Starting phenix.real_space_refine on Fri Aug 22 21:53:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i38_35145/08_2025/8i38_35145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i38_35145/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8i38_35145/08_2025/8i38_35145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i38_35145/08_2025/8i38_35145.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i38_35145/08_2025/8i38_35145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i38_35145/08_2025/8i38_35145.map" } resolution = 2.9 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= -0.002 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): 0.01s 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: 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: 2.68, per 1000 atoms: 0.33 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: 0.45 Conformation dependent library (CDL) restraints added in 399.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.27 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: 1.17 Time building geometry restraints manager: 0.63 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: 0.02 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: 1.700 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.250 Find NCS groups from input model: 0.050 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:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.970 ------------------------------------------------------------------------------- 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 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: -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 ARG 0.004 0.001 ARG B 293 TYR 0.011 0.002 TYR B 594 PHE 0.014 0.002 PHE A 308 TRP 0.021 0.002 TRP A 425 HIS 0.005 0.002 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 8296) covalent geometry : angle 1.19692 (11238) hydrogen bonds : bond 0.31584 ( 316) hydrogen bonds : angle 11.90223 ( 936) *********************** 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 : 0.290 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: 0.5503 time to fit residues: 82.2938 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 : 0.302 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.4386 r_free = 0.4386 target = 0.206776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.152015 restraints weight = 7680.146| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.96 r_work: 0.3719 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8296 Z= 0.125 Angle : 0.638 6.720 11238 Z= 0.327 Chirality : 0.041 0.136 1328 Planarity : 0.005 0.046 1378 Dihedral : 5.808 48.366 1130 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.98 % Rotamer: Outliers : 2.61 % Allowed : 11.90 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.50 (0.22), residues: 1026 helix: -2.96 (0.16), residues: 622 sheet: -2.76 (0.57), residues: 70 loop : -2.61 (0.31), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 436 TYR 0.016 0.002 TYR B 47 PHE 0.009 0.001 PHE A 308 TRP 0.009 0.001 TRP B 426 HIS 0.008 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8296) covalent geometry : angle 0.63758 (11238) hydrogen bonds : bond 0.03502 ( 316) hydrogen bonds : angle 5.02759 ( 936) *********************** 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 128 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.287 Fit side-chains REVERT: A 90 MET cc_start: 0.5922 (OUTLIER) cc_final: 0.4542 (mpp) REVERT: A 219 HIS cc_start: 0.6472 (m170) cc_final: 0.5197 (t70) REVERT: A 220 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7259 (mp0) REVERT: A 232 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: A 424 MET cc_start: 0.8017 (mmm) cc_final: 0.7782 (mmm) REVERT: A 546 LYS cc_start: 0.7588 (tttm) cc_final: 0.7230 (ttpt) REVERT: B 220 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7359 (mm-30) REVERT: B 230 LEU cc_start: 0.7129 (mp) cc_final: 0.6817 (mp) REVERT: B 232 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7584 (mp0) REVERT: B 244 ARG cc_start: 0.5204 (mtm180) cc_final: 0.4944 (mtm180) REVERT: B 274 MET cc_start: 0.4835 (OUTLIER) cc_final: 0.4455 (mpt) outliers start: 23 outliers final: 6 residues processed: 120 average time/residue: 0.5390 time to fit residues: 68.7464 Evaluate side-chains 106 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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 232 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 274 MET 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 53 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.198414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.141543 restraints weight = 7651.475| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.96 r_work: 0.3609 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 8296 Z= 0.293 Angle : 0.748 8.711 11238 Z= 0.379 Chirality : 0.048 0.158 1328 Planarity : 0.005 0.046 1378 Dihedral : 5.937 45.946 1130 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.48 % Favored : 91.33 % Rotamer: Outliers : 2.95 % Allowed : 14.40 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.80 (0.23), residues: 1026 helix: -2.42 (0.18), residues: 628 sheet: -2.76 (0.59), residues: 70 loop : -2.20 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 410 TYR 0.031 0.003 TYR A 649 PHE 0.016 0.002 PHE B 387 TRP 0.016 0.003 TRP B 425 HIS 0.006 0.001 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00706 ( 8296) covalent geometry : angle 0.74804 (11238) hydrogen bonds : bond 0.04003 ( 316) hydrogen bonds : angle 5.01776 ( 936) *********************** 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 126 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5209 (mpp) REVERT: A 95 GLU cc_start: 0.6066 (mt-10) cc_final: 0.4652 (mp0) REVERT: A 183 GLU cc_start: 0.6642 (tm-30) cc_final: 0.5397 (tp30) REVERT: A 219 HIS cc_start: 0.7144 (m170) cc_final: 0.5538 (t-170) REVERT: A 220 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7925 (mm-30) REVERT: A 279 LEU cc_start: 0.7363 (tt) cc_final: 0.7024 (tm) REVERT: A 477 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7043 (tp) REVERT: A 546 LYS cc_start: 0.7695 (tttm) cc_final: 0.7457 (ttpt) REVERT: A 576 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7215 (tmt) REVERT: B 219 HIS cc_start: 0.7106 (m170) cc_final: 0.5587 (t-170) REVERT: B 220 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7972 (mm-30) REVERT: B 232 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7594 (mp0) REVERT: B 244 ARG cc_start: 0.5430 (mtm180) cc_final: 0.5138 (mtm180) REVERT: B 477 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7003 (tp) outliers start: 26 outliers final: 9 residues processed: 114 average time/residue: 0.6170 time to fit residues: 73.9582 Evaluate side-chains 102 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 160 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 576 MET 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 397 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 477 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 24 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 chunk 47 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 18 optimal weight: 0.0370 chunk 82 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS B 266 GLN B 403 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.205236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.147593 restraints weight = 7762.778| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.90 r_work: 0.3654 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8296 Z= 0.101 Angle : 0.563 6.882 11238 Z= 0.285 Chirality : 0.040 0.147 1328 Planarity : 0.004 0.047 1378 Dihedral : 5.026 23.940 1128 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 3.06 % Allowed : 15.08 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.79 (0.25), residues: 1026 helix: -1.49 (0.20), residues: 618 sheet: -2.66 (0.57), residues: 70 loop : -2.00 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 410 TYR 0.009 0.001 TYR B 649 PHE 0.008 0.001 PHE B 387 TRP 0.009 0.001 TRP B 425 HIS 0.003 0.001 HIS B 434 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8296) covalent geometry : angle 0.56309 (11238) hydrogen bonds : bond 0.02610 ( 316) hydrogen bonds : angle 4.21585 ( 936) *********************** 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 121 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.5304 (mpp) REVERT: A 95 GLU cc_start: 0.5980 (mt-10) cc_final: 0.4659 (mp0) REVERT: A 220 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7587 (mm-30) REVERT: A 279 LEU cc_start: 0.7391 (tt) cc_final: 0.7182 (tp) REVERT: B 193 LYS cc_start: 0.8276 (tttm) cc_final: 0.7891 (mmpt) REVERT: B 205 ARG cc_start: 0.7997 (mmm-85) cc_final: 0.7774 (mmm-85) REVERT: B 219 HIS cc_start: 0.6898 (m170) cc_final: 0.5616 (t70) REVERT: B 220 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7625 (mm-30) REVERT: B 274 MET cc_start: 0.5123 (OUTLIER) cc_final: 0.4845 (mmt) outliers start: 27 outliers final: 8 residues processed: 106 average time/residue: 0.5732 time to fit residues: 64.1882 Evaluate side-chains 95 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 477 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 477 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 20 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 100 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 413 GLN B 413 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.199180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.143792 restraints weight = 7738.656| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.23 r_work: 0.3526 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8296 Z= 0.146 Angle : 0.597 6.506 11238 Z= 0.300 Chirality : 0.042 0.146 1328 Planarity : 0.004 0.046 1378 Dihedral : 4.962 22.972 1128 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.41 % Favored : 92.40 % Rotamer: Outliers : 2.72 % Allowed : 16.33 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.26), residues: 1026 helix: -1.24 (0.20), residues: 618 sheet: -2.58 (0.58), residues: 70 loop : -1.75 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 410 TYR 0.011 0.001 TYR A 649 PHE 0.014 0.001 PHE A 406 TRP 0.010 0.002 TRP A 425 HIS 0.004 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8296) covalent geometry : angle 0.59685 (11238) hydrogen bonds : bond 0.02882 ( 316) hydrogen bonds : angle 4.27107 ( 936) *********************** 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 119 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.194 Fit side-chains REVERT: A 90 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.5420 (mpp) REVERT: A 95 GLU cc_start: 0.5818 (mt-10) cc_final: 0.4475 (mp0) REVERT: A 211 GLU cc_start: 0.6358 (mt-10) cc_final: 0.6060 (mt-10) REVERT: A 220 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7684 (mm-30) REVERT: A 576 MET cc_start: 0.7229 (tmt) cc_final: 0.6950 (tmt) REVERT: B 40 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5682 (tp) REVERT: B 193 LYS cc_start: 0.8310 (tttm) cc_final: 0.7843 (mmpt) REVERT: B 219 HIS cc_start: 0.6909 (m170) cc_final: 0.5541 (t70) REVERT: B 220 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 244 ARG cc_start: 0.5658 (mtt-85) cc_final: 0.5236 (mtm180) REVERT: B 274 MET cc_start: 0.5077 (OUTLIER) cc_final: 0.4560 (mpm) REVERT: B 424 MET cc_start: 0.8195 (mmm) cc_final: 0.7987 (mmm) REVERT: B 576 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6690 (tpp) outliers start: 24 outliers final: 8 residues processed: 107 average time/residue: 0.4756 time to fit residues: 54.2001 Evaluate side-chains 102 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 B residue 40 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 274 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.200818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.134719 restraints weight = 7719.491| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.82 r_work: 0.3503 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8296 Z= 0.171 Angle : 0.623 10.076 11238 Z= 0.309 Chirality : 0.043 0.145 1328 Planarity : 0.004 0.045 1378 Dihedral : 5.012 23.501 1128 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.38 % Favored : 91.42 % Rotamer: Outliers : 3.06 % Allowed : 16.78 % 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 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: -2.27 (0.26), residues: 1026 helix: -1.15 (0.20), residues: 624 sheet: -2.00 (0.63), residues: 60 loop : -1.78 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 410 TYR 0.012 0.002 TYR B 649 PHE 0.016 0.001 PHE B 406 TRP 0.011 0.002 TRP B 425 HIS 0.004 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8296) covalent geometry : angle 0.62327 (11238) hydrogen bonds : bond 0.03048 ( 316) hydrogen bonds : angle 4.32442 ( 936) *********************** 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 120 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 93 time to evaluate : 0.313 Fit side-chains REVERT: A 90 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.5637 (mpp) REVERT: A 95 GLU cc_start: 0.5847 (mt-10) cc_final: 0.4451 (mp0) REVERT: A 193 LYS cc_start: 0.7803 (mmpt) cc_final: 0.7572 (ttpp) REVERT: A 220 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7902 (mm-30) REVERT: A 274 MET cc_start: 0.4877 (mpm) cc_final: 0.4669 (mpp) REVERT: A 576 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.7189 (tmt) REVERT: B 40 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5790 (tp) REVERT: B 95 GLU cc_start: 0.5540 (mt-10) cc_final: 0.4331 (mp0) REVERT: B 193 LYS cc_start: 0.8371 (tttm) cc_final: 0.7909 (mmpt) REVERT: B 219 HIS cc_start: 0.7025 (m170) cc_final: 0.5684 (t70) REVERT: B 220 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7809 (mm-30) REVERT: B 232 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: B 310 MET cc_start: 0.6584 (OUTLIER) cc_final: 0.6378 (ttm) REVERT: B 576 MET cc_start: 0.7215 (OUTLIER) cc_final: 0.6859 (tpp) outliers start: 27 outliers final: 9 residues processed: 106 average time/residue: 0.6312 time to fit residues: 70.9436 Evaluate side-chains 103 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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 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 174 THR Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 310 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.0570 chunk 65 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 0.0770 chunk 100 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.206867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.149789 restraints weight = 7676.294| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.04 r_work: 0.3662 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 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 : 0.002 0.032 8296 Z= 0.091 Angle : 0.565 9.826 11238 Z= 0.276 Chirality : 0.040 0.146 1328 Planarity : 0.003 0.045 1378 Dihedral : 4.573 23.900 1128 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.98 % Rotamer: Outliers : 2.61 % Allowed : 17.12 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.27), residues: 1026 helix: -0.50 (0.22), residues: 612 sheet: -2.03 (0.61), residues: 60 loop : -1.72 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 410 TYR 0.008 0.001 TYR B 649 PHE 0.008 0.001 PHE A 646 TRP 0.012 0.001 TRP A 425 HIS 0.003 0.001 HIS B 434 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 8296) covalent geometry : angle 0.56489 (11238) hydrogen bonds : bond 0.02473 ( 316) hydrogen bonds : angle 4.00529 ( 936) *********************** 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 121 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.286 Fit side-chains REVERT: A 90 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.5545 (mpp) REVERT: A 95 GLU cc_start: 0.5904 (mt-10) cc_final: 0.4535 (mp0) REVERT: A 158 ARG cc_start: 0.5622 (ttm170) cc_final: 0.5416 (ttm170) REVERT: A 220 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7594 (mm-30) REVERT: A 274 MET cc_start: 0.5037 (mpm) cc_final: 0.4829 (mpp) REVERT: A 279 LEU cc_start: 0.6324 (OUTLIER) cc_final: 0.6112 (tm) REVERT: B 40 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.6008 (tp) REVERT: B 95 GLU cc_start: 0.5669 (mt-10) cc_final: 0.4429 (mp0) REVERT: B 188 GLU cc_start: 0.6703 (tt0) cc_final: 0.6397 (tt0) REVERT: B 220 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7553 (mm-30) REVERT: B 244 ARG cc_start: 0.5845 (mtt-85) cc_final: 0.5453 (mtm180) REVERT: B 310 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.6111 (ttm) REVERT: B 424 MET cc_start: 0.8088 (mmm) cc_final: 0.7825 (mmm) REVERT: B 576 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6716 (tpp) outliers start: 23 outliers final: 12 residues processed: 111 average time/residue: 0.5325 time to fit residues: 63.1718 Evaluate side-chains 103 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 477 LEU 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 310 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 88 optimal weight: 0.0980 chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 63 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4333 r_free = 0.4333 target = 0.201415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145447 restraints weight = 7708.037| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.10 r_work: 0.3640 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3722 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= 0.157 Angle : 0.629 10.858 11238 Z= 0.305 Chirality : 0.043 0.140 1328 Planarity : 0.004 0.045 1378 Dihedral : 4.755 23.614 1128 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.41 % Favored : 92.40 % Rotamer: Outliers : 2.49 % Allowed : 18.71 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.26), residues: 1026 helix: -0.67 (0.21), residues: 624 sheet: -1.88 (0.62), residues: 60 loop : -1.70 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.008 0.001 TYR A 649 PHE 0.016 0.001 PHE B 406 TRP 0.011 0.002 TRP A 425 HIS 0.004 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8296) covalent geometry : angle 0.62875 (11238) hydrogen bonds : bond 0.02968 ( 316) hydrogen bonds : angle 4.21608 ( 936) *********************** 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 113 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.299 Fit side-chains REVERT: A 90 MET cc_start: 0.6523 (OUTLIER) cc_final: 0.5647 (mpp) REVERT: A 95 GLU cc_start: 0.5817 (mt-10) cc_final: 0.4379 (mp0) REVERT: A 193 LYS cc_start: 0.8138 (ttpp) cc_final: 0.7852 (mmpt) REVERT: A 220 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7742 (mm-30) REVERT: A 274 MET cc_start: 0.5177 (mpm) cc_final: 0.4948 (mpp) REVERT: A 546 LYS cc_start: 0.7480 (tttm) cc_final: 0.7243 (ttmt) REVERT: B 40 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.5967 (tp) REVERT: B 95 GLU cc_start: 0.5667 (mt-10) cc_final: 0.4468 (mp0) REVERT: B 188 GLU cc_start: 0.6669 (tt0) cc_final: 0.6423 (tt0) REVERT: B 219 HIS cc_start: 0.6984 (m170) cc_final: 0.5637 (t70) REVERT: B 220 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7720 (mm-30) REVERT: B 310 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6337 (ttm) REVERT: B 424 MET cc_start: 0.8188 (mmm) cc_final: 0.7943 (mmm) REVERT: B 546 LYS cc_start: 0.7471 (tttm) cc_final: 0.7236 (ttmt) REVERT: B 576 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6804 (tpp) outliers start: 22 outliers final: 10 residues processed: 107 average time/residue: 0.5442 time to fit residues: 62.0545 Evaluate side-chains 102 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 310 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 Chi-restraints excluded: chain B residue 576 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 15 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 60 optimal weight: 0.0270 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.204607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.138852 restraints weight = 7635.122| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.82 r_work: 0.3547 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8296 Z= 0.113 Angle : 0.607 11.379 11238 Z= 0.292 Chirality : 0.042 0.145 1328 Planarity : 0.004 0.045 1378 Dihedral : 4.619 23.849 1128 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.92 % Favored : 92.88 % Rotamer: Outliers : 1.93 % Allowed : 19.05 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.26), residues: 1026 helix: -0.33 (0.21), residues: 612 sheet: -1.74 (0.65), residues: 60 loop : -1.71 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.007 0.001 TYR A 649 PHE 0.019 0.001 PHE B 406 TRP 0.010 0.001 TRP A 425 HIS 0.003 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8296) covalent geometry : angle 0.60679 (11238) hydrogen bonds : bond 0.02693 ( 316) hydrogen bonds : angle 4.09904 ( 936) *********************** 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 109 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.287 Fit side-chains REVERT: A 40 LEU cc_start: 0.6033 (OUTLIER) cc_final: 0.5746 (tp) REVERT: A 90 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.5595 (mpp) REVERT: A 95 GLU cc_start: 0.5792 (mt-10) cc_final: 0.4505 (mp0) REVERT: A 157 VAL cc_start: 0.7343 (m) cc_final: 0.7104 (t) REVERT: A 188 GLU cc_start: 0.6608 (tt0) cc_final: 0.6227 (tt0) REVERT: A 220 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7804 (mm-30) REVERT: A 310 MET cc_start: 0.6137 (ttm) cc_final: 0.5896 (ttm) REVERT: B 40 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5765 (tp) REVERT: B 95 GLU cc_start: 0.5507 (mt-10) cc_final: 0.4309 (mp0) REVERT: B 188 GLU cc_start: 0.6674 (tt0) cc_final: 0.6357 (tt0) REVERT: B 219 HIS cc_start: 0.6896 (m170) cc_final: 0.5578 (t70) REVERT: B 220 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7664 (mm-30) REVERT: B 244 ARG cc_start: 0.5577 (mtt-85) cc_final: 0.5275 (mtm180) REVERT: B 310 MET cc_start: 0.6396 (OUTLIER) cc_final: 0.6026 (ttm) REVERT: B 576 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6754 (tpp) outliers start: 17 outliers final: 10 residues processed: 104 average time/residue: 0.5050 time to fit residues: 55.6635 Evaluate side-chains 105 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU 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 174 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 385 THR 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 310 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 Chi-restraints excluded: chain B residue 576 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4345 r_free = 0.4345 target = 0.202637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.146211 restraints weight = 7601.179| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.92 r_work: 0.3615 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8296 Z= 0.140 Angle : 0.629 11.395 11238 Z= 0.304 Chirality : 0.043 0.143 1328 Planarity : 0.004 0.045 1378 Dihedral : 4.700 23.739 1128 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.60 % Favored : 92.20 % Rotamer: Outliers : 2.04 % Allowed : 19.39 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.26), residues: 1026 helix: -0.39 (0.21), residues: 620 sheet: -1.59 (0.67), residues: 60 loop : -1.63 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.007 0.001 TYR A 649 PHE 0.008 0.001 PHE B 387 TRP 0.010 0.002 TRP A 425 HIS 0.004 0.001 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8296) covalent geometry : angle 0.62863 (11238) hydrogen bonds : bond 0.02862 ( 316) hydrogen bonds : angle 4.20383 ( 936) ********************** 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 108 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.274 Fit side-chains REVERT: A 40 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.6008 (tp) REVERT: A 90 MET cc_start: 0.6468 (OUTLIER) cc_final: 0.5672 (mpp) REVERT: A 95 GLU cc_start: 0.5857 (mt-10) cc_final: 0.4522 (mp0) REVERT: A 157 VAL cc_start: 0.7419 (m) cc_final: 0.7192 (t) REVERT: A 188 GLU cc_start: 0.6641 (tt0) cc_final: 0.6247 (tt0) REVERT: A 220 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7787 (mm-30) REVERT: A 293 ARG cc_start: 0.6288 (mmt180) cc_final: 0.5820 (ttp80) REVERT: A 310 MET cc_start: 0.6285 (ttm) cc_final: 0.6074 (ttm) REVERT: B 95 GLU cc_start: 0.5708 (mt-10) cc_final: 0.4491 (mp0) REVERT: B 188 GLU cc_start: 0.6842 (tt0) cc_final: 0.6541 (tt0) REVERT: B 193 LYS cc_start: 0.8257 (ttpp) cc_final: 0.7932 (mmpt) REVERT: B 219 HIS cc_start: 0.6959 (m170) cc_final: 0.5674 (t70) REVERT: B 220 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7807 (mm-30) REVERT: B 244 ARG cc_start: 0.5837 (mtt-85) cc_final: 0.5498 (mtm180) REVERT: B 310 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.6205 (ttm) REVERT: B 424 MET cc_start: 0.8107 (mmm) cc_final: 0.7850 (mmm) REVERT: B 576 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6827 (tpp) outliers start: 18 outliers final: 9 residues processed: 102 average time/residue: 0.5486 time to fit residues: 59.3484 Evaluate side-chains 101 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU 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 174 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 310 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 Chi-restraints excluded: chain B residue 576 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 32 optimal weight: 0.4980 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 66 optimal weight: 3.9990 chunk 10 optimal weight: 0.0040 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 5 optimal weight: 0.0370 chunk 87 optimal weight: 0.9980 overall best weight: 0.2548 ------------------------------------------------------------------------------- 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 = 0.4399 r_free = 0.4399 target = 0.208687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.152549 restraints weight = 7576.193| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.96 r_work: 0.3732 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8296 Z= 0.090 Angle : 0.582 11.090 11238 Z= 0.281 Chirality : 0.041 0.147 1328 Planarity : 0.003 0.045 1378 Dihedral : 4.375 24.227 1128 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.53 % Favored : 93.27 % Rotamer: Outliers : 2.15 % Allowed : 19.50 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.27), residues: 1026 helix: 0.13 (0.22), residues: 608 sheet: -1.41 (0.68), residues: 60 loop : -1.51 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 205 TYR 0.007 0.001 TYR B 480 PHE 0.009 0.001 PHE A 646 TRP 0.014 0.001 TRP A 425 HIS 0.003 0.001 HIS B 434 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 8296) covalent geometry : angle 0.58178 (11238) hydrogen bonds : bond 0.02468 ( 316) hydrogen bonds : angle 3.97048 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3016.54 seconds wall clock time: 52 minutes 3.75 seconds (3123.75 seconds total)