Starting phenix.real_space_refine on Fri Jun 6 20:40:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i38_35145/06_2025/8i38_35145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i38_35145/06_2025/8i38_35145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i38_35145/06_2025/8i38_35145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i38_35145/06_2025/8i38_35145.map" model { file = "/net/cci-nas-00/data/ceres_data/8i38_35145/06_2025/8i38_35145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i38_35145/06_2025/8i38_35145.cif" } resolution = 2.9 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= -0.002 sd= 0.123 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 50 5.16 5 C 5306 2.51 5 N 1354 2.21 5 O 1412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8122 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4061 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 17, 'TRANS': 503} Chain breaks: 3 Restraints were copied for chains: B Time building chain proxies: 7.41, per 1000 atoms: 0.91 Number of scatterers: 8122 At special positions: 0 Unit cell: (88.54, 90.404, 122.092, 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 50 16.00 O 1412 8.00 N 1354 7.00 C 5306 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: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 52.0% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 106 through 115 Processing helix chain 'A' and resid 156 through 169 removed outlier: 3.719A pdb=" N VAL A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 removed outlier: 5.616A pdb=" N ALA A 182 " --> pdb=" O LYS A 178 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 removed outlier: 3.512A pdb=" N SER A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 255 removed outlier: 3.803A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 294 through 300 removed outlier: 3.547A pdb=" N TYR A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.648A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 397 removed outlier: 3.511A pdb=" N LEU A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.713A pdb=" N GLU A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 405' Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.728A pdb=" N ALA A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.552A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 455 removed outlier: 3.626A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 472 Processing helix chain 'A' and resid 477 through 492 removed outlier: 4.383A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 512 through 541 removed outlier: 3.938A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.513A pdb=" N THR A 549 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 580 through 594 removed outlier: 4.315A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 643 through 657 removed outlier: 3.678A pdb=" N TYR A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 156 through 169 removed outlier: 3.718A pdb=" N VAL B 164 " --> pdb=" O THR B 160 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 169 " --> pdb=" O ALA B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 removed outlier: 5.616A pdb=" N ALA B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 219 removed outlier: 3.512A pdb=" N SER B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 255 removed outlier: 3.803A pdb=" N ALA B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 Processing helix chain 'B' and resid 294 through 300 removed outlier: 3.547A pdb=" N TYR B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 322 removed outlier: 3.648A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASP B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 397 removed outlier: 3.511A pdb=" N LEU B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 removed outlier: 3.713A pdb=" N GLU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 405' Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.728A pdb=" N ALA B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TRP B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.553A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 455 removed outlier: 3.626A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix Processing helix chain 'B' and resid 459 through 461 No H-bonds generated for 'chain 'B' and resid 459 through 461' Processing helix chain 'B' and resid 462 through 472 Processing helix chain 'B' and resid 477 through 492 removed outlier: 4.383A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 503 Processing helix chain 'B' and resid 512 through 541 removed outlier: 3.937A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 555 removed outlier: 3.512A pdb=" N THR B 549 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 580 through 594 removed outlier: 4.315A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N CYS B 585 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 605 Processing helix chain 'B' and resid 643 through 657 removed outlier: 3.678A pdb=" N TYR B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 90 removed outlier: 6.923A pdb=" N THR A 88 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL A 43 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N MET A 90 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS A 41 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ASP A 44 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS A 126 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR A 124 " --> pdb=" O CYS A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 227 through 229 removed outlier: 6.142A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 290 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 85 through 90 removed outlier: 6.923A pdb=" N THR B 88 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL B 43 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N MET B 90 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS B 41 " --> pdb=" O MET B 90 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ASP B 44 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LYS B 126 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 124 " --> pdb=" O CYS B 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 227 through 229 removed outlier: 6.141A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY B 290 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 936 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: 2.05 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1256 1.32 - 1.45: 2324 1.45 - 1.58: 4629 1.58 - 1.71: 3 1.71 - 1.84: 84 Bond restraints: 8296 Sorted by residual: bond pdb=" CA SER A 85 " pdb=" C SER A 85 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.61e-02 3.86e+03 1.72e+01 bond pdb=" CA THR A 88 " pdb=" C THR A 88 " ideal model delta sigma weight residual 1.521 1.467 0.054 1.30e-02 5.92e+03 1.70e+01 bond pdb=" CA SER B 85 " pdb=" C SER B 85 " ideal model delta sigma weight residual 1.523 1.456 0.066 1.61e-02 3.86e+03 1.70e+01 bond pdb=" CA THR B 88 " pdb=" C THR B 88 " ideal model delta sigma weight residual 1.521 1.468 0.053 1.30e-02 5.92e+03 1.65e+01 bond pdb=" N SER A 85 " pdb=" CA SER A 85 " ideal model delta sigma weight residual 1.460 1.404 0.056 1.45e-02 4.76e+03 1.49e+01 ... (remaining 8291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.57: 11126 4.57 - 9.13: 100 9.13 - 13.70: 6 13.70 - 18.27: 4 18.27 - 22.83: 2 Bond angle restraints: 11238 Sorted by residual: angle pdb=" N SER B 85 " pdb=" CA SER B 85 " pdb=" C SER B 85 " ideal model delta sigma weight residual 110.44 87.61 22.83 1.20e+00 6.94e-01 3.62e+02 angle pdb=" N SER A 85 " pdb=" CA SER A 85 " pdb=" C SER A 85 " ideal model delta sigma weight residual 110.44 87.62 22.82 1.20e+00 6.94e-01 3.62e+02 angle pdb=" CA GLU B 599 " pdb=" CB GLU B 599 " pdb=" CG GLU B 599 " ideal model delta sigma weight residual 114.10 128.46 -14.36 2.00e+00 2.50e-01 5.15e+01 angle pdb=" CA GLU A 599 " pdb=" CB GLU A 599 " pdb=" CG GLU A 599 " ideal model delta sigma weight residual 114.10 128.42 -14.32 2.00e+00 2.50e-01 5.13e+01 angle pdb=" N VAL B 87 " pdb=" CA VAL B 87 " pdb=" C VAL B 87 " ideal model delta sigma weight residual 109.34 124.15 -14.81 2.08e+00 2.31e-01 5.07e+01 ... (remaining 11233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 4437 16.60 - 33.20: 347 33.20 - 49.80: 62 49.80 - 66.40: 18 66.40 - 83.00: 4 Dihedral angle restraints: 4868 sinusoidal: 1892 harmonic: 2976 Sorted by residual: dihedral pdb=" C VAL A 87 " pdb=" N VAL A 87 " pdb=" CA VAL A 87 " pdb=" CB VAL A 87 " ideal model delta harmonic sigma weight residual -122.00 -149.46 27.46 0 2.50e+00 1.60e-01 1.21e+02 dihedral pdb=" C VAL B 87 " pdb=" N VAL B 87 " pdb=" CA VAL B 87 " pdb=" CB VAL B 87 " ideal model delta harmonic sigma weight residual -122.00 -149.40 27.40 0 2.50e+00 1.60e-01 1.20e+02 dihedral pdb=" N VAL A 87 " pdb=" C VAL A 87 " pdb=" CA VAL A 87 " pdb=" CB VAL A 87 " ideal model delta harmonic sigma weight residual 123.40 148.99 -25.59 0 2.50e+00 1.60e-01 1.05e+02 ... (remaining 4865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.229: 1322 0.229 - 0.458: 4 0.458 - 0.687: 0 0.687 - 0.916: 0 0.916 - 1.145: 2 Chirality restraints: 1328 Sorted by residual: chirality pdb=" CA VAL A 87 " pdb=" N VAL A 87 " pdb=" C VAL A 87 " pdb=" CB VAL A 87 " both_signs ideal model delta sigma weight residual False 2.44 1.30 1.14 2.00e-01 2.50e+01 3.28e+01 chirality pdb=" CA VAL B 87 " pdb=" N VAL B 87 " pdb=" C VAL B 87 " pdb=" CB VAL B 87 " both_signs ideal model delta sigma weight residual False 2.44 1.30 1.14 2.00e-01 2.50e+01 3.27e+01 chirality pdb=" CB THR A 142 " pdb=" CA THR A 142 " pdb=" OG1 THR A 142 " pdb=" CG2 THR A 142 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.36 2.00e-01 2.50e+01 3.26e+00 ... (remaining 1325 not shown) Planarity restraints: 1378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 459 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO A 460 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 460 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 460 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 459 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO B 460 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 460 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 460 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 84 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C LEU B 84 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU B 84 " 0.014 2.00e-02 2.50e+03 pdb=" N SER B 85 " 0.012 2.00e-02 2.50e+03 ... (remaining 1375 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 71 2.56 - 3.15: 5824 3.15 - 3.73: 12120 3.73 - 4.32: 17946 4.32 - 4.90: 29069 Nonbonded interactions: 65030 Sorted by model distance: nonbonded pdb=" O GLY A 631 " pdb=" OD1 ASP A 632 " model vdw 1.981 3.040 nonbonded pdb=" O GLY B 631 " pdb=" OD1 ASP B 632 " model vdw 1.981 3.040 nonbonded pdb=" OH TYR A 47 " pdb=" CG2 VAL A 49 " model vdw 2.089 3.460 nonbonded pdb=" OH TYR B 47 " pdb=" CG2 VAL B 49 " model vdw 2.090 3.460 nonbonded pdb=" O MET B 645 " pdb=" CD2 TYR B 649 " model vdw 2.143 3.340 ... (remaining 65025 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.500 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.020 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 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 : 0.006 0.078 8296 Z= 0.300 Angle : 1.197 22.833 11238 Z= 0.719 Chirality : 0.071 1.145 1328 Planarity : 0.007 0.053 1378 Dihedral : 12.795 83.001 2960 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.77 % Favored : 91.03 % Rotamer: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 0.00 % 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: -6.34 (0.17), residues: 1026 helix: -4.65 (0.09), residues: 602 sheet: -3.32 (0.52), residues: 70 loop : -3.07 (0.27), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 425 HIS 0.005 0.002 HIS A 395 PHE 0.014 0.002 PHE A 308 TYR 0.011 0.002 TYR B 594 ARG 0.004 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.31584 ( 316) hydrogen bonds : angle 11.90223 ( 936) covalent geometry : bond 0.00566 ( 8296) covalent geometry : angle 1.19692 (11238) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.858 Fit side-chains REVERT: A 219 HIS cc_start: 0.6604 (m170) cc_final: 0.5250 (t-90) REVERT: A 220 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7008 (mp0) REVERT: B 220 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7218 (mp0) REVERT: B 232 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7523 (mp0) REVERT: B 244 ARG cc_start: 0.5489 (mtm180) cc_final: 0.5076 (mtm180) outliers start: 0 outliers final: 1 residues processed: 141 average time/residue: 1.2669 time to fit residues: 189.6434 Evaluate side-chains 104 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 94 optimal weight: 0.4980 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 273 GLN A 395 HIS A 403 HIS B 266 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.206269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.153020 restraints weight = 7609.193| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.07 r_work: 0.3691 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8296 Z= 0.130 Angle : 0.635 6.530 11238 Z= 0.326 Chirality : 0.041 0.133 1328 Planarity : 0.005 0.046 1378 Dihedral : 5.826 48.119 1130 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.98 % Rotamer: Outliers : 3.06 % Allowed : 11.22 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.51 (0.22), residues: 1026 helix: -2.98 (0.16), residues: 624 sheet: -2.76 (0.57), residues: 70 loop : -2.59 (0.31), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 426 HIS 0.007 0.001 HIS A 395 PHE 0.010 0.001 PHE A 308 TYR 0.017 0.002 TYR B 47 ARG 0.003 0.000 ARG B 436 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 316) hydrogen bonds : angle 5.02837 ( 936) covalent geometry : bond 0.00301 ( 8296) covalent geometry : angle 0.63506 (11238) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.900 Fit side-chains REVERT: A 90 MET cc_start: 0.5946 (OUTLIER) cc_final: 0.4581 (mpp) REVERT: A 219 HIS cc_start: 0.6750 (m170) cc_final: 0.5527 (t70) REVERT: A 220 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7441 (mm-30) REVERT: A 424 MET cc_start: 0.8029 (mmm) cc_final: 0.7770 (mmm) REVERT: A 546 LYS cc_start: 0.7644 (tttm) cc_final: 0.7292 (ttpt) REVERT: B 219 HIS cc_start: 0.7054 (m170) cc_final: 0.5498 (t70) REVERT: B 220 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7494 (mm-30) REVERT: B 232 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7574 (mp0) REVERT: B 244 ARG cc_start: 0.5243 (mtm180) cc_final: 0.4980 (mtm180) REVERT: B 274 MET cc_start: 0.4864 (OUTLIER) cc_final: 0.4512 (mpt) REVERT: B 635 MET cc_start: 0.7855 (ttt) cc_final: 0.7612 (ttt) outliers start: 27 outliers final: 8 residues processed: 123 average time/residue: 1.4237 time to fit residues: 187.0434 Evaluate side-chains 105 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN B 403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.204642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.149347 restraints weight = 7728.882| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.06 r_work: 0.3636 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8296 Z= 0.142 Angle : 0.607 7.962 11238 Z= 0.308 Chirality : 0.041 0.138 1328 Planarity : 0.004 0.046 1378 Dihedral : 5.377 47.296 1130 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.73 % Favored : 93.08 % Rotamer: Outliers : 3.17 % Allowed : 12.70 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.36 (0.24), residues: 1026 helix: -1.99 (0.19), residues: 622 sheet: -2.54 (0.58), residues: 70 loop : -2.24 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 426 HIS 0.004 0.001 HIS B 484 PHE 0.012 0.001 PHE B 387 TYR 0.018 0.002 TYR A 649 ARG 0.003 0.000 ARG A 650 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 316) hydrogen bonds : angle 4.37906 ( 936) covalent geometry : bond 0.00330 ( 8296) covalent geometry : angle 0.60663 (11238) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.5905 (OUTLIER) cc_final: 0.4760 (mpp) REVERT: A 219 HIS cc_start: 0.6974 (m170) cc_final: 0.5613 (t70) REVERT: A 220 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7576 (mm-30) REVERT: A 279 LEU cc_start: 0.7308 (tt) cc_final: 0.7092 (tp) REVERT: A 546 LYS cc_start: 0.7630 (tttm) cc_final: 0.7390 (ttpt) REVERT: A 576 MET cc_start: 0.7303 (OUTLIER) cc_final: 0.7085 (tmt) REVERT: B 117 ARG cc_start: 0.5947 (mmm-85) cc_final: 0.5190 (mmm-85) REVERT: B 193 LYS cc_start: 0.8250 (tttm) cc_final: 0.7818 (mmpt) REVERT: B 205 ARG cc_start: 0.7556 (mtt180) cc_final: 0.7286 (mmm-85) REVERT: B 219 HIS cc_start: 0.7098 (m170) cc_final: 0.5605 (t70) REVERT: B 220 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7624 (mm-30) REVERT: B 232 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7682 (mp0) REVERT: B 274 MET cc_start: 0.5065 (OUTLIER) cc_final: 0.4794 (mmt) REVERT: B 546 LYS cc_start: 0.7718 (tttm) cc_final: 0.7478 (ttpt) outliers start: 28 outliers final: 8 residues processed: 114 average time/residue: 1.3242 time to fit residues: 159.8554 Evaluate side-chains 106 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN B 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.200925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.147439 restraints weight = 7705.879| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.17 r_work: 0.3537 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8296 Z= 0.145 Angle : 0.584 6.876 11238 Z= 0.297 Chirality : 0.042 0.143 1328 Planarity : 0.004 0.046 1378 Dihedral : 5.026 24.150 1128 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.80 % Favored : 92.01 % Rotamer: Outliers : 2.83 % Allowed : 14.85 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.74 (0.25), residues: 1026 helix: -1.46 (0.20), residues: 620 sheet: -2.47 (0.59), residues: 70 loop : -2.02 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 425 HIS 0.004 0.001 HIS A 484 PHE 0.014 0.001 PHE A 406 TYR 0.014 0.002 TYR A 649 ARG 0.003 0.000 ARG B 410 Details of bonding type rmsd hydrogen bonds : bond 0.02877 ( 316) hydrogen bonds : angle 4.28926 ( 936) covalent geometry : bond 0.00342 ( 8296) covalent geometry : angle 0.58406 (11238) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5349 (mpp) REVERT: A 95 GLU cc_start: 0.5806 (mt-10) cc_final: 0.4511 (mp0) REVERT: A 205 ARG cc_start: 0.7603 (mtt180) cc_final: 0.7237 (mmm-85) REVERT: A 219 HIS cc_start: 0.6895 (m170) cc_final: 0.5458 (t70) REVERT: A 220 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7666 (mm-30) REVERT: A 576 MET cc_start: 0.7259 (tmt) cc_final: 0.7038 (tmt) REVERT: B 117 ARG cc_start: 0.5764 (mmm-85) cc_final: 0.5048 (mmm-85) REVERT: B 193 LYS cc_start: 0.8232 (tttm) cc_final: 0.7784 (mmpt) REVERT: B 205 ARG cc_start: 0.7518 (mtt180) cc_final: 0.7084 (mmm-85) REVERT: B 219 HIS cc_start: 0.6919 (m170) cc_final: 0.5430 (t70) REVERT: B 220 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7626 (mm-30) REVERT: B 232 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7594 (mp0) REVERT: B 274 MET cc_start: 0.4984 (OUTLIER) cc_final: 0.4697 (mmt) outliers start: 25 outliers final: 7 residues processed: 114 average time/residue: 1.3106 time to fit residues: 158.1465 Evaluate side-chains 107 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 40 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN B 413 GLN B 454 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.204455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.147264 restraints weight = 7625.083| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.02 r_work: 0.3636 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8296 Z= 0.120 Angle : 0.562 6.322 11238 Z= 0.283 Chirality : 0.041 0.141 1328 Planarity : 0.004 0.046 1378 Dihedral : 4.782 23.083 1128 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.02 % Favored : 92.79 % Rotamer: Outliers : 2.49 % Allowed : 15.42 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.26 (0.26), residues: 1026 helix: -1.08 (0.21), residues: 624 sheet: -2.40 (0.59), residues: 70 loop : -1.80 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 425 HIS 0.003 0.001 HIS A 484 PHE 0.012 0.001 PHE B 406 TYR 0.011 0.001 TYR B 649 ARG 0.003 0.000 ARG B 510 Details of bonding type rmsd hydrogen bonds : bond 0.02675 ( 316) hydrogen bonds : angle 4.13105 ( 936) covalent geometry : bond 0.00282 ( 8296) covalent geometry : angle 0.56152 (11238) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.6360 (OUTLIER) cc_final: 0.5386 (mpp) REVERT: A 95 GLU cc_start: 0.5938 (mt-10) cc_final: 0.4668 (mp0) REVERT: A 97 MET cc_start: 0.6548 (OUTLIER) cc_final: 0.6125 (tpt) REVERT: A 219 HIS cc_start: 0.7017 (m170) cc_final: 0.5706 (t70) REVERT: A 220 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7767 (mm-30) REVERT: B 97 MET cc_start: 0.6421 (OUTLIER) cc_final: 0.5978 (tpt) REVERT: B 117 ARG cc_start: 0.5907 (mmm-85) cc_final: 0.5228 (mmm-85) REVERT: B 193 LYS cc_start: 0.8341 (tttm) cc_final: 0.7925 (mmpt) REVERT: B 219 HIS cc_start: 0.7063 (m170) cc_final: 0.5679 (t70) REVERT: B 220 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7641 (mm-30) REVERT: B 232 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7789 (mp0) REVERT: B 274 MET cc_start: 0.5160 (OUTLIER) cc_final: 0.4911 (mmt) REVERT: B 576 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6738 (tpp) outliers start: 22 outliers final: 9 residues processed: 114 average time/residue: 1.1856 time to fit residues: 143.6857 Evaluate side-chains 110 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 3 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4331 r_free = 0.4331 target = 0.201253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.144441 restraints weight = 7672.594| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.05 r_work: 0.3637 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8296 Z= 0.161 Angle : 0.593 6.501 11238 Z= 0.299 Chirality : 0.043 0.149 1328 Planarity : 0.004 0.044 1378 Dihedral : 4.898 23.448 1128 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.99 % Favored : 91.81 % Rotamer: Outliers : 2.72 % Allowed : 16.55 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.14 (0.26), residues: 1026 helix: -1.08 (0.20), residues: 624 sheet: -1.89 (0.65), residues: 60 loop : -1.68 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 425 HIS 0.004 0.001 HIS A 484 PHE 0.011 0.001 PHE B 387 TYR 0.010 0.002 TYR A 649 ARG 0.004 0.000 ARG B 410 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 316) hydrogen bonds : angle 4.28790 ( 936) covalent geometry : bond 0.00386 ( 8296) covalent geometry : angle 0.59262 (11238) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.802 Fit side-chains REVERT: A 90 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.5565 (mpp) REVERT: A 95 GLU cc_start: 0.5872 (mt-10) cc_final: 0.4545 (mp0) REVERT: A 157 VAL cc_start: 0.7369 (OUTLIER) cc_final: 0.7121 (t) REVERT: A 193 LYS cc_start: 0.8163 (ttpp) cc_final: 0.7831 (mmpt) REVERT: A 211 GLU cc_start: 0.6476 (mt-10) cc_final: 0.6078 (mt-10) REVERT: A 219 HIS cc_start: 0.6977 (m170) cc_final: 0.5526 (t-170) REVERT: A 220 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7738 (mm-30) REVERT: A 576 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6810 (tpp) REVERT: B 40 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5789 (tp) REVERT: B 97 MET cc_start: 0.6252 (OUTLIER) cc_final: 0.5798 (tpt) REVERT: B 193 LYS cc_start: 0.8348 (tttm) cc_final: 0.7885 (mmpt) REVERT: B 219 HIS cc_start: 0.7026 (m170) cc_final: 0.5578 (t-170) REVERT: B 220 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7676 (mm-30) REVERT: B 232 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7658 (mp0) REVERT: B 576 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6717 (tpp) outliers start: 24 outliers final: 8 residues processed: 105 average time/residue: 1.2222 time to fit residues: 136.4361 Evaluate side-chains 101 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 576 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 0.0010 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- 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 = 0.4351 r_free = 0.4351 target = 0.203361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.146901 restraints weight = 7671.354| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.04 r_work: 0.3658 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8296 Z= 0.118 Angle : 0.573 9.200 11238 Z= 0.283 Chirality : 0.041 0.139 1328 Planarity : 0.004 0.045 1378 Dihedral : 4.718 23.465 1128 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 2.49 % Allowed : 17.35 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.81 (0.26), residues: 1026 helix: -0.78 (0.21), residues: 624 sheet: -1.89 (0.65), residues: 60 loop : -1.60 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 425 HIS 0.003 0.001 HIS A 484 PHE 0.017 0.001 PHE A 406 TYR 0.009 0.001 TYR B 649 ARG 0.002 0.000 ARG B 410 Details of bonding type rmsd hydrogen bonds : bond 0.02657 ( 316) hydrogen bonds : angle 4.11959 ( 936) covalent geometry : bond 0.00277 ( 8296) covalent geometry : angle 0.57253 (11238) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.880 Fit side-chains REVERT: A 90 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.5637 (mpp) REVERT: A 95 GLU cc_start: 0.5891 (mt-10) cc_final: 0.4593 (mp0) REVERT: A 97 MET cc_start: 0.6409 (tpp) cc_final: 0.6038 (tpt) REVERT: A 157 VAL cc_start: 0.7346 (OUTLIER) cc_final: 0.7066 (t) REVERT: A 193 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7804 (mmpt) REVERT: A 195 GLU cc_start: 0.6163 (tt0) cc_final: 0.5529 (tt0) REVERT: A 205 ARG cc_start: 0.7900 (mmm-85) cc_final: 0.7689 (mmm-85) REVERT: A 211 GLU cc_start: 0.6646 (mt-10) cc_final: 0.6336 (mt-10) REVERT: A 219 HIS cc_start: 0.6892 (m170) cc_final: 0.5513 (t70) REVERT: A 220 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 546 LYS cc_start: 0.7441 (tttm) cc_final: 0.7166 (ttmt) REVERT: A 576 MET cc_start: 0.7151 (OUTLIER) cc_final: 0.6814 (tpp) REVERT: B 40 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5948 (tp) REVERT: B 188 GLU cc_start: 0.6559 (tt0) cc_final: 0.6260 (tt0) REVERT: B 193 LYS cc_start: 0.8177 (tttm) cc_final: 0.7930 (mmpt) REVERT: B 219 HIS cc_start: 0.6956 (m170) cc_final: 0.5513 (t-170) REVERT: B 220 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 232 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7693 (mp0) REVERT: B 274 MET cc_start: 0.4986 (OUTLIER) cc_final: 0.4743 (mmt) REVERT: B 576 MET cc_start: 0.7066 (OUTLIER) cc_final: 0.6581 (tpp) outliers start: 22 outliers final: 11 residues processed: 103 average time/residue: 1.4886 time to fit residues: 162.2168 Evaluate side-chains 104 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 54 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4324 r_free = 0.4324 target = 0.200518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.144110 restraints weight = 7679.431| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.98 r_work: 0.3592 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8296 Z= 0.188 Angle : 0.643 9.936 11238 Z= 0.316 Chirality : 0.045 0.146 1328 Planarity : 0.004 0.044 1378 Dihedral : 4.936 23.666 1128 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.41 % Favored : 92.40 % Rotamer: Outliers : 2.95 % Allowed : 16.89 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.02 (0.26), residues: 1026 helix: -0.96 (0.20), residues: 624 sheet: -1.50 (0.56), residues: 80 loop : -1.73 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 425 HIS 0.004 0.001 HIS A 484 PHE 0.014 0.001 PHE A 406 TYR 0.010 0.002 TYR B 475 ARG 0.003 0.000 ARG B 410 Details of bonding type rmsd hydrogen bonds : bond 0.03099 ( 316) hydrogen bonds : angle 4.32246 ( 936) covalent geometry : bond 0.00454 ( 8296) covalent geometry : angle 0.64254 (11238) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.937 Fit side-chains REVERT: A 90 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.5712 (mpp) REVERT: A 95 GLU cc_start: 0.6046 (mt-10) cc_final: 0.4633 (mp0) REVERT: A 97 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.6113 (tpt) REVERT: A 157 VAL cc_start: 0.7494 (OUTLIER) cc_final: 0.7275 (t) REVERT: A 193 LYS cc_start: 0.8228 (ttpp) cc_final: 0.7876 (mmpt) REVERT: A 195 GLU cc_start: 0.6341 (tt0) cc_final: 0.5951 (tt0) REVERT: A 211 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6379 (mt-10) REVERT: A 219 HIS cc_start: 0.7125 (m170) cc_final: 0.5701 (t-170) REVERT: A 220 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 280 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5706 (mt) REVERT: A 293 ARG cc_start: 0.6320 (mmt180) cc_final: 0.5964 (ttp80) REVERT: A 546 LYS cc_start: 0.7558 (tttm) cc_final: 0.7305 (ttmt) REVERT: A 576 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6882 (tpp) REVERT: B 40 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6067 (tp) REVERT: B 95 GLU cc_start: 0.5802 (mt-10) cc_final: 0.4620 (mp0) REVERT: B 188 GLU cc_start: 0.6824 (tt0) cc_final: 0.6447 (tt0) REVERT: B 219 HIS cc_start: 0.7126 (m170) cc_final: 0.5729 (t70) REVERT: B 220 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7814 (mm-30) REVERT: B 232 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7739 (mp0) REVERT: B 576 MET cc_start: 0.7207 (OUTLIER) cc_final: 0.6764 (tpp) outliers start: 26 outliers final: 10 residues processed: 105 average time/residue: 1.2860 time to fit residues: 143.4230 Evaluate side-chains 106 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 63 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 53 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.202628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.148173 restraints weight = 7771.554| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.14 r_work: 0.3599 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8296 Z= 0.128 Angle : 0.607 9.243 11238 Z= 0.297 Chirality : 0.042 0.143 1328 Planarity : 0.004 0.045 1378 Dihedral : 4.743 23.659 1128 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.02 % Favored : 92.79 % Rotamer: Outliers : 2.04 % Allowed : 18.03 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.81 (0.26), residues: 1026 helix: -0.69 (0.21), residues: 618 sheet: -2.05 (0.63), residues: 60 loop : -1.75 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 425 HIS 0.003 0.001 HIS A 484 PHE 0.015 0.001 PHE A 406 TYR 0.008 0.001 TYR B 649 ARG 0.004 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.02728 ( 316) hydrogen bonds : angle 4.13227 ( 936) covalent geometry : bond 0.00305 ( 8296) covalent geometry : angle 0.60704 (11238) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.827 Fit side-chains REVERT: A 90 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.5640 (mpp) REVERT: A 95 GLU cc_start: 0.5960 (mt-10) cc_final: 0.4602 (mp0) REVERT: A 97 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.6084 (tpt) REVERT: A 157 VAL cc_start: 0.7507 (OUTLIER) cc_final: 0.7291 (t) REVERT: A 195 GLU cc_start: 0.6185 (tt0) cc_final: 0.5795 (tt0) REVERT: A 211 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6390 (mt-10) REVERT: A 219 HIS cc_start: 0.7068 (m170) cc_final: 0.5700 (t70) REVERT: A 220 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7738 (mm-30) REVERT: A 280 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5300 (mt) REVERT: A 293 ARG cc_start: 0.6194 (mmt180) cc_final: 0.5832 (ttp80) REVERT: A 546 LYS cc_start: 0.7441 (tttm) cc_final: 0.7227 (ttmt) REVERT: A 576 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6853 (tpp) REVERT: B 40 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6118 (tp) REVERT: B 95 GLU cc_start: 0.5781 (mt-10) cc_final: 0.4585 (mp0) REVERT: B 188 GLU cc_start: 0.6781 (tt0) cc_final: 0.6449 (tt0) REVERT: B 219 HIS cc_start: 0.7106 (m170) cc_final: 0.5756 (t70) REVERT: B 220 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7709 (mm-30) REVERT: B 232 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7777 (mp0) REVERT: B 546 LYS cc_start: 0.7483 (tttm) cc_final: 0.7272 (ttmt) REVERT: B 576 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.6717 (tpp) outliers start: 18 outliers final: 10 residues processed: 103 average time/residue: 1.3150 time to fit residues: 143.5998 Evaluate side-chains 105 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 75 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.0570 chunk 19 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.203849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.138034 restraints weight = 7628.760| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.84 r_work: 0.3537 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8296 Z= 0.116 Angle : 0.588 8.798 11238 Z= 0.289 Chirality : 0.041 0.146 1328 Planarity : 0.004 0.044 1378 Dihedral : 4.638 24.045 1128 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 2.15 % Allowed : 17.91 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.54 (0.26), residues: 1026 helix: -0.45 (0.21), residues: 618 sheet: -2.00 (0.64), residues: 60 loop : -1.69 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 425 HIS 0.003 0.001 HIS A 484 PHE 0.020 0.001 PHE B 406 TYR 0.007 0.001 TYR A 649 ARG 0.004 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.02645 ( 316) hydrogen bonds : angle 4.07173 ( 936) covalent geometry : bond 0.00274 ( 8296) covalent geometry : angle 0.58809 (11238) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.818 Fit side-chains REVERT: A 90 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.5652 (mpp) REVERT: A 95 GLU cc_start: 0.5831 (mt-10) cc_final: 0.4534 (mp0) REVERT: A 97 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5948 (tpt) REVERT: A 195 GLU cc_start: 0.6048 (tt0) cc_final: 0.5687 (tt0) REVERT: A 219 HIS cc_start: 0.6854 (m170) cc_final: 0.5544 (t70) REVERT: A 220 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7789 (mm-30) REVERT: A 280 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5158 (mt) REVERT: A 293 ARG cc_start: 0.6161 (mmt180) cc_final: 0.5685 (ttp80) REVERT: A 576 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6814 (tpp) REVERT: B 40 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5804 (tp) REVERT: B 95 GLU cc_start: 0.5551 (mt-10) cc_final: 0.4400 (mp0) REVERT: B 188 GLU cc_start: 0.6782 (tt0) cc_final: 0.6439 (tt0) REVERT: B 193 LYS cc_start: 0.8249 (ttpp) cc_final: 0.7889 (mmpt) REVERT: B 219 HIS cc_start: 0.6895 (m170) cc_final: 0.5627 (t70) REVERT: B 220 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7685 (mm-30) REVERT: B 232 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7727 (mp0) REVERT: B 274 MET cc_start: 0.5007 (mpp) cc_final: 0.4767 (mmt) REVERT: B 576 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6708 (tpp) REVERT: B 632 ASP cc_start: 0.5269 (OUTLIER) cc_final: 0.4597 (t0) outliers start: 19 outliers final: 10 residues processed: 96 average time/residue: 1.3254 time to fit residues: 135.3020 Evaluate side-chains 104 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 576 MET Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 573 MET Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 12 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 7 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.204568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.151149 restraints weight = 7771.896| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 2.21 r_work: 0.3658 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8296 Z= 0.107 Angle : 0.592 9.728 11238 Z= 0.287 Chirality : 0.041 0.149 1328 Planarity : 0.004 0.045 1378 Dihedral : 4.542 23.978 1128 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.92 % Favored : 92.88 % Rotamer: Outliers : 1.93 % Allowed : 18.37 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.23 (0.27), residues: 1026 helix: -0.16 (0.21), residues: 614 sheet: -1.88 (0.66), residues: 60 loop : -1.63 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 425 HIS 0.003 0.001 HIS A 484 PHE 0.024 0.001 PHE B 406 TYR 0.006 0.001 TYR B 480 ARG 0.004 0.000 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.02606 ( 316) hydrogen bonds : angle 3.98917 ( 936) covalent geometry : bond 0.00250 ( 8296) covalent geometry : angle 0.59154 (11238) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6760.84 seconds wall clock time: 118 minutes 45.77 seconds (7125.77 seconds total)