Starting phenix.real_space_refine on Thu Jul 2 09:04:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8avv_15684/07_2026/8avv_15684.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avv_15684/07_2026/8avv_15684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8avv_15684/07_2026/8avv_15684.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8avv_15684/07_2026/8avv_15684.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8avv_15684/07_2026/8avv_15684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avv_15684/07_2026/8avv_15684.map" model { file = "/net/cci-nas-00/data/ceres_data/8avv_15684/07_2026/8avv_15684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avv_15684/07_2026/8avv_15684.cif" } resolution = 3.4 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= 0.022 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 22 5.16 5 C 4958 2.51 5 N 1378 2.21 5 O 1436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7794 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3849 Classifications: {'peptide': 504} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 463} Chain breaks: 2 Chain: "B" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3859 Classifications: {'peptide': 506} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 465} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'LBV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.58, per 1000 atoms: 0.20 Number of scatterers: 7794 At special positions: 0 Unit cell: (93.0636, 98.2338, 115.468, 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 22 16.00 O 1436 8.00 N 1378 7.00 C 4958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.54 Conformation dependent library (CDL) restraints added in 374.5 milliseconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1856 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 36.8% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 81 through 89 removed outlier: 3.645A pdb=" N ALA A 87 " --> pdb=" O PRO A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 148 removed outlier: 3.592A pdb=" N GLU A 148 " --> pdb=" O MET A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 169 removed outlier: 3.518A pdb=" N THR A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.520A pdb=" N GLN A 262 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 328 removed outlier: 3.619A pdb=" N THR A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLN A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 removed outlier: 3.753A pdb=" N VAL A 338 " --> pdb=" O HIS A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.572A pdb=" N THR A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 396 removed outlier: 3.769A pdb=" N ASP A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 412 removed outlier: 4.159A pdb=" N LEU A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 416 Processing helix chain 'A' and resid 455 through 460 removed outlier: 3.867A pdb=" N ALA A 459 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS A 460 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 501 removed outlier: 3.610A pdb=" N ILE A 488 " --> pdb=" O HIS A 484 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 496 " --> pdb=" O GLN A 492 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 497 " --> pdb=" O ASP A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 519 removed outlier: 3.664A pdb=" N ARG A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP A 511 " --> pdb=" O SER A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 65 through 70 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.643A pdb=" N ALA B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 148 removed outlier: 3.583A pdb=" N GLU B 148 " --> pdb=" O MET B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 169 removed outlier: 3.525A pdb=" N THR B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 216 Processing helix chain 'B' and resid 257 through 267 removed outlier: 3.518A pdb=" N GLN B 262 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 328 removed outlier: 3.617A pdb=" N THR B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 314 " --> pdb=" O ARG B 310 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 removed outlier: 3.746A pdb=" N VAL B 338 " --> pdb=" O HIS B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.578A pdb=" N THR B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 396 removed outlier: 3.773A pdb=" N ASP B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 4.159A pdb=" N LEU B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 416 Processing helix chain 'B' and resid 455 through 460 removed outlier: 3.868A pdb=" N ALA B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LYS B 460 " --> pdb=" O ASP B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 501 removed outlier: 3.615A pdb=" N ILE B 488 " --> pdb=" O HIS B 484 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 493 " --> pdb=" O GLU B 489 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP B 496 " --> pdb=" O GLN B 492 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR B 497 " --> pdb=" O ASP B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 519 removed outlier: 3.683A pdb=" N ARG B 505 " --> pdb=" O ALA B 501 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.493A pdb=" N THR A 43 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N MET A 54 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 41 " --> pdb=" O MET A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.962A pdb=" N LEU A 175 " --> pdb=" O ILE A 187 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLU A 189 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL A 173 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TRP A 284 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU A 283 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL A 279 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 285 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 238 through 239 removed outlier: 3.548A pdb=" N ALA A 244 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 380 removed outlier: 3.528A pdb=" N PHE A 372 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 452 removed outlier: 4.616A pdb=" N TYR A 479 " --> pdb=" O LEU A 445 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU A 447 " --> pdb=" O ARG A 477 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ARG A 477 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N VAL A 449 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLU A 475 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TRP A 451 " --> pdb=" O LEU A 473 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N LEU A 473 " --> pdb=" O TRP A 451 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.498A pdb=" N THR B 43 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET B 54 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 41 " --> pdb=" O MET B 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 202 through 203 removed outlier: 6.974A pdb=" N LEU B 175 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLU B 189 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL B 173 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TRP B 284 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 283 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL B 279 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 285 " --> pdb=" O VAL B 277 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 238 through 239 removed outlier: 3.538A pdb=" N ALA B 244 " --> pdb=" O ASN B 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 375 through 380 removed outlier: 3.529A pdb=" N PHE B 372 " --> pdb=" O ARG B 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 445 through 452 removed outlier: 4.557A pdb=" N TYR B 479 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LEU B 447 " --> pdb=" O ARG B 477 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ARG B 477 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL B 449 " --> pdb=" O GLU B 475 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N GLU B 475 " --> pdb=" O VAL B 449 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N TRP B 451 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU B 473 " --> pdb=" O TRP B 451 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 918 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: 1.13 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1984 1.34 - 1.46: 2367 1.46 - 1.58: 3608 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 7995 Sorted by residual: bond pdb=" C2D LBV A1000 " pdb=" C3D LBV A1000 " ideal model delta sigma weight residual 1.358 1.435 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C2D LBV B1000 " pdb=" C3D LBV B1000 " ideal model delta sigma weight residual 1.358 1.432 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C3A LBV B1000 " pdb=" C4A LBV B1000 " ideal model delta sigma weight residual 1.463 1.392 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C4C LBV B1000 " pdb=" CHD LBV B1000 " ideal model delta sigma weight residual 1.428 1.360 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C4C LBV A1000 " pdb=" CHD LBV A1000 " ideal model delta sigma weight residual 1.428 1.363 0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 7990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 8756 1.69 - 3.37: 1910 3.37 - 5.06: 255 5.06 - 6.75: 18 6.75 - 8.43: 4 Bond angle restraints: 10943 Sorted by residual: angle pdb=" N LEU B 346 " pdb=" CA LEU B 346 " pdb=" C LEU B 346 " ideal model delta sigma weight residual 114.31 108.90 5.41 1.29e+00 6.01e-01 1.76e+01 angle pdb=" N LEU A 346 " pdb=" CA LEU A 346 " pdb=" C LEU A 346 " ideal model delta sigma weight residual 114.31 109.14 5.17 1.29e+00 6.01e-01 1.61e+01 angle pdb=" C LEU A 297 " pdb=" N PRO A 298 " pdb=" CA PRO A 298 " ideal model delta sigma weight residual 119.66 122.50 -2.84 7.20e-01 1.93e+00 1.56e+01 angle pdb=" C GLN B 398 " pdb=" CA GLN B 398 " pdb=" CB GLN B 398 " ideal model delta sigma weight residual 109.26 114.91 -5.65 1.47e+00 4.63e-01 1.48e+01 angle pdb=" C GLN A 398 " pdb=" CA GLN A 398 " pdb=" CB GLN A 398 " ideal model delta sigma weight residual 109.26 114.88 -5.62 1.47e+00 4.63e-01 1.46e+01 ... (remaining 10938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.78: 4015 15.78 - 31.55: 464 31.55 - 47.32: 181 47.32 - 63.10: 54 63.10 - 78.87: 41 Dihedral angle restraints: 4755 sinusoidal: 1876 harmonic: 2879 Sorted by residual: dihedral pdb=" CA HIS B 219 " pdb=" C HIS B 219 " pdb=" N LEU B 220 " pdb=" CA LEU B 220 " ideal model delta harmonic sigma weight residual -180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA HIS A 219 " pdb=" C HIS A 219 " pdb=" N LEU A 220 " pdb=" CA LEU A 220 " ideal model delta harmonic sigma weight residual -180.00 -157.74 -22.26 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA MET B 54 " pdb=" C MET B 54 " pdb=" N SER B 55 " pdb=" CA SER B 55 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 4752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 665 0.055 - 0.110: 337 0.110 - 0.165: 165 0.165 - 0.221: 55 0.221 - 0.276: 8 Chirality restraints: 1230 Sorted by residual: chirality pdb=" CA ARG B 337 " pdb=" N ARG B 337 " pdb=" C ARG B 337 " pdb=" CB ARG B 337 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA ASN A 243 " pdb=" N ASN A 243 " pdb=" C ASN A 243 " pdb=" CB ASN A 243 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA ASN B 243 " pdb=" N ASN B 243 " pdb=" C ASN B 243 " pdb=" CB ASN B 243 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1227 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D LBV B1000 " 0.021 2.00e-02 2.50e+03 2.03e-01 9.27e+02 pdb=" C2D LBV B1000 " -0.088 2.00e-02 2.50e+03 pdb=" C3D LBV B1000 " 0.053 2.00e-02 2.50e+03 pdb=" C4D LBV B1000 " -0.071 2.00e-02 2.50e+03 pdb=" CAD LBV B1000 " 0.269 2.00e-02 2.50e+03 pdb=" CHD LBV B1000 " 0.362 2.00e-02 2.50e+03 pdb=" CMD LBV B1000 " -0.265 2.00e-02 2.50e+03 pdb=" N_D LBV B1000 " -0.285 2.00e-02 2.50e+03 pdb=" O_D LBV B1000 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D LBV A1000 " 0.024 2.00e-02 2.50e+03 1.68e-01 6.32e+02 pdb=" C2D LBV A1000 " 0.055 2.00e-02 2.50e+03 pdb=" C3D LBV A1000 " -0.003 2.00e-02 2.50e+03 pdb=" C4D LBV A1000 " 0.040 2.00e-02 2.50e+03 pdb=" CAD LBV A1000 " -0.101 2.00e-02 2.50e+03 pdb=" CHD LBV A1000 " -0.290 2.00e-02 2.50e+03 pdb=" CMD LBV A1000 " 0.089 2.00e-02 2.50e+03 pdb=" N_D LBV A1000 " 0.346 2.00e-02 2.50e+03 pdb=" O_D LBV A1000 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C LBV A1000 " 0.033 2.00e-02 2.50e+03 1.36e-01 4.17e+02 pdb=" C2C LBV A1000 " -0.009 2.00e-02 2.50e+03 pdb=" C3C LBV A1000 " 0.019 2.00e-02 2.50e+03 pdb=" C4C LBV A1000 " 0.011 2.00e-02 2.50e+03 pdb=" CAC LBV A1000 " -0.048 2.00e-02 2.50e+03 pdb=" CHC LBV A1000 " -0.148 2.00e-02 2.50e+03 pdb=" CHD LBV A1000 " -0.217 2.00e-02 2.50e+03 pdb=" CMC LBV A1000 " 0.058 2.00e-02 2.50e+03 pdb=" N_C LBV A1000 " 0.301 2.00e-02 2.50e+03 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.04: 3437 3.04 - 3.51: 7725 3.51 - 3.97: 11916 3.97 - 4.44: 13620 4.44 - 4.90: 22326 Nonbonded interactions: 59024 Sorted by model distance: nonbonded pdb=" O ARG A 514 " pdb=" OG1 THR A 517 " model vdw 2.580 3.040 nonbonded pdb=" O ARG B 514 " pdb=" OG1 THR B 517 " model vdw 2.581 3.040 nonbonded pdb=" N ALA B 401 " pdb=" N LEU B 402 " model vdw 2.618 2.560 nonbonded pdb=" N HIS B 344 " pdb=" N SER B 345 " model vdw 2.619 2.560 nonbonded pdb=" OD2 ASP B 45 " pdb=" N SER B 48 " model vdw 2.620 3.120 ... (remaining 59019 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 'A' selection = (chain 'B' and (resid 7 through 106 or resid 109 through 1000)) } 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: 7.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.160 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 : 0.008 0.077 7995 Z= 0.505 Angle : 1.381 8.435 10943 Z= 0.921 Chirality : 0.081 0.276 1230 Planarity : 0.009 0.203 1437 Dihedral : 18.268 78.875 2899 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.70 % Favored : 95.10 % Rotamer: Outliers : 5.03 % Allowed : 12.94 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -3.08 (0.22), residues: 1000 helix: -3.09 (0.22), residues: 316 sheet: 0.12 (0.37), residues: 174 loop : -2.11 (0.22), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 154 TYR 0.016 0.002 TYR A 263 PHE 0.016 0.003 PHE A 170 TRP 0.009 0.002 TRP A 412 HIS 0.008 0.002 HIS B 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00773 / 0.51 ( 7995) covalent geometry : angle 1.38120 / 0.92 (10943) hydrogen bonds : bond 0.31349 / 21.28 ( 336) hydrogen bonds : angle 9.28641 / 6.48 ( 918) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7002 (pm20) REVERT: A 148 GLU cc_start: 0.8703 (mt-10) cc_final: 0.7809 (mp0) REVERT: A 154 ARG cc_start: 0.8383 (ptt180) cc_final: 0.7959 (tpt-90) REVERT: A 218 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7740 (tpt-90) REVERT: A 259 MET cc_start: 0.8754 (tpp) cc_final: 0.8541 (mmm) REVERT: A 261 MET cc_start: 0.7975 (mmm) cc_final: 0.7718 (mtt) REVERT: A 340 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7668 (tt) REVERT: A 408 LEU cc_start: 0.7990 (tp) cc_final: 0.7724 (tt) REVERT: A 493 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8079 (m-30) REVERT: B 31 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8425 (pt) REVERT: B 261 MET cc_start: 0.8331 (mmm) cc_final: 0.8114 (mtp) REVERT: B 282 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7584 (mm-40) REVERT: B 317 GLN cc_start: 0.8582 (mt0) cc_final: 0.8308 (tt0) REVERT: B 363 MET cc_start: 0.8898 (mmt) cc_final: 0.8504 (mmt) REVERT: B 411 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8298 (tp) outliers start: 40 outliers final: 16 residues processed: 158 average time/residue: 0.1011 time to fit residues: 20.5476 Evaluate side-chains 100 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 ARG Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 508 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 GLN A 290 HIS A 349 HIS B 266 ASN B 290 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.148029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121864 restraints weight = 10616.025| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.77 r_work: 0.3202 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7995 Z= 0.135 Angle : 0.652 9.652 10943 Z= 0.322 Chirality : 0.042 0.145 1230 Planarity : 0.005 0.031 1437 Dihedral : 8.803 83.444 1162 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.40 % Favored : 98.40 % Rotamer: Outliers : 2.89 % Allowed : 16.08 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.47 (0.24), residues: 1000 helix: -1.17 (0.27), residues: 320 sheet: 0.40 (0.34), residues: 184 loop : -1.33 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 505 TYR 0.019 0.002 TYR A 307 PHE 0.010 0.001 PHE B 170 TRP 0.020 0.001 TRP A 82 HIS 0.005 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 7995) covalent geometry : angle 0.65193 / 0.32 (10943) hydrogen bonds : bond 0.05697 / 4.02 ( 336) hydrogen bonds : angle 5.36201 / 3.75 ( 918) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.172 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6831 (pm20) REVERT: A 218 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.7796 (mmm160) REVERT: A 243 ASN cc_start: 0.7983 (t0) cc_final: 0.7764 (t0) REVERT: B 31 ILE cc_start: 0.8960 (OUTLIER) cc_final: 0.8709 (pt) REVERT: B 154 ARG cc_start: 0.8287 (mmm-85) cc_final: 0.8017 (ttm-80) REVERT: B 282 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7444 (mm-40) REVERT: B 311 LEU cc_start: 0.8062 (mt) cc_final: 0.7772 (mt) outliers start: 23 outliers final: 11 residues processed: 113 average time/residue: 0.0976 time to fit residues: 14.3557 Evaluate side-chains 85 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 349 HIS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 0 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 291 HIS B 329 GLN B 349 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.144265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116262 restraints weight = 10572.809| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.96 r_work: 0.3135 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7995 Z= 0.197 Angle : 0.641 7.695 10943 Z= 0.313 Chirality : 0.043 0.187 1230 Planarity : 0.005 0.041 1437 Dihedral : 7.678 86.421 1132 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.64 % Allowed : 17.71 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.25), residues: 1000 helix: -0.40 (0.28), residues: 320 sheet: 0.76 (0.37), residues: 158 loop : -1.18 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 191 TYR 0.020 0.002 TYR A 176 PHE 0.009 0.001 PHE A 9 TRP 0.015 0.002 TRP A 82 HIS 0.008 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 ( 7995) covalent geometry : angle 0.64078 / 0.31 (10943) hydrogen bonds : bond 0.05893 / 4.14 ( 336) hydrogen bonds : angle 5.08858 / 3.55 ( 918) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6800 (pm20) REVERT: A 218 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.7765 (mtp85) REVERT: A 222 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7519 (pmm150) REVERT: A 243 ASN cc_start: 0.7991 (t0) cc_final: 0.7729 (t0) REVERT: B 26 ARG cc_start: 0.7201 (mtp180) cc_final: 0.6867 (mmm160) REVERT: B 154 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8103 (ttm-80) REVERT: B 222 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7556 (pmm150) REVERT: B 282 GLN cc_start: 0.8277 (OUTLIER) cc_final: 0.7726 (tm-30) outliers start: 21 outliers final: 12 residues processed: 97 average time/residue: 0.0806 time to fit residues: 10.3638 Evaluate side-chains 84 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.0470 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 84 optimal weight: 0.0570 chunk 46 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 GLN B 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.118701 restraints weight = 10736.755| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.99 r_work: 0.3182 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7995 Z= 0.114 Angle : 0.538 7.963 10943 Z= 0.262 Chirality : 0.041 0.188 1230 Planarity : 0.004 0.035 1437 Dihedral : 7.095 86.322 1126 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.89 % Allowed : 18.84 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.25), residues: 1000 helix: 0.29 (0.29), residues: 325 sheet: 0.92 (0.37), residues: 170 loop : -0.97 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 191 TYR 0.013 0.001 TYR B 176 PHE 0.007 0.001 PHE B 469 TRP 0.010 0.001 TRP B 451 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 7995) covalent geometry : angle 0.53773 / 0.26 (10943) hydrogen bonds : bond 0.04300 / 3.03 ( 336) hydrogen bonds : angle 4.59325 / 3.20 ( 918) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6797 (pm20) REVERT: A 85 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8151 (mt) REVERT: A 218 ARG cc_start: 0.8589 (ttm-80) cc_final: 0.7754 (mtp85) REVERT: A 222 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7283 (pmm150) REVERT: A 514 ARG cc_start: 0.8548 (tpp80) cc_final: 0.8186 (tpp-160) REVERT: B 24 CYS cc_start: 0.7718 (p) cc_final: 0.7255 (m) REVERT: B 154 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.8183 (ttm-80) REVERT: B 222 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7117 (pmm150) REVERT: B 282 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: B 510 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6480 (mtm110) outliers start: 23 outliers final: 9 residues processed: 93 average time/residue: 0.0890 time to fit residues: 10.9655 Evaluate side-chains 83 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 0.0020 chunk 10 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 291 HIS B 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.143563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115477 restraints weight = 10917.055| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.12 r_work: 0.3185 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7995 Z= 0.165 Angle : 0.584 6.465 10943 Z= 0.283 Chirality : 0.042 0.193 1230 Planarity : 0.005 0.042 1437 Dihedral : 7.103 87.733 1124 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.52 % Allowed : 18.59 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.26), residues: 1000 helix: 0.37 (0.29), residues: 335 sheet: 1.02 (0.38), residues: 170 loop : -0.90 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 191 TYR 0.022 0.002 TYR A 176 PHE 0.013 0.001 PHE A 198 TRP 0.010 0.001 TRP A 284 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 7995) covalent geometry : angle 0.58448 / 0.28 (10943) hydrogen bonds : bond 0.04832 / 3.40 ( 336) hydrogen bonds : angle 4.67265 / 3.24 ( 918) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6771 (pm20) REVERT: A 85 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8091 (mt) REVERT: A 218 ARG cc_start: 0.8574 (ttm-80) cc_final: 0.7683 (mtp85) REVERT: A 222 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7384 (pmm150) REVERT: A 514 ARG cc_start: 0.8611 (tpp80) cc_final: 0.8218 (tpp-160) REVERT: B 26 ARG cc_start: 0.7190 (mtp180) cc_final: 0.6842 (mmm160) REVERT: B 154 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8264 (ttm-80) REVERT: B 222 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7549 (pmm150) REVERT: B 274 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8556 (p) REVERT: B 282 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: B 510 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6499 (mtm110) outliers start: 28 outliers final: 16 residues processed: 100 average time/residue: 0.1028 time to fit residues: 13.4076 Evaluate side-chains 91 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 0.0980 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.145268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117362 restraints weight = 10825.566| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.09 r_work: 0.3187 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7995 Z= 0.113 Angle : 0.530 7.470 10943 Z= 0.255 Chirality : 0.040 0.189 1230 Planarity : 0.004 0.038 1437 Dihedral : 6.949 87.777 1124 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.14 % Allowed : 19.72 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.26), residues: 1000 helix: 0.71 (0.29), residues: 334 sheet: 1.00 (0.38), residues: 175 loop : -0.73 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 191 TYR 0.013 0.001 TYR B 176 PHE 0.005 0.001 PHE A 9 TRP 0.009 0.001 TRP A 284 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 7995) covalent geometry : angle 0.52976 / 0.26 (10943) hydrogen bonds : bond 0.04119 / 2.91 ( 336) hydrogen bonds : angle 4.46105 / 3.10 ( 918) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6743 (pm20) REVERT: A 85 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8040 (mt) REVERT: A 181 ASP cc_start: 0.7785 (t70) cc_final: 0.7570 (t0) REVERT: A 218 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.7613 (mtp85) REVERT: A 222 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7248 (pmm150) REVERT: A 514 ARG cc_start: 0.8591 (tpp80) cc_final: 0.8233 (tpp-160) REVERT: B 154 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.8185 (ttm-80) REVERT: B 222 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7263 (pmm150) REVERT: B 274 SER cc_start: 0.8727 (OUTLIER) cc_final: 0.8503 (p) REVERT: B 282 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7567 (tm-30) REVERT: B 510 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6477 (mtm110) outliers start: 25 outliers final: 15 residues processed: 93 average time/residue: 0.0929 time to fit residues: 11.3245 Evaluate side-chains 91 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.144569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.117111 restraints weight = 10781.667| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.13 r_work: 0.3112 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7995 Z= 0.175 Angle : 0.595 7.656 10943 Z= 0.286 Chirality : 0.043 0.185 1230 Planarity : 0.005 0.041 1437 Dihedral : 7.181 89.666 1124 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.89 % Allowed : 19.35 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.26), residues: 1000 helix: 0.58 (0.29), residues: 335 sheet: 0.87 (0.38), residues: 179 loop : -0.75 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 191 TYR 0.015 0.001 TYR B 176 PHE 0.007 0.001 PHE A 9 TRP 0.011 0.001 TRP A 284 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 7995) covalent geometry : angle 0.59520 / 0.29 (10943) hydrogen bonds : bond 0.04849 / 3.41 ( 336) hydrogen bonds : angle 4.68097 / 3.24 ( 918) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6701 (pm20) REVERT: A 85 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8061 (mt) REVERT: A 181 ASP cc_start: 0.7925 (t70) cc_final: 0.7659 (t0) REVERT: A 218 ARG cc_start: 0.8556 (ttm-80) cc_final: 0.7619 (mtp85) REVERT: A 222 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7344 (pmm150) REVERT: A 514 ARG cc_start: 0.8631 (tpp80) cc_final: 0.8220 (tpp-160) REVERT: B 26 ARG cc_start: 0.7096 (mtp180) cc_final: 0.6627 (mmm160) REVERT: B 154 ARG cc_start: 0.8600 (mmm-85) cc_final: 0.8256 (ttm-80) REVERT: B 222 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7495 (pmm150) REVERT: B 510 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6462 (mtm110) outliers start: 31 outliers final: 20 residues processed: 98 average time/residue: 0.0944 time to fit residues: 11.9278 Evaluate side-chains 98 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 502 LEU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 0.0470 chunk 51 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.145959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118968 restraints weight = 10691.679| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.07 r_work: 0.3156 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7995 Z= 0.109 Angle : 0.530 8.060 10943 Z= 0.255 Chirality : 0.040 0.179 1230 Planarity : 0.004 0.037 1437 Dihedral : 6.988 88.764 1124 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.14 % Allowed : 20.73 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.26), residues: 1000 helix: 0.91 (0.29), residues: 338 sheet: 1.11 (0.39), residues: 174 loop : -0.66 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 191 TYR 0.013 0.001 TYR B 176 PHE 0.005 0.001 PHE A 9 TRP 0.010 0.001 TRP A 284 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 7995) covalent geometry : angle 0.53023 / 0.25 (10943) hydrogen bonds : bond 0.04007 / 2.82 ( 336) hydrogen bonds : angle 4.43785 / 3.07 ( 918) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6691 (pm20) REVERT: A 85 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8052 (mt) REVERT: A 218 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.7593 (mtp85) REVERT: A 222 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7149 (pmm150) REVERT: A 514 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8169 (tpp-160) REVERT: B 26 ARG cc_start: 0.7102 (mtp180) cc_final: 0.6749 (mmm160) REVERT: B 154 ARG cc_start: 0.8534 (mmm-85) cc_final: 0.8163 (ttm-80) REVERT: B 222 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7242 (pmm150) REVERT: B 274 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8480 (p) REVERT: B 510 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6429 (mtm110) outliers start: 25 outliers final: 16 residues processed: 95 average time/residue: 0.0960 time to fit residues: 12.0535 Evaluate side-chains 94 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 54 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 84 optimal weight: 0.0050 chunk 66 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.147830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120783 restraints weight = 10689.387| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.98 r_work: 0.3251 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7995 Z= 0.097 Angle : 0.518 7.831 10943 Z= 0.249 Chirality : 0.040 0.162 1230 Planarity : 0.004 0.034 1437 Dihedral : 6.807 87.324 1124 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.51 % Allowed : 20.73 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.26), residues: 1000 helix: 1.21 (0.29), residues: 338 sheet: 1.21 (0.39), residues: 175 loop : -0.55 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 510 TYR 0.012 0.001 TYR B 176 PHE 0.004 0.001 PHE A 9 TRP 0.010 0.001 TRP A 376 HIS 0.003 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 ( 7995) covalent geometry : angle 0.51837 / 0.25 (10943) hydrogen bonds : bond 0.03615 / 2.55 ( 336) hydrogen bonds : angle 4.27203 / 2.97 ( 918) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6666 (pm20) REVERT: A 85 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8078 (mt) REVERT: A 218 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.7615 (mtp85) REVERT: A 222 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7122 (pmm150) REVERT: A 513 ASN cc_start: 0.8439 (t0) cc_final: 0.8019 (t0) REVERT: A 514 ARG cc_start: 0.8421 (tpp80) cc_final: 0.8059 (tpp-160) REVERT: B 26 ARG cc_start: 0.7117 (mtp180) cc_final: 0.6653 (mtp180) REVERT: B 154 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.8048 (ttm-80) REVERT: B 222 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7136 (pmm150) REVERT: B 274 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8394 (p) REVERT: B 282 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7613 (tm-30) outliers start: 20 outliers final: 14 residues processed: 95 average time/residue: 0.0983 time to fit residues: 12.3495 Evaluate side-chains 92 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain A residue 473 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.119793 restraints weight = 10617.271| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.03 r_work: 0.3177 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7995 Z= 0.113 Angle : 0.528 7.781 10943 Z= 0.253 Chirality : 0.040 0.188 1230 Planarity : 0.004 0.045 1437 Dihedral : 6.833 87.138 1124 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.39 % Allowed : 20.98 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.26), residues: 1000 helix: 1.25 (0.29), residues: 338 sheet: 1.10 (0.39), residues: 180 loop : -0.50 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 510 TYR 0.022 0.001 TYR A 176 PHE 0.005 0.001 PHE A 9 TRP 0.009 0.001 TRP A 284 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 ( 7995) covalent geometry : angle 0.52804 / 0.25 (10943) hydrogen bonds : bond 0.03847 / 2.70 ( 336) hydrogen bonds : angle 4.30374 / 2.99 ( 918) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6677 (pm20) REVERT: A 85 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8050 (mt) REVERT: A 218 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.7591 (mtp85) REVERT: A 222 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7195 (pmm150) REVERT: A 513 ASN cc_start: 0.8493 (t0) cc_final: 0.8080 (t0) REVERT: A 514 ARG cc_start: 0.8458 (tpp80) cc_final: 0.8105 (tpp-160) REVERT: B 26 ARG cc_start: 0.7086 (mtp180) cc_final: 0.6352 (mmm160) REVERT: B 154 ARG cc_start: 0.8513 (mmm-85) cc_final: 0.8120 (ttm-80) REVERT: B 222 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7314 (pmm150) REVERT: B 274 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8440 (p) REVERT: B 282 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7620 (tm-30) outliers start: 19 outliers final: 12 residues processed: 91 average time/residue: 0.1047 time to fit residues: 12.6609 Evaluate side-chains 92 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 349 HIS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 511 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.146448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.119093 restraints weight = 10680.408| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.06 r_work: 0.3155 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7995 Z= 0.127 Angle : 0.554 8.810 10943 Z= 0.264 Chirality : 0.041 0.229 1230 Planarity : 0.005 0.047 1437 Dihedral : 6.889 87.193 1124 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.51 % Allowed : 21.61 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.26), residues: 1000 helix: 1.19 (0.29), residues: 338 sheet: 1.11 (0.39), residues: 180 loop : -0.50 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 191 TYR 0.013 0.001 TYR B 176 PHE 0.005 0.001 PHE A 9 TRP 0.009 0.001 TRP A 284 HIS 0.004 0.001 HIS B 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 7995) covalent geometry : angle 0.55369 / 0.26 (10943) hydrogen bonds : bond 0.03996 / 2.80 ( 336) hydrogen bonds : angle 4.34802 / 3.01 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1793.57 seconds wall clock time: 31 minutes 17.82 seconds (1877.82 seconds total)