Starting phenix.real_space_refine on Wed Feb 4 04:46:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yfo_39225/02_2026/8yfo_39225.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yfo_39225/02_2026/8yfo_39225.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yfo_39225/02_2026/8yfo_39225.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yfo_39225/02_2026/8yfo_39225.map" model { file = "/net/cci-nas-00/data/ceres_data/8yfo_39225/02_2026/8yfo_39225.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yfo_39225/02_2026/8yfo_39225.cif" } resolution = 2.71 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= 0.001 sd= 0.057 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 54 5.16 5 C 5536 2.51 5 N 1520 2.21 5 O 1591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8701 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1948 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2610 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "P" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 274 Unusual residues: {'ACE': 1} Classifications: {'peptide': 32, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 31} Chain: "R" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2450 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 292} Chain breaks: 4 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 1.68, per 1000 atoms: 0.19 Number of scatterers: 8701 At special positions: 0 Unit cell: (87.6, 98.55, 151.84, 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 54 16.00 O 1591 8.00 N 1520 7.00 C 5536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " 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 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 198.1 milliseconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2058 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 11 sheets defined 43.8% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.573A pdb=" N ALA A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.523A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 246 through 250 removed outlier: 3.901A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.244A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 removed outlier: 4.150A pdb=" N ARG A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.540A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 358 removed outlier: 4.469A pdb=" N ARG A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.762A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.547A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 32 removed outlier: 3.574A pdb=" N ARG P 20 " --> pdb=" O GLN P 16 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU P 30 " --> pdb=" O LYS P 26 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE P 31 " --> pdb=" O LEU P 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 212 removed outlier: 3.539A pdb=" N PHE R 212 " --> pdb=" O ILE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 245 Processing helix chain 'R' and resid 278 through 309 removed outlier: 3.597A pdb=" N ARG R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY R 303 " --> pdb=" O ILE R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 347 removed outlier: 4.074A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 356 through 359 removed outlier: 3.617A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 388 Proline residue: R 366 - end of helix Processing helix chain 'R' and resid 388 through 393 Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 418 through 426 removed outlier: 4.396A pdb=" N ILE R 422 " --> pdb=" O GLY R 418 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL R 423 " --> pdb=" O VAL R 419 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE R 424 " --> pdb=" O HIS R 420 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA R 426 " --> pdb=" O ILE R 422 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 461 removed outlier: 4.017A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 481 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.493A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL A 254 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N HIS A 329 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 256 " --> pdb=" O HIS A 329 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.219A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.114A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.426A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.552A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.067A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.570A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.784A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.667A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 129 through 130 453 hydrogen bonds defined for protein. 1302 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: 0.99 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1397 1.31 - 1.44: 2543 1.44 - 1.56: 4871 1.56 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 8889 Sorted by residual: bond pdb=" N PHE R 314 " pdb=" CA PHE R 314 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.24e-02 6.50e+03 6.96e+00 bond pdb=" N SER R 316 " pdb=" CA SER R 316 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.28e-02 6.10e+03 6.64e+00 bond pdb=" N ALA R 313 " pdb=" CA ALA R 313 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 4.82e+00 bond pdb=" CA SER R 316 " pdb=" CB SER R 316 " ideal model delta sigma weight residual 1.533 1.498 0.034 1.72e-02 3.38e+03 3.96e+00 bond pdb=" N PHE R 315 " pdb=" CA PHE R 315 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.50e-02 4.44e+03 3.35e+00 ... (remaining 8884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 11744 1.01 - 2.02: 220 2.02 - 3.03: 53 3.03 - 4.03: 8 4.03 - 5.04: 5 Bond angle restraints: 12030 Sorted by residual: angle pdb=" CA ALA R 313 " pdb=" C ALA R 313 " pdb=" O ALA R 313 " ideal model delta sigma weight residual 121.00 117.45 3.55 1.05e+00 9.07e-01 1.14e+01 angle pdb=" C SER R 316 " pdb=" N GLU R 317 " pdb=" CA GLU R 317 " ideal model delta sigma weight residual 121.56 116.71 4.85 1.56e+00 4.11e-01 9.65e+00 angle pdb=" CA SER R 316 " pdb=" C SER R 316 " pdb=" O SER R 316 " ideal model delta sigma weight residual 121.10 118.02 3.08 1.10e+00 8.26e-01 7.84e+00 angle pdb=" CA TYR R 191 " pdb=" CB TYR R 191 " pdb=" CG TYR R 191 " ideal model delta sigma weight residual 113.90 118.49 -4.59 1.80e+00 3.09e-01 6.49e+00 angle pdb=" N ILE R 38 " pdb=" CA ILE R 38 " pdb=" C ILE R 38 " ideal model delta sigma weight residual 112.29 109.90 2.39 9.40e-01 1.13e+00 6.44e+00 ... (remaining 12025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.96: 4937 13.96 - 27.91: 236 27.91 - 41.87: 66 41.87 - 55.82: 8 55.82 - 69.78: 4 Dihedral angle restraints: 5251 sinusoidal: 2067 harmonic: 3184 Sorted by residual: dihedral pdb=" N LYS B 15 " pdb=" CA LYS B 15 " pdb=" CB LYS B 15 " pdb=" CG LYS B 15 " ideal model delta sinusoidal sigma weight residual -60.00 -118.22 58.22 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N TYR B 59 " pdb=" CA TYR B 59 " pdb=" CB TYR B 59 " pdb=" CG TYR B 59 " ideal model delta sinusoidal sigma weight residual -180.00 -124.26 -55.74 3 1.50e+01 4.44e-03 9.36e+00 dihedral pdb=" CB ARG B 22 " pdb=" CG ARG B 22 " pdb=" CD ARG B 22 " pdb=" NE ARG B 22 " ideal model delta sinusoidal sigma weight residual 60.00 112.30 -52.30 3 1.50e+01 4.44e-03 9.10e+00 ... (remaining 5248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 864 0.027 - 0.055: 300 0.055 - 0.082: 101 0.082 - 0.110: 55 0.110 - 0.137: 17 Chirality restraints: 1337 Sorted by residual: chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE B 273 " pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CB ILE B 273 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 1334 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 343 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C PHE A 343 " 0.024 2.00e-02 2.50e+03 pdb=" O PHE A 343 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN A 344 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 348 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ASP A 348 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP A 348 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 349 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 349 " -0.007 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C ILE A 349 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE A 349 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE A 350 " -0.008 2.00e-02 2.50e+03 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1429 2.77 - 3.30: 8447 3.30 - 3.83: 14808 3.83 - 4.37: 16955 4.37 - 4.90: 29712 Nonbonded interactions: 71351 Sorted by model distance: nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.232 3.040 nonbonded pdb=" OE1 GLN R 364 " pdb=" OH TYR R 429 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.265 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.267 3.040 nonbonded pdb=" NE2 GLN B 75 " pdb=" O VAL B 100 " model vdw 2.267 3.120 ... (remaining 71346 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.780 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 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 : 0.002 0.034 8890 Z= 0.102 Angle : 0.390 5.042 12032 Z= 0.230 Chirality : 0.037 0.137 1337 Planarity : 0.003 0.028 1526 Dihedral : 8.998 69.779 3190 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.32 % Allowed : 5.70 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.27), residues: 1071 helix: 2.68 (0.25), residues: 436 sheet: 1.36 (0.35), residues: 218 loop : 0.05 (0.32), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 19 TYR 0.022 0.001 TYR R 191 PHE 0.009 0.001 PHE R 335 TRP 0.013 0.001 TRP P 14 HIS 0.002 0.000 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00158 ( 8889) covalent geometry : angle 0.38975 (12030) SS BOND : bond 0.00222 ( 1) SS BOND : angle 0.34428 ( 2) hydrogen bonds : bond 0.12290 ( 453) hydrogen bonds : angle 4.98740 ( 1302) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: B 186 ASP cc_start: 0.6458 (m-30) cc_final: 0.6168 (m-30) REVERT: B 217 MET cc_start: 0.7799 (pmm) cc_final: 0.7413 (pp-130) REVERT: R 362 ILE cc_start: 0.6955 (mt) cc_final: 0.6453 (mt) outliers start: 3 outliers final: 1 residues processed: 192 average time/residue: 0.4265 time to fit residues: 87.2479 Evaluate side-chains 125 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 8 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0370 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 88 ASN B 239 ASN B 311 HIS N 35 ASN N 82 GLN ** P 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.181194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.140311 restraints weight = 10441.863| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.11 r_work: 0.3631 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8890 Z= 0.189 Angle : 0.571 10.794 12032 Z= 0.311 Chirality : 0.044 0.216 1337 Planarity : 0.004 0.051 1526 Dihedral : 4.032 24.819 1203 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.12 % Allowed : 12.80 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.26), residues: 1071 helix: 2.64 (0.25), residues: 432 sheet: 1.01 (0.35), residues: 208 loop : 0.01 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 233 TYR 0.027 0.002 TYR R 191 PHE 0.028 0.002 PHE R 335 TRP 0.021 0.002 TRP P 14 HIS 0.012 0.002 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 8889) covalent geometry : angle 0.57053 (12030) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.48018 ( 2) hydrogen bonds : bond 0.04311 ( 453) hydrogen bonds : angle 4.10355 ( 1302) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7462 (ttmt) cc_final: 0.6835 (ttpp) REVERT: A 24 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.6924 (mp10) REVERT: A 186 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6365 (tp30) REVERT: A 198 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8056 (ttp) REVERT: A 266 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: A 281 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5716 (mp0) REVERT: B 122 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8337 (t) REVERT: B 217 MET cc_start: 0.8145 (pmm) cc_final: 0.7184 (pp-130) REVERT: B 234 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.6794 (t80) REVERT: N 31 ASN cc_start: 0.7782 (m-40) cc_final: 0.7342 (m-40) REVERT: R 32 MET cc_start: 0.6660 (tmt) cc_final: 0.6285 (tmm) REVERT: R 190 ILE cc_start: 0.7469 (mt) cc_final: 0.7251 (tp) outliers start: 29 outliers final: 10 residues processed: 153 average time/residue: 0.5546 time to fit residues: 89.7573 Evaluate side-chains 127 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 475 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 77 optimal weight: 0.0070 chunk 23 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN P 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.182514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.142737 restraints weight = 10302.412| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.01 r_work: 0.3609 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8890 Z= 0.137 Angle : 0.479 5.540 12032 Z= 0.265 Chirality : 0.041 0.150 1337 Planarity : 0.004 0.036 1526 Dihedral : 3.783 15.280 1200 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.87 % Allowed : 14.30 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.26), residues: 1071 helix: 2.73 (0.25), residues: 428 sheet: 0.88 (0.34), residues: 219 loop : 0.09 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 181 TYR 0.025 0.002 TYR R 191 PHE 0.026 0.001 PHE R 335 TRP 0.016 0.002 TRP B 82 HIS 0.008 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8889) covalent geometry : angle 0.47881 (12030) SS BOND : bond 0.00268 ( 1) SS BOND : angle 0.42748 ( 2) hydrogen bonds : bond 0.03933 ( 453) hydrogen bonds : angle 3.94274 ( 1302) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 123 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7480 (ttmt) cc_final: 0.6911 (ttpp) REVERT: A 24 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7112 (mp10) REVERT: A 51 LYS cc_start: 0.8635 (tptm) cc_final: 0.7819 (mtpt) REVERT: A 186 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6347 (tp30) REVERT: A 198 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8154 (ttp) REVERT: A 266 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: A 284 ARG cc_start: 0.6772 (mtm-85) cc_final: 0.6420 (mtt180) REVERT: A 357 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.6828 (mp-120) REVERT: B 122 SER cc_start: 0.8481 (OUTLIER) cc_final: 0.8246 (t) REVERT: B 191 SER cc_start: 0.9010 (m) cc_final: 0.8786 (t) REVERT: B 217 MET cc_start: 0.8150 (pmm) cc_final: 0.7260 (pp-130) REVERT: B 234 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.6897 (t80) REVERT: B 269 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7385 (tp) REVERT: G 47 GLU cc_start: 0.6790 (tp30) cc_final: 0.6586 (tp30) REVERT: N 31 ASN cc_start: 0.7749 (m-40) cc_final: 0.7366 (m-40) REVERT: R 190 ILE cc_start: 0.7683 (mt) cc_final: 0.7476 (tp) outliers start: 36 outliers final: 11 residues processed: 137 average time/residue: 0.4975 time to fit residues: 72.6099 Evaluate side-chains 128 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 475 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 101 optimal weight: 0.0010 chunk 80 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 16 GLN R 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.185659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.149456 restraints weight = 10544.447| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.97 r_work: 0.3639 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3530 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8890 Z= 0.123 Angle : 0.459 5.521 12032 Z= 0.256 Chirality : 0.041 0.148 1337 Planarity : 0.004 0.043 1526 Dihedral : 3.763 15.602 1200 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.33 % Allowed : 16.34 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.26), residues: 1071 helix: 2.72 (0.25), residues: 427 sheet: 0.80 (0.34), residues: 214 loop : 0.04 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 31 TYR 0.025 0.001 TYR R 191 PHE 0.028 0.001 PHE R 335 TRP 0.014 0.001 TRP R 298 HIS 0.007 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8889) covalent geometry : angle 0.45856 (12030) SS BOND : bond 0.00121 ( 1) SS BOND : angle 0.54804 ( 2) hydrogen bonds : bond 0.03728 ( 453) hydrogen bonds : angle 3.88994 ( 1302) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7454 (ttmt) cc_final: 0.6881 (ttpp) REVERT: A 51 LYS cc_start: 0.8604 (tptm) cc_final: 0.7858 (mtpt) REVERT: A 186 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6367 (tp30) REVERT: A 198 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8167 (ttp) REVERT: A 217 ASP cc_start: 0.8226 (p0) cc_final: 0.8025 (p0) REVERT: A 266 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: A 314 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7764 (ttp80) REVERT: A 357 GLN cc_start: 0.7872 (OUTLIER) cc_final: 0.7168 (mp10) REVERT: B 122 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.8238 (t) REVERT: B 136 SER cc_start: 0.8548 (t) cc_final: 0.8344 (p) REVERT: B 191 SER cc_start: 0.9031 (m) cc_final: 0.8803 (t) REVERT: B 217 MET cc_start: 0.8206 (pmm) cc_final: 0.7338 (pp-130) REVERT: B 234 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.6790 (t80) REVERT: B 269 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7307 (tp) REVERT: G 21 MET cc_start: 0.6654 (tmm) cc_final: 0.6451 (tmm) REVERT: G 47 GLU cc_start: 0.6848 (tp30) cc_final: 0.6593 (tp30) REVERT: N 31 ASN cc_start: 0.7790 (m-40) cc_final: 0.7466 (m-40) REVERT: N 76 LYS cc_start: 0.8482 (mtpp) cc_final: 0.8095 (mtpp) REVERT: R 190 ILE cc_start: 0.7707 (mt) cc_final: 0.7454 (mm) outliers start: 31 outliers final: 12 residues processed: 129 average time/residue: 0.5687 time to fit residues: 77.9098 Evaluate side-chains 127 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 379 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** P 9 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 = 0.4172 r_free = 0.4172 target = 0.183686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.146840 restraints weight = 10462.849| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.04 r_work: 0.3599 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8890 Z= 0.136 Angle : 0.469 5.573 12032 Z= 0.261 Chirality : 0.041 0.152 1337 Planarity : 0.004 0.035 1526 Dihedral : 3.846 16.214 1200 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.66 % Allowed : 16.77 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.26), residues: 1071 helix: 2.75 (0.25), residues: 425 sheet: 0.65 (0.34), residues: 213 loop : -0.15 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 31 TYR 0.025 0.001 TYR R 191 PHE 0.031 0.001 PHE R 335 TRP 0.014 0.002 TRP R 298 HIS 0.008 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8889) covalent geometry : angle 0.46854 (12030) SS BOND : bond 0.00139 ( 1) SS BOND : angle 0.59251 ( 2) hydrogen bonds : bond 0.03873 ( 453) hydrogen bonds : angle 3.93203 ( 1302) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7552 (ttmt) cc_final: 0.7018 (ttpp) REVERT: A 24 GLN cc_start: 0.7834 (tp40) cc_final: 0.7548 (mm110) REVERT: A 51 LYS cc_start: 0.8613 (tptm) cc_final: 0.7898 (mtpt) REVERT: A 186 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6340 (tp30) REVERT: A 198 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8203 (ttp) REVERT: A 266 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6990 (mp0) REVERT: A 357 GLN cc_start: 0.7925 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: B 122 SER cc_start: 0.8500 (OUTLIER) cc_final: 0.8272 (t) REVERT: B 191 SER cc_start: 0.9055 (m) cc_final: 0.8828 (t) REVERT: B 197 ARG cc_start: 0.7665 (mmm160) cc_final: 0.7263 (mtt-85) REVERT: B 214 ARG cc_start: 0.8164 (mpp-170) cc_final: 0.7654 (mmt180) REVERT: B 234 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.6953 (t80) REVERT: B 269 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7397 (tp) REVERT: G 21 MET cc_start: 0.6706 (tmm) cc_final: 0.6458 (tmm) REVERT: N 28 THR cc_start: 0.8170 (p) cc_final: 0.7759 (t) REVERT: N 76 LYS cc_start: 0.8503 (mtpp) cc_final: 0.8122 (mtpp) REVERT: R 32 MET cc_start: 0.6926 (OUTLIER) cc_final: 0.6641 (tmm) REVERT: R 190 ILE cc_start: 0.7788 (mt) cc_final: 0.7562 (mm) outliers start: 34 outliers final: 13 residues processed: 133 average time/residue: 0.4963 time to fit residues: 70.2153 Evaluate side-chains 129 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 475 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 0.0870 chunk 18 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN P 9 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.181181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.144452 restraints weight = 10465.046| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.01 r_work: 0.3624 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8890 Z= 0.113 Angle : 0.453 5.761 12032 Z= 0.253 Chirality : 0.040 0.144 1337 Planarity : 0.004 0.038 1526 Dihedral : 3.772 18.429 1200 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.19 % Allowed : 17.31 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.26), residues: 1071 helix: 2.81 (0.25), residues: 425 sheet: 0.65 (0.34), residues: 207 loop : -0.13 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 31 TYR 0.025 0.001 TYR R 191 PHE 0.029 0.001 PHE R 335 TRP 0.013 0.001 TRP R 298 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8889) covalent geometry : angle 0.45331 (12030) SS BOND : bond 0.00141 ( 1) SS BOND : angle 0.59111 ( 2) hydrogen bonds : bond 0.03640 ( 453) hydrogen bonds : angle 3.81521 ( 1302) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 109 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7576 (ttmt) cc_final: 0.7059 (ttpp) REVERT: A 24 GLN cc_start: 0.7782 (tp40) cc_final: 0.7482 (mm110) REVERT: A 51 LYS cc_start: 0.8583 (tptm) cc_final: 0.7950 (mtpt) REVERT: A 186 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6299 (tp30) REVERT: A 198 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8189 (ttp) REVERT: A 258 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8086 (mm) REVERT: A 266 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6981 (mp0) REVERT: B 122 SER cc_start: 0.8439 (OUTLIER) cc_final: 0.8217 (t) REVERT: B 191 SER cc_start: 0.9021 (m) cc_final: 0.8798 (t) REVERT: B 197 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7230 (mtt-85) REVERT: B 214 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7612 (mmt180) REVERT: B 234 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.6831 (t80) REVERT: B 269 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7395 (tp) REVERT: G 21 MET cc_start: 0.6757 (tmm) cc_final: 0.6462 (tmm) REVERT: N 28 THR cc_start: 0.8217 (p) cc_final: 0.7814 (t) REVERT: N 46 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6883 (pp20) REVERT: N 76 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8111 (mtpp) REVERT: R 190 ILE cc_start: 0.7728 (mt) cc_final: 0.7504 (mm) outliers start: 39 outliers final: 15 residues processed: 132 average time/residue: 0.4963 time to fit residues: 69.6421 Evaluate side-chains 129 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 325 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 475 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.181424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.145465 restraints weight = 10580.266| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.94 r_work: 0.3615 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8890 Z= 0.123 Angle : 0.459 5.489 12032 Z= 0.256 Chirality : 0.040 0.146 1337 Planarity : 0.003 0.034 1526 Dihedral : 3.783 17.667 1200 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.87 % Allowed : 17.85 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.26), residues: 1071 helix: 2.75 (0.25), residues: 430 sheet: 0.64 (0.34), residues: 211 loop : -0.22 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 31 TYR 0.024 0.001 TYR R 191 PHE 0.030 0.001 PHE R 335 TRP 0.016 0.001 TRP B 82 HIS 0.006 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8889) covalent geometry : angle 0.45928 (12030) SS BOND : bond 0.00141 ( 1) SS BOND : angle 0.59591 ( 2) hydrogen bonds : bond 0.03716 ( 453) hydrogen bonds : angle 3.83406 ( 1302) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7570 (ttmt) cc_final: 0.6986 (ttpp) REVERT: A 186 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6273 (tp30) REVERT: A 198 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8181 (ttp) REVERT: A 250 ARG cc_start: 0.6628 (mmt90) cc_final: 0.6081 (mtp-110) REVERT: A 258 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8089 (mm) REVERT: A 266 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: A 284 ARG cc_start: 0.6838 (mtm-85) cc_final: 0.6609 (mtt180) REVERT: B 122 SER cc_start: 0.8498 (OUTLIER) cc_final: 0.8253 (t) REVERT: B 191 SER cc_start: 0.9063 (m) cc_final: 0.8840 (t) REVERT: B 197 ARG cc_start: 0.7617 (mmm160) cc_final: 0.7203 (mtt-85) REVERT: B 214 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7553 (mmt180) REVERT: B 234 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.6847 (t80) REVERT: B 269 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7256 (tp) REVERT: G 21 MET cc_start: 0.6767 (tmm) cc_final: 0.6515 (tmm) REVERT: N 28 THR cc_start: 0.8204 (p) cc_final: 0.7795 (t) REVERT: R 32 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6652 (tmm) REVERT: R 190 ILE cc_start: 0.7786 (mt) cc_final: 0.7549 (mm) outliers start: 36 outliers final: 14 residues processed: 128 average time/residue: 0.5071 time to fit residues: 68.9139 Evaluate side-chains 127 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 321 LEU Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 475 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.176141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.139741 restraints weight = 10479.082| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 1.94 r_work: 0.3560 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8890 Z= 0.192 Angle : 0.543 5.919 12032 Z= 0.302 Chirality : 0.043 0.174 1337 Planarity : 0.004 0.052 1526 Dihedral : 4.160 18.129 1200 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.55 % Allowed : 18.28 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.26), residues: 1071 helix: 2.38 (0.25), residues: 430 sheet: 0.34 (0.33), residues: 215 loop : -0.30 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 181 TYR 0.026 0.002 TYR R 191 PHE 0.035 0.002 PHE R 335 TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 8889) covalent geometry : angle 0.54308 (12030) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.66155 ( 2) hydrogen bonds : bond 0.04353 ( 453) hydrogen bonds : angle 4.16192 ( 1302) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7679 (ttmt) cc_final: 0.7122 (ttpp) REVERT: A 24 GLN cc_start: 0.7868 (tp40) cc_final: 0.7585 (mm110) REVERT: A 51 LYS cc_start: 0.8622 (tptm) cc_final: 0.7894 (mtmt) REVERT: A 266 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: A 284 ARG cc_start: 0.6916 (mtm-85) cc_final: 0.6581 (mtt180) REVERT: B 122 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8362 (t) REVERT: B 191 SER cc_start: 0.9106 (m) cc_final: 0.8868 (t) REVERT: B 197 ARG cc_start: 0.7729 (mmm160) cc_final: 0.7326 (mtt-85) REVERT: B 214 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7540 (mmt180) REVERT: B 234 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7047 (t80) REVERT: G 21 MET cc_start: 0.6885 (tmm) cc_final: 0.6604 (tmm) REVERT: N 2 VAL cc_start: 0.7626 (OUTLIER) cc_final: 0.7336 (t) REVERT: N 31 ASN cc_start: 0.7995 (m-40) cc_final: 0.7730 (m-40) REVERT: R 32 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6731 (tmm) REVERT: R 190 ILE cc_start: 0.7945 (mt) cc_final: 0.7739 (mm) outliers start: 33 outliers final: 15 residues processed: 131 average time/residue: 0.5249 time to fit residues: 73.0144 Evaluate side-chains 125 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 475 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.182327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.146309 restraints weight = 10468.324| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.97 r_work: 0.3613 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8890 Z= 0.126 Angle : 0.480 6.878 12032 Z= 0.267 Chirality : 0.041 0.151 1337 Planarity : 0.004 0.084 1526 Dihedral : 3.991 18.954 1200 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.37 % Allowed : 19.46 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.26), residues: 1071 helix: 2.56 (0.25), residues: 430 sheet: 0.34 (0.33), residues: 215 loop : -0.28 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG R 181 TYR 0.024 0.002 TYR R 191 PHE 0.032 0.001 PHE R 335 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 8889) covalent geometry : angle 0.47949 (12030) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.63439 ( 2) hydrogen bonds : bond 0.03814 ( 453) hydrogen bonds : angle 3.93638 ( 1302) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7624 (ttmt) cc_final: 0.7111 (ttpp) REVERT: A 24 GLN cc_start: 0.7854 (tp40) cc_final: 0.7551 (mm110) REVERT: A 36 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8431 (mt) REVERT: A 51 LYS cc_start: 0.8627 (tptm) cc_final: 0.7831 (mtpt) REVERT: A 250 ARG cc_start: 0.6642 (mmt90) cc_final: 0.6058 (mtp-110) REVERT: A 266 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: A 284 ARG cc_start: 0.6923 (mtm-85) cc_final: 0.6702 (mtt180) REVERT: B 122 SER cc_start: 0.8472 (OUTLIER) cc_final: 0.8269 (t) REVERT: B 191 SER cc_start: 0.9043 (m) cc_final: 0.8821 (t) REVERT: B 197 ARG cc_start: 0.7667 (mmm160) cc_final: 0.7239 (mtt-85) REVERT: B 214 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7666 (mmt180) REVERT: B 234 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.6958 (t80) REVERT: G 21 MET cc_start: 0.6827 (tmm) cc_final: 0.6557 (tmm) REVERT: N 2 VAL cc_start: 0.7594 (OUTLIER) cc_final: 0.7295 (t) REVERT: N 31 ASN cc_start: 0.7776 (m-40) cc_final: 0.7443 (m-40) REVERT: R 32 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6707 (tmm) REVERT: R 190 ILE cc_start: 0.7880 (mt) cc_final: 0.7663 (mm) outliers start: 22 outliers final: 12 residues processed: 118 average time/residue: 0.5159 time to fit residues: 64.7598 Evaluate side-chains 119 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 457 ILE Chi-restraints excluded: chain R residue 475 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 55 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.177103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.140044 restraints weight = 10538.957| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.11 r_work: 0.3575 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8890 Z= 0.157 Angle : 0.514 6.369 12032 Z= 0.285 Chirality : 0.042 0.163 1337 Planarity : 0.004 0.075 1526 Dihedral : 4.083 17.780 1200 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.37 % Allowed : 19.46 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.26), residues: 1071 helix: 2.50 (0.25), residues: 428 sheet: 0.40 (0.33), residues: 211 loop : -0.32 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 181 TYR 0.025 0.002 TYR R 191 PHE 0.034 0.002 PHE R 335 TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8889) covalent geometry : angle 0.51362 (12030) SS BOND : bond 0.00113 ( 1) SS BOND : angle 0.67147 ( 2) hydrogen bonds : bond 0.04053 ( 453) hydrogen bonds : angle 4.03330 ( 1302) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7602 (ttmt) cc_final: 0.7055 (ttpp) REVERT: A 24 GLN cc_start: 0.7853 (tp40) cc_final: 0.7531 (mm110) REVERT: A 36 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8422 (mt) REVERT: A 51 LYS cc_start: 0.8602 (tptm) cc_final: 0.7770 (mtpt) REVERT: A 250 ARG cc_start: 0.6578 (mmt90) cc_final: 0.5935 (mtp-110) REVERT: A 266 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: A 284 ARG cc_start: 0.6987 (mtm-85) cc_final: 0.6737 (mtt180) REVERT: B 122 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8308 (t) REVERT: B 191 SER cc_start: 0.9057 (m) cc_final: 0.8834 (t) REVERT: B 214 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7682 (mmt180) REVERT: B 234 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7021 (t80) REVERT: B 270 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8447 (pp) REVERT: G 21 MET cc_start: 0.6869 (tmm) cc_final: 0.6662 (tmm) REVERT: N 2 VAL cc_start: 0.7634 (OUTLIER) cc_final: 0.7350 (t) REVERT: N 31 ASN cc_start: 0.7750 (m-40) cc_final: 0.7435 (m-40) REVERT: R 32 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6684 (tmm) outliers start: 22 outliers final: 12 residues processed: 117 average time/residue: 0.5152 time to fit residues: 64.1738 Evaluate side-chains 118 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 32 MET Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 387 THR Chi-restraints excluded: chain R residue 475 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 100 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.178736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142095 restraints weight = 10508.546| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.97 r_work: 0.3603 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8890 Z= 0.119 Angle : 0.470 5.936 12032 Z= 0.261 Chirality : 0.040 0.150 1337 Planarity : 0.004 0.056 1526 Dihedral : 3.926 17.583 1200 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.37 % Allowed : 19.46 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.26), residues: 1071 helix: 2.62 (0.25), residues: 428 sheet: 0.48 (0.33), residues: 209 loop : -0.28 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 181 TYR 0.025 0.001 TYR R 191 PHE 0.031 0.001 PHE R 335 TRP 0.014 0.001 TRP R 298 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8889) covalent geometry : angle 0.47024 (12030) SS BOND : bond 0.00149 ( 1) SS BOND : angle 0.61516 ( 2) hydrogen bonds : bond 0.03747 ( 453) hydrogen bonds : angle 3.89817 ( 1302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3282.03 seconds wall clock time: 56 minutes 28.65 seconds (3388.65 seconds total)