Starting phenix.real_space_refine on Sun May 11 12:40:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8avv_15684/05_2025/8avv_15684.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avv_15684/05_2025/8avv_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8avv_15684/05_2025/8avv_15684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avv_15684/05_2025/8avv_15684.map" model { file = "/net/cci-nas-00/data/ceres_data/8avv_15684/05_2025/8avv_15684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avv_15684/05_2025/8avv_15684.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.31, per 1000 atoms: 0.81 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: 1.87 Conformation dependent library (CDL) restraints added in 864.7 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: 1.02 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: 2.33 Time building geometry restraints manager: 2.17 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: 4031 15.78 - 31.55: 464 31.55 - 47.32: 181 47.32 - 63.10: 54 63.10 - 78.87: 41 Dihedral angle restraints: 4771 sinusoidal: 1892 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 4768 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 519 or resid 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: 7.660 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.380 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 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 : 18.227 78.875 2915 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.002 TRP A 412 HIS 0.008 0.002 HIS B 484 PHE 0.016 0.003 PHE A 170 TYR 0.016 0.002 TYR A 263 ARG 0.004 0.001 ARG B 154 Details of bonding type rmsd hydrogen bonds : bond 0.31349 ( 336) hydrogen bonds : angle 9.28641 ( 918) covalent geometry : bond 0.00773 ( 7995) covalent geometry : angle 1.38120 (10943) *********************** 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 : 0.879 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: 0.2492 time to fit residues: 50.4349 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 : 0.778 ------------------------------------------------------------------------------- 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 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.0070 chunk 90 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 290 HIS A 349 HIS B 72 GLN B 266 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.123293 restraints weight = 10493.420| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.75 r_work: 0.3134 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2127 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= 0.146 Angle : 0.658 9.016 10943 Z= 0.327 Chirality : 0.042 0.149 1230 Planarity : 0.005 0.034 1437 Dihedral : 8.875 83.405 1178 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.14 % Allowed : 16.08 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.24), residues: 1000 helix: -1.07 (0.27), residues: 320 sheet: 0.40 (0.34), residues: 185 loop : -1.32 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 82 HIS 0.005 0.001 HIS A 334 PHE 0.009 0.001 PHE B 170 TYR 0.019 0.002 TYR A 307 ARG 0.005 0.001 ARG B 332 Details of bonding type rmsd hydrogen bonds : bond 0.06050 ( 336) hydrogen bonds : angle 5.40958 ( 918) covalent geometry : bond 0.00317 ( 7995) covalent geometry : angle 0.65797 (10943) *********************** 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 115 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 90 time to evaluate : 0.773 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6721 (pm20) REVERT: A 218 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.7806 (mmm160) REVERT: A 243 ASN cc_start: 0.7986 (t0) cc_final: 0.7782 (t0) REVERT: B 31 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8718 (pt) REVERT: B 154 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8021 (ttm-80) REVERT: B 282 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7366 (mm-40) REVERT: B 311 LEU cc_start: 0.8080 (mt) cc_final: 0.7810 (mt) outliers start: 25 outliers final: 12 residues processed: 112 average time/residue: 0.2452 time to fit residues: 35.6041 Evaluate side-chains 84 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.767 ------------------------------------------------------------------------------- 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 402 LEU Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 60 THR 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 324 VAL 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 13 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 8 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN B 291 HIS B 329 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.149696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123842 restraints weight = 10568.642| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.76 r_work: 0.3172 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7995 Z= 0.104 Angle : 0.540 7.092 10943 Z= 0.263 Chirality : 0.040 0.171 1230 Planarity : 0.004 0.032 1437 Dihedral : 7.208 82.607 1149 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.14 % Allowed : 17.21 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1000 helix: 0.14 (0.29), residues: 319 sheet: 0.80 (0.37), residues: 158 loop : -1.09 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 82 HIS 0.003 0.001 HIS A 334 PHE 0.005 0.001 PHE B 327 TYR 0.023 0.002 TYR A 176 ARG 0.006 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04591 ( 336) hydrogen bonds : angle 4.73066 ( 918) covalent geometry : bond 0.00223 ( 7995) covalent geometry : angle 0.53984 (10943) *********************** 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 91 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6745 (pm20) REVERT: A 218 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.7850 (mtp85) REVERT: A 222 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7236 (pmm150) REVERT: A 243 ASN cc_start: 0.8054 (t0) cc_final: 0.7731 (t0) REVERT: A 514 ARG cc_start: 0.8540 (tpp80) cc_final: 0.8258 (tpp-160) REVERT: B 24 CYS cc_start: 0.7683 (p) cc_final: 0.7317 (m) REVERT: B 154 ARG cc_start: 0.8318 (mmm-85) cc_final: 0.7992 (ttm-80) REVERT: B 222 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.6952 (pmm150) REVERT: B 282 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: B 311 LEU cc_start: 0.8015 (mt) cc_final: 0.7763 (mt) REVERT: B 411 LEU cc_start: 0.8562 (mp) cc_final: 0.8303 (tp) outliers start: 17 outliers final: 11 residues processed: 88 average time/residue: 0.2497 time to fit residues: 28.9452 Evaluate side-chains 84 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU 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 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 349 HIS 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 37 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN B 349 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118347 restraints weight = 10597.112| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.98 r_work: 0.3130 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2979 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= 0.141 Angle : 0.570 8.609 10943 Z= 0.277 Chirality : 0.042 0.199 1230 Planarity : 0.005 0.045 1437 Dihedral : 7.087 84.621 1144 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.39 % Allowed : 17.71 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1000 helix: 0.45 (0.29), residues: 326 sheet: 1.02 (0.39), residues: 158 loop : -0.96 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 82 HIS 0.006 0.001 HIS A 334 PHE 0.007 0.001 PHE A 9 TYR 0.016 0.002 TYR B 176 ARG 0.008 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 336) hydrogen bonds : angle 4.60846 ( 918) covalent geometry : bond 0.00331 ( 7995) covalent geometry : angle 0.56961 (10943) *********************** 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 106 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6770 (pm20) REVERT: A 218 ARG cc_start: 0.8549 (ttm-80) cc_final: 0.7707 (mtp85) REVERT: A 514 ARG cc_start: 0.8554 (tpp80) cc_final: 0.8268 (tpp-160) REVERT: B 154 ARG cc_start: 0.8419 (mmm-85) cc_final: 0.8106 (ttm-80) REVERT: B 222 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7060 (pmm150) REVERT: B 282 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7665 (tm-30) REVERT: B 311 LEU cc_start: 0.7977 (mt) cc_final: 0.7735 (mt) REVERT: B 510 ARG cc_start: 0.7246 (OUTLIER) cc_final: 0.6525 (mtm110) outliers start: 27 outliers final: 14 residues processed: 99 average time/residue: 0.2569 time to fit residues: 33.0424 Evaluate side-chains 88 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 187 ILE 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 54 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.3980 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS A 291 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116620 restraints weight = 10648.273| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.12 r_work: 0.3179 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7995 Z= 0.127 Angle : 0.536 7.434 10943 Z= 0.261 Chirality : 0.041 0.187 1230 Planarity : 0.004 0.042 1437 Dihedral : 6.732 85.939 1140 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.89 % Allowed : 19.85 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.26), residues: 1000 helix: 0.63 (0.29), residues: 335 sheet: 1.15 (0.38), residues: 169 loop : -0.83 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 451 HIS 0.004 0.001 HIS A 334 PHE 0.006 0.001 PHE B 469 TYR 0.014 0.001 TYR B 176 ARG 0.008 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04338 ( 336) hydrogen bonds : angle 4.50199 ( 918) covalent geometry : bond 0.00298 ( 7995) covalent geometry : angle 0.53577 (10943) *********************** 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 98 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6752 (pm20) REVERT: A 85 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8053 (mt) REVERT: A 218 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.7665 (mtp85) REVERT: A 222 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7371 (pmm150) REVERT: A 514 ARG cc_start: 0.8645 (tpp80) cc_final: 0.8344 (tpp-160) REVERT: B 24 CYS cc_start: 0.7742 (p) cc_final: 0.7286 (m) REVERT: B 154 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.8050 (ttm-80) REVERT: B 282 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7638 (tm-30) REVERT: B 311 LEU cc_start: 0.7983 (mt) cc_final: 0.7720 (mt) outliers start: 23 outliers final: 12 residues processed: 94 average time/residue: 0.2357 time to fit residues: 29.4969 Evaluate side-chains 87 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 349 HIS Chi-restraints excluded: chain A residue 378 THR 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 187 ILE 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 506 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 90 optimal weight: 0.0770 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS B 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.142744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.115178 restraints weight = 10614.041| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.99 r_work: 0.3109 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7995 Z= 0.229 Angle : 0.662 7.230 10943 Z= 0.322 Chirality : 0.045 0.199 1230 Planarity : 0.005 0.049 1437 Dihedral : 7.404 89.479 1140 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.39 % Allowed : 19.35 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1000 helix: 0.22 (0.29), residues: 332 sheet: 0.81 (0.38), residues: 176 loop : -0.91 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 284 HIS 0.008 0.001 HIS A 334 PHE 0.011 0.002 PHE A 9 TYR 0.016 0.002 TYR B 176 ARG 0.008 0.001 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.05625 ( 336) hydrogen bonds : angle 4.96202 ( 918) covalent geometry : bond 0.00561 ( 7995) covalent geometry : angle 0.66227 (10943) *********************** 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 105 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6747 (pm20) REVERT: A 85 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8121 (mt) REVERT: A 218 ARG cc_start: 0.8660 (ttm-80) cc_final: 0.7711 (mtp85) REVERT: A 222 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7711 (pmm150) REVERT: B 26 ARG cc_start: 0.7104 (mtp180) cc_final: 0.6744 (mmm160) REVERT: B 154 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.8215 (ttm-80) REVERT: B 222 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7537 (pmm150) REVERT: B 311 LEU cc_start: 0.8037 (mt) cc_final: 0.7813 (mt) REVERT: B 510 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6513 (mtm110) outliers start: 27 outliers final: 16 residues processed: 103 average time/residue: 0.2490 time to fit residues: 33.3941 Evaluate side-chains 91 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE 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 349 HIS Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 54 MET 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 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 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 89 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.145365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.117781 restraints weight = 10573.508| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.00 r_work: 0.3161 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7995 Z= 0.120 Angle : 0.540 7.082 10943 Z= 0.263 Chirality : 0.041 0.172 1230 Planarity : 0.004 0.040 1437 Dihedral : 7.107 89.449 1140 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.02 % Allowed : 20.10 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1000 helix: 0.65 (0.29), residues: 331 sheet: 0.97 (0.39), residues: 174 loop : -0.72 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.004 0.001 HIS B 38 PHE 0.008 0.001 PHE B 469 TYR 0.013 0.001 TYR B 176 ARG 0.006 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 336) hydrogen bonds : angle 4.53372 ( 918) covalent geometry : bond 0.00279 ( 7995) covalent geometry : angle 0.54016 (10943) *********************** 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 98 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6727 (pm20) REVERT: A 85 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8012 (mt) REVERT: A 181 ASP cc_start: 0.8053 (t70) cc_final: 0.7851 (t0) REVERT: A 218 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.7592 (mtp85) REVERT: A 222 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7231 (pmm150) REVERT: A 514 ARG cc_start: 0.8614 (tpp80) cc_final: 0.8235 (tpp-160) REVERT: B 26 ARG cc_start: 0.7116 (mtp180) cc_final: 0.6630 (mmm160) REVERT: B 154 ARG cc_start: 0.8346 (mmm-85) cc_final: 0.8000 (ttm-80) REVERT: B 222 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7071 (pmm150) REVERT: B 311 LEU cc_start: 0.7966 (mt) cc_final: 0.7727 (mt) REVERT: B 510 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6448 (mtm110) outliers start: 24 outliers final: 16 residues processed: 95 average time/residue: 0.2426 time to fit residues: 30.5040 Evaluate side-chains 95 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 378 THR Chi-restraints excluded: chain B residue 54 MET 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 274 SER Chi-restraints excluded: chain B residue 282 GLN Chi-restraints excluded: chain B residue 293 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 458 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.142173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.115095 restraints weight = 10756.283| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.08 r_work: 0.3151 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 7995 Z= 0.269 Angle : 0.669 7.513 10943 Z= 0.325 Chirality : 0.046 0.200 1230 Planarity : 0.005 0.047 1437 Dihedral : 7.496 89.806 1140 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.39 % Allowed : 19.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1000 helix: 0.20 (0.29), residues: 333 sheet: 0.79 (0.39), residues: 175 loop : -0.88 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 284 HIS 0.006 0.001 HIS A 116 PHE 0.010 0.002 PHE A 145 TYR 0.018 0.002 TYR B 176 ARG 0.005 0.001 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.05583 ( 336) hydrogen bonds : angle 4.93083 ( 918) covalent geometry : bond 0.00662 ( 7995) covalent geometry : angle 0.66900 (10943) *********************** 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 98 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6774 (pm20) REVERT: A 85 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8198 (mt) REVERT: A 218 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.7469 (tpt-90) REVERT: A 222 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7918 (pmm150) REVERT: A 514 ARG cc_start: 0.8745 (tpp80) cc_final: 0.8416 (tpp-160) REVERT: B 26 ARG cc_start: 0.7187 (mtp180) cc_final: 0.6789 (mmm160) REVERT: B 154 ARG cc_start: 0.8524 (mmm-85) cc_final: 0.8206 (ttm-80) REVERT: B 222 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7590 (pmm150) REVERT: B 510 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6530 (mtm110) outliers start: 27 outliers final: 17 residues processed: 96 average time/residue: 0.2488 time to fit residues: 31.5067 Evaluate side-chains 90 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE 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 378 THR Chi-restraints excluded: chain B residue 54 MET 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 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 502 LEU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 510 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 72 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.144753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.117500 restraints weight = 10855.658| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.00 r_work: 0.3138 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7995 Z= 0.127 Angle : 0.554 7.428 10943 Z= 0.268 Chirality : 0.041 0.187 1230 Planarity : 0.005 0.041 1437 Dihedral : 7.260 89.923 1140 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.76 % Allowed : 20.73 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.26), residues: 1000 helix: 0.60 (0.29), residues: 332 sheet: 0.97 (0.39), residues: 174 loop : -0.75 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.004 0.001 HIS B 38 PHE 0.006 0.001 PHE A 9 TYR 0.013 0.001 TYR B 176 ARG 0.006 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 336) hydrogen bonds : angle 4.59946 ( 918) covalent geometry : bond 0.00297 ( 7995) covalent geometry : angle 0.55365 (10943) *********************** 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 96 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6755 (pm20) REVERT: A 85 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8060 (mt) REVERT: A 181 ASP cc_start: 0.8105 (t70) cc_final: 0.7891 (t0) REVERT: A 218 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.7619 (mtp85) REVERT: A 222 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7265 (pmm150) REVERT: A 513 ASN cc_start: 0.8612 (t0) cc_final: 0.8306 (t0) REVERT: A 514 ARG cc_start: 0.8594 (tpp80) cc_final: 0.8271 (tpp-160) REVERT: B 26 ARG cc_start: 0.7130 (mtp180) cc_final: 0.6661 (mmm160) REVERT: B 154 ARG cc_start: 0.8355 (mmm-85) cc_final: 0.8009 (ttm-80) REVERT: B 222 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7173 (pmm150) REVERT: B 510 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6473 (mtm110) outliers start: 22 outliers final: 16 residues processed: 93 average time/residue: 0.2463 time to fit residues: 30.1105 Evaluate side-chains 94 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE 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 378 THR Chi-restraints excluded: chain B residue 54 MET 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 274 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.144408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118083 restraints weight = 10697.353| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.08 r_work: 0.3131 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7995 Z= 0.142 Angle : 0.565 7.446 10943 Z= 0.272 Chirality : 0.042 0.190 1230 Planarity : 0.005 0.040 1437 Dihedral : 7.223 89.829 1140 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.64 % Allowed : 21.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1000 helix: 0.74 (0.29), residues: 332 sheet: 1.00 (0.39), residues: 175 loop : -0.72 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 284 HIS 0.005 0.001 HIS B 38 PHE 0.006 0.001 PHE A 9 TYR 0.014 0.001 TYR B 176 ARG 0.007 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 336) hydrogen bonds : angle 4.57418 ( 918) covalent geometry : bond 0.00339 ( 7995) covalent geometry : angle 0.56490 (10943) ********************** 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 99 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6739 (pm20) REVERT: A 85 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8077 (mt) REVERT: A 181 ASP cc_start: 0.8163 (t70) cc_final: 0.7948 (t0) REVERT: A 218 ARG cc_start: 0.8581 (ttm-80) cc_final: 0.7428 (tpt-90) REVERT: A 222 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7343 (pmm150) REVERT: A 513 ASN cc_start: 0.8626 (t0) cc_final: 0.8335 (t0) REVERT: A 514 ARG cc_start: 0.8516 (tpp80) cc_final: 0.7821 (mpt-90) REVERT: B 26 ARG cc_start: 0.7156 (mtp180) cc_final: 0.6396 (mmm160) REVERT: B 154 ARG cc_start: 0.8455 (mmm-85) cc_final: 0.8103 (ttm-80) REVERT: B 222 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7232 (pmm150) REVERT: B 510 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6537 (mtm110) outliers start: 21 outliers final: 17 residues processed: 95 average time/residue: 0.2379 time to fit residues: 29.8220 Evaluate side-chains 97 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 237 VAL 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 378 THR Chi-restraints excluded: chain B residue 54 MET 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 0.1980 chunk 23 optimal weight: 0.2980 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.144427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116932 restraints weight = 10725.767| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.06 r_work: 0.3136 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3848 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= 0.142 Angle : 0.581 9.897 10943 Z= 0.278 Chirality : 0.042 0.206 1230 Planarity : 0.005 0.047 1437 Dihedral : 7.205 89.656 1140 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.89 % Allowed : 21.23 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1000 helix: 0.67 (0.29), residues: 338 sheet: 1.04 (0.39), residues: 175 loop : -0.68 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 284 HIS 0.005 0.001 HIS B 38 PHE 0.006 0.001 PHE A 9 TYR 0.014 0.001 TYR B 176 ARG 0.010 0.000 ARG B 191 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 336) hydrogen bonds : angle 4.56492 ( 918) covalent geometry : bond 0.00340 ( 7995) covalent geometry : angle 0.58108 (10943) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4271.11 seconds wall clock time: 74 minutes 26.99 seconds (4466.99 seconds total)