Starting phenix.real_space_refine on Fri Aug 22 21:22:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8avv_15684/08_2025/8avv_15684.cif Found real_map, /net/cci-nas-00/data/ceres_data/8avv_15684/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8avv_15684/08_2025/8avv_15684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8avv_15684/08_2025/8avv_15684.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8avv_15684/08_2025/8avv_15684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8avv_15684/08_2025/8avv_15684.map" } 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-2.0-5787/lib/python3.9/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: 1.75, per 1000 atoms: 0.22 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: 0.53 Conformation dependent library (CDL) restraints added in 373.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.24 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: 0.96 Time building geometry restraints manager: 0.74 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 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: 6.810 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.670 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.010 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00773 ( 7995) covalent geometry : angle 1.38120 (10943) hydrogen bonds : bond 0.31349 ( 336) hydrogen bonds : angle 9.28641 ( 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 : 0.283 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: 0.0993 time to fit residues: 19.7929 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 : 0.199 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3677 r_free = 0.3677 target = 0.147971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121830 restraints weight = 10605.001| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.76 r_work: 0.3199 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2194 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= 0.137 Angle : 0.654 9.879 10943 Z= 0.323 Chirality : 0.042 0.148 1230 Planarity : 0.005 0.031 1437 Dihedral : 8.781 83.393 1178 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.50 % Favored : 98.30 % Rotamer: Outliers : 2.89 % Allowed : 16.21 % Favored : 80.90 % 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 aren not related in a simple way. whole: -1.50 (0.24), residues: 1000 helix: -1.21 (0.27), residues: 320 sheet: 0.39 (0.34), residues: 184 loop : -1.33 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 332 TYR 0.019 0.002 TYR A 307 PHE 0.009 0.001 PHE B 170 TRP 0.019 0.001 TRP A 82 HIS 0.005 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 7995) covalent geometry : angle 0.65432 (10943) hydrogen bonds : bond 0.05992 ( 336) hydrogen bonds : angle 5.42114 ( 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 : 0.222 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6812 (pm20) REVERT: A 218 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.7799 (mmm160) REVERT: A 243 ASN cc_start: 0.7989 (t0) cc_final: 0.7777 (t0) REVERT: B 154 ARG cc_start: 0.8314 (mmm-85) cc_final: 0.8039 (ttm-80) REVERT: B 282 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7446 (mm-40) REVERT: B 311 LEU cc_start: 0.8068 (mt) cc_final: 0.7797 (mt) outliers start: 23 outliers final: 11 residues processed: 113 average time/residue: 0.0867 time to fit residues: 12.6842 Evaluate side-chains 85 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3655 r_free = 0.3655 target = 0.145403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117266 restraints weight = 10557.120| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.98 r_work: 0.3134 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7995 Z= 0.171 Angle : 0.613 7.945 10943 Z= 0.300 Chirality : 0.042 0.168 1230 Planarity : 0.005 0.039 1437 Dihedral : 7.482 85.609 1146 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.64 % Allowed : 16.96 % Favored : 80.40 % 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 aren not related in a simple way. whole: -0.82 (0.25), residues: 1000 helix: -0.24 (0.28), residues: 320 sheet: 0.77 (0.37), residues: 158 loop : -1.15 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 191 TYR 0.021 0.002 TYR A 176 PHE 0.008 0.001 PHE A 9 TRP 0.014 0.002 TRP A 82 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 7995) covalent geometry : angle 0.61323 (10943) hydrogen bonds : bond 0.05443 ( 336) hydrogen bonds : angle 4.97874 ( 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 97 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6803 (pm20) REVERT: A 218 ARG cc_start: 0.8595 (ttm-80) cc_final: 0.7786 (mtp85) REVERT: A 222 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7881 (pmm150) REVERT: A 243 ASN cc_start: 0.8041 (t0) cc_final: 0.7762 (t0) REVERT: B 154 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8087 (ttm-80) REVERT: B 222 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7482 (pmm150) REVERT: B 282 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: B 311 LEU cc_start: 0.8042 (mt) cc_final: 0.7831 (mt) outliers start: 21 outliers final: 12 residues processed: 94 average time/residue: 0.0890 time to fit residues: 11.1667 Evaluate side-chains 79 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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: 0.0050 chunk 89 optimal weight: 0.0670 chunk 93 optimal weight: 0.4980 chunk 57 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.148185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119932 restraints weight = 10716.330| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.01 r_work: 0.3198 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7995 Z= 0.100 Angle : 0.520 8.249 10943 Z= 0.253 Chirality : 0.040 0.186 1230 Planarity : 0.004 0.033 1437 Dihedral : 6.883 85.013 1142 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.39 % Allowed : 18.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.26), residues: 1000 helix: 0.43 (0.29), residues: 326 sheet: 0.93 (0.37), residues: 171 loop : -0.92 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 191 TYR 0.012 0.001 TYR B 176 PHE 0.006 0.001 PHE B 469 TRP 0.011 0.001 TRP B 451 HIS 0.003 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 7995) covalent geometry : angle 0.52041 (10943) hydrogen bonds : bond 0.04074 ( 336) hydrogen bonds : angle 4.52137 ( 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 93 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6764 (pm20) REVERT: A 218 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.7781 (mtp85) REVERT: A 222 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7362 (pmm150) REVERT: A 514 ARG cc_start: 0.8580 (tpp80) cc_final: 0.8317 (tpp-160) REVERT: B 24 CYS cc_start: 0.7733 (p) cc_final: 0.7258 (m) REVERT: B 154 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.8052 (ttm-80) REVERT: B 222 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7078 (pmm150) REVERT: B 282 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: B 311 LEU cc_start: 0.8007 (mt) cc_final: 0.7750 (mt) REVERT: B 510 ARG cc_start: 0.7240 (OUTLIER) cc_final: 0.6520 (mtm110) outliers start: 19 outliers final: 8 residues processed: 88 average time/residue: 0.0879 time to fit residues: 10.2267 Evaluate side-chains 83 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 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 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: 0.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 B 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.116196 restraints weight = 10807.424| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.15 r_work: 0.3179 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3245 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= 0.169 Angle : 0.580 7.509 10943 Z= 0.282 Chirality : 0.042 0.191 1230 Planarity : 0.005 0.040 1437 Dihedral : 6.939 87.276 1140 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.14 % Allowed : 19.10 % Favored : 77.76 % 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 aren not related in a simple way. whole: -0.14 (0.25), residues: 1000 helix: 0.45 (0.29), residues: 328 sheet: 1.08 (0.38), residues: 169 loop : -0.86 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 191 TYR 0.020 0.002 TYR A 176 PHE 0.009 0.001 PHE B 469 TRP 0.010 0.001 TRP A 284 HIS 0.006 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 7995) covalent geometry : angle 0.58014 (10943) hydrogen bonds : bond 0.04764 ( 336) hydrogen bonds : angle 4.63817 ( 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 98 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6750 (pm20) REVERT: A 218 ARG cc_start: 0.8650 (ttm-80) cc_final: 0.7724 (mtp85) REVERT: A 222 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7566 (pmm150) REVERT: A 514 ARG cc_start: 0.8647 (tpp80) cc_final: 0.8375 (tpp-160) REVERT: B 154 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8176 (ttm-80) REVERT: B 222 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7518 (pmm150) REVERT: B 274 SER cc_start: 0.8772 (OUTLIER) cc_final: 0.8544 (p) REVERT: B 282 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: B 311 LEU cc_start: 0.8021 (mt) cc_final: 0.7773 (mt) REVERT: B 510 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6533 (mtm110) outliers start: 25 outliers final: 13 residues processed: 95 average time/residue: 0.1008 time to fit residues: 12.3635 Evaluate side-chains 87 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 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 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 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: 0.9980 chunk 72 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.118179 restraints weight = 10666.948| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.97 r_work: 0.3133 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3413 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= 0.123 Angle : 0.533 6.914 10943 Z= 0.258 Chirality : 0.041 0.184 1230 Planarity : 0.004 0.038 1437 Dihedral : 6.860 87.504 1140 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.02 % Allowed : 19.97 % Favored : 77.01 % 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 aren not related in a simple way. whole: 0.12 (0.26), residues: 1000 helix: 0.70 (0.29), residues: 334 sheet: 1.22 (0.39), residues: 169 loop : -0.74 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 191 TYR 0.014 0.001 TYR B 176 PHE 0.006 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 covalent geometry : bond 0.00288 ( 7995) covalent geometry : angle 0.53267 (10943) hydrogen bonds : bond 0.04218 ( 336) hydrogen bonds : angle 4.46380 ( 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 101 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6773 (pm20) REVERT: A 181 ASP cc_start: 0.7989 (t70) cc_final: 0.7784 (t0) REVERT: A 218 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.7630 (mtp85) REVERT: A 222 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7622 (pmm150) REVERT: A 514 ARG cc_start: 0.8640 (tpp80) cc_final: 0.8347 (tpp-160) REVERT: B 26 ARG cc_start: 0.7108 (mtp180) cc_final: 0.6765 (mmm160) REVERT: B 31 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8667 (pt) REVERT: B 154 ARG cc_start: 0.8404 (mmm-85) cc_final: 0.8058 (ttm-80) REVERT: B 222 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7248 (pmm150) REVERT: B 274 SER cc_start: 0.8715 (OUTLIER) cc_final: 0.8492 (p) REVERT: B 282 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: B 311 LEU cc_start: 0.7959 (mt) cc_final: 0.7730 (mt) REVERT: B 510 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6478 (mtm110) outliers start: 24 outliers final: 11 residues processed: 97 average time/residue: 0.1056 time to fit residues: 13.2118 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 : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 349 HIS 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 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 50 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 0.2980 chunk 63 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.147471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.119131 restraints weight = 10671.804| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.98 r_work: 0.3172 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7995 Z= 0.105 Angle : 0.513 8.219 10943 Z= 0.247 Chirality : 0.040 0.187 1230 Planarity : 0.004 0.035 1437 Dihedral : 6.716 87.227 1140 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.64 % Allowed : 20.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 1000 helix: 1.13 (0.29), residues: 331 sheet: 1.12 (0.39), residues: 176 loop : -0.61 (0.26), residues: 493 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 0.004 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 covalent geometry : bond 0.00240 ( 7995) covalent geometry : angle 0.51300 (10943) hydrogen bonds : bond 0.03840 ( 336) hydrogen bonds : angle 4.31733 ( 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 96 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6743 (pm20) REVERT: A 181 ASP cc_start: 0.8050 (t70) cc_final: 0.7843 (t0) REVERT: A 218 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.7615 (mtp85) REVERT: A 222 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7247 (pmm150) REVERT: A 514 ARG cc_start: 0.8650 (tpp80) cc_final: 0.8333 (tpp-160) REVERT: B 31 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8655 (pt) REVERT: B 154 ARG cc_start: 0.8309 (mmm-85) cc_final: 0.7971 (ttm-80) REVERT: B 222 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7195 (pmm150) REVERT: B 274 SER cc_start: 0.8704 (OUTLIER) cc_final: 0.8461 (p) REVERT: B 282 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: B 311 LEU cc_start: 0.7946 (mt) cc_final: 0.7707 (mt) outliers start: 21 outliers final: 14 residues processed: 92 average time/residue: 0.0996 time to fit residues: 12.0203 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 : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 382 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 506 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 0.0270 chunk 29 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.9642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.144681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116960 restraints weight = 10710.972| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.12 r_work: 0.3123 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 7995 Z= 0.148 Angle : 0.562 8.253 10943 Z= 0.270 Chirality : 0.042 0.183 1230 Planarity : 0.004 0.037 1437 Dihedral : 6.923 88.521 1140 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.89 % Allowed : 19.97 % 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 aren not related in a simple way. whole: 0.35 (0.26), residues: 1000 helix: 1.00 (0.29), residues: 332 sheet: 1.02 (0.38), residues: 180 loop : -0.58 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 191 TYR 0.020 0.002 TYR A 176 PHE 0.009 0.001 PHE A 198 TRP 0.010 0.001 TRP A 376 HIS 0.005 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 7995) covalent geometry : angle 0.56186 (10943) hydrogen bonds : bond 0.04497 ( 336) hydrogen bonds : angle 4.50201 ( 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 96 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6665 (pm20) REVERT: A 181 ASP cc_start: 0.8085 (t70) cc_final: 0.7866 (t0) REVERT: A 218 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.7637 (mtp85) REVERT: A 222 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7551 (pmm150) REVERT: A 514 ARG cc_start: 0.8669 (tpp80) cc_final: 0.8344 (tpp-160) REVERT: B 26 ARG cc_start: 0.7120 (mtp180) cc_final: 0.6706 (mtp180) REVERT: B 154 ARG cc_start: 0.8494 (mmm-85) cc_final: 0.8150 (ttm-80) REVERT: B 222 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7477 (pmm150) REVERT: B 274 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8502 (p) REVERT: B 282 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: B 311 LEU cc_start: 0.8008 (mt) cc_final: 0.7780 (mt) REVERT: B 510 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6503 (mtm110) outliers start: 23 outliers final: 12 residues processed: 94 average time/residue: 0.0984 time to fit residues: 11.8172 Evaluate side-chains 89 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 0.5980 chunk 26 optimal weight: 0.0270 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3684 r_free = 0.3684 target = 0.147138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118932 restraints weight = 10663.515| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.97 r_work: 0.3170 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7995 Z= 0.107 Angle : 0.518 7.958 10943 Z= 0.249 Chirality : 0.040 0.176 1230 Planarity : 0.004 0.035 1437 Dihedral : 6.805 87.869 1140 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.26 % Allowed : 20.73 % Favored : 77.01 % 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 aren not related in a simple way. whole: 0.55 (0.26), residues: 1000 helix: 1.23 (0.29), residues: 332 sheet: 1.08 (0.39), residues: 180 loop : -0.48 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 510 TYR 0.013 0.001 TYR B 176 PHE 0.004 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 covalent geometry : bond 0.00247 ( 7995) covalent geometry : angle 0.51803 (10943) hydrogen bonds : bond 0.03863 ( 336) hydrogen bonds : angle 4.32435 ( 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 92 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6704 (pm20) REVERT: A 181 ASP cc_start: 0.8059 (t70) cc_final: 0.7857 (t0) REVERT: A 218 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.7600 (mtp85) REVERT: A 222 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7316 (pmm150) REVERT: A 514 ARG cc_start: 0.8527 (tpp80) cc_final: 0.8262 (tpp-160) REVERT: B 26 ARG cc_start: 0.7093 (mtp180) cc_final: 0.6668 (mtp180) REVERT: B 154 ARG cc_start: 0.8289 (mmm-85) cc_final: 0.7942 (ttm-80) REVERT: B 222 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7184 (pmm150) REVERT: B 274 SER cc_start: 0.8707 (OUTLIER) cc_final: 0.8452 (p) REVERT: B 282 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: B 311 LEU cc_start: 0.7939 (mt) cc_final: 0.7690 (mt) outliers start: 18 outliers final: 12 residues processed: 90 average time/residue: 0.1059 time to fit residues: 12.4068 Evaluate side-chains 88 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 378 THR Chi-restraints excluded: chain A residue 473 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 513 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.146783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.118647 restraints weight = 10604.606| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.96 r_work: 0.3208 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7995 Z= 0.119 Angle : 0.537 8.111 10943 Z= 0.256 Chirality : 0.041 0.188 1230 Planarity : 0.004 0.045 1437 Dihedral : 6.813 87.634 1140 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.26 % Allowed : 20.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.26), residues: 1000 helix: 1.19 (0.29), residues: 338 sheet: 1.10 (0.39), residues: 180 loop : -0.45 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 510 TYR 0.019 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 covalent geometry : bond 0.00281 ( 7995) covalent geometry : angle 0.53750 (10943) hydrogen bonds : bond 0.03984 ( 336) hydrogen bonds : angle 4.34769 ( 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 91 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6693 (pm20) REVERT: A 181 ASP cc_start: 0.8084 (t70) cc_final: 0.7882 (t0) REVERT: A 218 ARG cc_start: 0.8566 (ttm-80) cc_final: 0.7644 (mtp85) REVERT: A 222 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7376 (pmm150) REVERT: A 514 ARG cc_start: 0.8486 (tpp80) cc_final: 0.7784 (mpt-90) REVERT: B 26 ARG cc_start: 0.7096 (mtp180) cc_final: 0.6369 (mmm160) REVERT: B 154 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.7961 (ttm-80) REVERT: B 222 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7304 (pmm150) REVERT: B 274 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8448 (p) REVERT: B 282 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7644 (tm-30) REVERT: B 311 LEU cc_start: 0.7989 (mt) cc_final: 0.7735 (mt) REVERT: B 510 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6578 (mtm110) outliers start: 18 outliers final: 13 residues processed: 89 average time/residue: 0.1262 time to fit residues: 14.5207 Evaluate side-chains 90 residues out of total 796 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 21 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.146263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118100 restraints weight = 10648.426| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.95 r_work: 0.3210 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7995 Z= 0.113 Angle : 0.536 7.835 10943 Z= 0.256 Chirality : 0.041 0.204 1230 Planarity : 0.004 0.047 1437 Dihedral : 6.790 87.144 1140 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.51 % Allowed : 20.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.26), residues: 1000 helix: 1.19 (0.29), residues: 338 sheet: 1.12 (0.39), residues: 180 loop : -0.41 (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 covalent geometry : bond 0.00264 ( 7995) covalent geometry : angle 0.53614 (10943) hydrogen bonds : bond 0.03915 ( 336) hydrogen bonds : angle 4.29827 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1945.02 seconds wall clock time: 33 minutes 51.25 seconds (2031.25 seconds total)