Starting phenix.real_space_refine on Wed Feb 12 17:26:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i38_35145/02_2025/8i38_35145.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i38_35145/02_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_35145/02_2025/8i38_35145.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i38_35145/02_2025/8i38_35145.map" model { file = "/net/cci-nas-00/data/ceres_data/8i38_35145/02_2025/8i38_35145.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i38_35145/02_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-5592/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: 6.50, per 1000 atoms: 0.80 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: 1.91 Conformation dependent library (CDL) restraints added in 1.2 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: 0.75 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: 2.06 Time building geometry restraints manager: 2.18 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: 1.520 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.150 Find NCS groups from input model: 0.140 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:12.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.000 ------------------------------------------------------------------------------- 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= 0.372 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 *********************** 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 : 0.807 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: 1.2389 time to fit residues: 185.3316 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 : 0.883 ------------------------------------------------------------------------------- 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: 0.3692 rms_B_bonded: 2.33 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= 0.197 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 *********************** 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 : 0.861 Fit side-chains REVERT: A 90 MET cc_start: 0.5946 (OUTLIER) cc_final: 0.4582 (mpp) REVERT: A 219 HIS cc_start: 0.6752 (m170) cc_final: 0.5529 (t70) REVERT: A 220 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7442 (mm-30) REVERT: A 424 MET cc_start: 0.8029 (mmm) cc_final: 0.7770 (mmm) REVERT: A 546 LYS cc_start: 0.7643 (tttm) cc_final: 0.7291 (ttpt) REVERT: B 219 HIS cc_start: 0.7056 (m170) cc_final: 0.5500 (t70) REVERT: B 220 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7495 (mm-30) REVERT: B 232 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7576 (mp0) REVERT: B 244 ARG cc_start: 0.5246 (mtm180) cc_final: 0.4983 (mtm180) REVERT: B 274 MET cc_start: 0.4868 (OUTLIER) cc_final: 0.4516 (mpt) REVERT: B 635 MET cc_start: 0.7854 (ttt) cc_final: 0.7612 (ttt) outliers start: 27 outliers final: 8 residues processed: 123 average time/residue: 1.2156 time to fit residues: 159.7869 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 : 0.922 ------------------------------------------------------------------------------- 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: 0.6980 chunk 42 optimal weight: 0.0870 chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 48 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 0.4556 ------------------------------------------------------------------------------- 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 = 0.4393 r_free = 0.4393 target = 0.208154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.153375 restraints weight = 7711.167| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.03 r_work: 0.3718 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8296 Z= 0.154 Angle : 0.572 7.856 11238 Z= 0.289 Chirality : 0.040 0.142 1328 Planarity : 0.004 0.045 1378 Dihedral : 5.223 47.907 1130 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.53 % Favored : 93.27 % Rotamer: Outliers : 3.29 % Allowed : 11.90 % Favored : 84.81 % 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: -3.19 (0.24), residues: 1026 helix: -1.83 (0.19), residues: 624 sheet: -2.51 (0.58), residues: 70 loop : -2.20 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 447 HIS 0.003 0.001 HIS B 434 PHE 0.009 0.001 PHE B 387 TYR 0.009 0.001 TYR A 47 ARG 0.002 0.000 ARG A 650 *********************** 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 134 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.5903 (OUTLIER) cc_final: 0.4634 (mpp) REVERT: A 219 HIS cc_start: 0.6778 (m170) cc_final: 0.5471 (t70) REVERT: A 220 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7315 (mp0) REVERT: A 546 LYS cc_start: 0.7526 (tttm) cc_final: 0.7241 (ttpt) REVERT: A 576 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.7003 (tmt) REVERT: B 117 ARG cc_start: 0.5795 (mmm-85) cc_final: 0.5107 (mmm-85) REVERT: B 205 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7219 (mmm-85) REVERT: B 220 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7313 (mm-30) REVERT: B 232 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7607 (mp0) REVERT: B 274 MET cc_start: 0.4909 (OUTLIER) cc_final: 0.4675 (mmt) REVERT: B 546 LYS cc_start: 0.7619 (tttm) cc_final: 0.7318 (ttpt) outliers start: 29 outliers final: 10 residues processed: 118 average time/residue: 1.2785 time to fit residues: 160.2730 Evaluate side-chains 108 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 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 477 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: 0.3980 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 101 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN B 266 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 = 0.4329 r_free = 0.4329 target = 0.204109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.150213 restraints weight = 7658.668| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.14 r_work: 0.3548 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2958 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= 0.170 Angle : 0.552 6.645 11238 Z= 0.279 Chirality : 0.040 0.147 1328 Planarity : 0.004 0.045 1378 Dihedral : 4.802 24.247 1128 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.70 % Favored : 92.11 % Rotamer: Outliers : 2.83 % Allowed : 14.63 % Favored : 82.54 % 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: -2.44 (0.26), residues: 1026 helix: -1.18 (0.21), residues: 620 sheet: -2.35 (0.61), residues: 70 loop : -1.99 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 447 HIS 0.003 0.001 HIS B 484 PHE 0.014 0.001 PHE A 406 TYR 0.011 0.001 TYR A 649 ARG 0.002 0.000 ARG B 410 *********************** 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 117 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.6091 (OUTLIER) cc_final: 0.4957 (mpp) REVERT: A 220 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7528 (mm-30) REVERT: A 546 LYS cc_start: 0.7493 (tttm) cc_final: 0.7149 (ttpt) REVERT: A 576 MET cc_start: 0.7172 (tmt) cc_final: 0.6881 (tmt) REVERT: B 205 ARG cc_start: 0.7580 (mtt180) cc_final: 0.7139 (mmm-85) REVERT: B 220 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7460 (mm-30) REVERT: B 232 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7608 (mp0) REVERT: B 274 MET cc_start: 0.4984 (OUTLIER) cc_final: 0.4718 (mmt) REVERT: B 277 THR cc_start: 0.6265 (OUTLIER) cc_final: 0.6050 (t) REVERT: B 546 LYS cc_start: 0.7540 (tttm) cc_final: 0.7216 (ttpt) REVERT: B 603 MET cc_start: 0.5634 (mpt) cc_final: 0.5341 (mpt) outliers start: 25 outliers final: 11 residues processed: 105 average time/residue: 1.2523 time to fit residues: 139.8011 Evaluate side-chains 103 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 277 THR 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 632 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 B 454 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.202514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.146829 restraints weight = 7647.399| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.99 r_work: 0.3649 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8296 Z= 0.250 Angle : 0.593 6.473 11238 Z= 0.299 Chirality : 0.043 0.138 1328 Planarity : 0.004 0.046 1378 Dihedral : 4.922 22.770 1128 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.50 % Favored : 92.30 % Rotamer: Outliers : 2.61 % Allowed : 15.53 % 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 (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: -2.38 (0.26), residues: 1026 helix: -1.17 (0.21), residues: 616 sheet: -2.35 (0.61), residues: 70 loop : -1.87 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 426 HIS 0.004 0.001 HIS A 484 PHE 0.011 0.001 PHE B 387 TYR 0.014 0.002 TYR A 649 ARG 0.004 0.000 ARG B 410 *********************** 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 121 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5466 (mpp) REVERT: A 95 GLU cc_start: 0.5817 (mt-10) cc_final: 0.4539 (mp0) REVERT: A 219 HIS cc_start: 0.6986 (m170) cc_final: 0.5621 (t70) REVERT: A 220 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 576 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.7086 (tmt) REVERT: B 205 ARG cc_start: 0.7452 (mtt180) cc_final: 0.7247 (mmm-85) REVERT: B 219 HIS cc_start: 0.6934 (m170) cc_final: 0.5404 (t-170) REVERT: B 220 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7739 (mm-30) REVERT: B 232 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7661 (mp0) REVERT: B 274 MET cc_start: 0.4982 (OUTLIER) cc_final: 0.4699 (mmt) REVERT: B 576 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6769 (tpp) outliers start: 23 outliers final: 10 residues processed: 108 average time/residue: 1.2384 time to fit residues: 142.2808 Evaluate side-chains 106 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 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 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 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 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 72 optimal weight: 0.0770 chunk 54 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.203220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.147319 restraints weight = 7675.747| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.00 r_work: 0.3615 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.3307 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= 0.217 Angle : 0.574 5.750 11238 Z= 0.289 Chirality : 0.042 0.138 1328 Planarity : 0.004 0.044 1378 Dihedral : 4.811 23.705 1128 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.50 % Favored : 92.30 % Rotamer: Outliers : 2.38 % Allowed : 16.55 % Favored : 81.07 % 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: -2.16 (0.26), residues: 1026 helix: -0.96 (0.21), residues: 624 sheet: -2.41 (0.60), residues: 70 loop : -1.84 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 425 HIS 0.004 0.001 HIS A 484 PHE 0.014 0.001 PHE A 406 TYR 0.012 0.001 TYR B 649 ARG 0.003 0.000 ARG A 293 *********************** 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 114 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.5620 (mpp) REVERT: A 95 GLU cc_start: 0.5886 (mt-10) cc_final: 0.4620 (mp0) REVERT: A 193 LYS cc_start: 0.7698 (mmpt) cc_final: 0.7441 (tttm) REVERT: A 219 HIS cc_start: 0.7034 (m170) cc_final: 0.5684 (t70) REVERT: A 220 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7693 (mm-30) REVERT: B 193 LYS cc_start: 0.8355 (tttm) cc_final: 0.7907 (mmpt) REVERT: B 220 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7671 (mm-30) REVERT: B 232 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7699 (mp0) REVERT: B 274 MET cc_start: 0.5203 (OUTLIER) cc_final: 0.4929 (mmt) REVERT: B 310 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6659 (ttm) REVERT: B 576 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6804 (tpp) outliers start: 21 outliers final: 10 residues processed: 102 average time/residue: 1.3792 time to fit residues: 148.7202 Evaluate side-chains 100 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.833 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 95 optimal weight: 0.0570 chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7898 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.203307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137566 restraints weight = 7692.175| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.83 r_work: 0.3532 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8296 Z= 0.192 Angle : 0.571 9.778 11238 Z= 0.283 Chirality : 0.041 0.139 1328 Planarity : 0.004 0.045 1378 Dihedral : 4.684 23.474 1128 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.31 % Favored : 92.50 % Rotamer: Outliers : 3.17 % Allowed : 16.21 % Favored : 80.61 % 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 (0.27), residues: 1026 helix: -0.74 (0.21), residues: 626 sheet: -1.88 (0.66), residues: 60 loop : -1.69 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 425 HIS 0.004 0.001 HIS A 484 PHE 0.011 0.001 PHE A 406 TYR 0.009 0.001 TYR B 649 ARG 0.003 0.000 ARG A 293 *********************** 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 122 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.777 Fit side-chains REVERT: A 90 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.5582 (mpp) REVERT: A 95 GLU cc_start: 0.5732 (mt-10) cc_final: 0.4490 (mp0) REVERT: A 157 VAL cc_start: 0.7338 (OUTLIER) cc_final: 0.7102 (t) REVERT: A 193 LYS cc_start: 0.7754 (mmpt) cc_final: 0.7521 (ttpp) REVERT: A 211 GLU cc_start: 0.6549 (mt-10) cc_final: 0.6158 (mt-10) REVERT: A 219 HIS cc_start: 0.6923 (m170) cc_final: 0.5593 (t70) REVERT: A 220 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7814 (mm-30) REVERT: A 546 LYS cc_start: 0.7509 (tttm) cc_final: 0.7238 (ttmt) REVERT: B 40 LEU cc_start: 0.5911 (OUTLIER) cc_final: 0.5648 (tp) REVERT: B 193 LYS cc_start: 0.8396 (tttm) cc_final: 0.7887 (mmpt) REVERT: B 205 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7768 (mmm-85) REVERT: B 220 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7626 (mm-30) REVERT: B 232 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7758 (mp0) REVERT: B 274 MET cc_start: 0.5107 (OUTLIER) cc_final: 0.4830 (mmt) REVERT: B 310 MET cc_start: 0.6502 (OUTLIER) cc_final: 0.6151 (ttm) REVERT: B 576 MET cc_start: 0.7160 (OUTLIER) cc_final: 0.6759 (tpp) outliers start: 28 outliers final: 11 residues processed: 109 average time/residue: 1.2608 time to fit residues: 146.0885 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 : 0.833 ------------------------------------------------------------------------------- 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 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 274 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.194373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140579 restraints weight = 7751.069| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.44 r_work: 0.3468 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8296 Z= 0.351 Angle : 0.674 10.021 11238 Z= 0.333 Chirality : 0.046 0.145 1328 Planarity : 0.004 0.043 1378 Dihedral : 5.065 23.388 1128 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.89 % Favored : 91.91 % Rotamer: Outliers : 2.72 % Allowed : 16.78 % Favored : 80.50 % 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: -1.06 (0.20), residues: 618 sheet: -1.48 (0.56), residues: 80 loop : -1.79 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 425 HIS 0.005 0.001 HIS B 484 PHE 0.017 0.002 PHE B 406 TYR 0.014 0.002 TYR B 649 ARG 0.004 0.001 ARG B 410 *********************** 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 114 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.931 Fit side-chains REVERT: A 90 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.5585 (mpp) REVERT: A 95 GLU cc_start: 0.5827 (mt-10) cc_final: 0.4394 (mp0) REVERT: A 183 GLU cc_start: 0.6347 (tm-30) cc_final: 0.5051 (tp30) REVERT: A 219 HIS cc_start: 0.7057 (m170) cc_final: 0.5516 (t-170) REVERT: A 220 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7850 (mm-30) REVERT: A 293 ARG cc_start: 0.6326 (mmt180) cc_final: 0.5923 (ttp80) REVERT: A 546 LYS cc_start: 0.7587 (tttm) cc_final: 0.7275 (ttmt) REVERT: B 40 LEU cc_start: 0.6183 (OUTLIER) cc_final: 0.5876 (tp) REVERT: B 95 GLU cc_start: 0.5639 (mt-10) cc_final: 0.4430 (mp0) REVERT: B 188 GLU cc_start: 0.6486 (tt0) cc_final: 0.6138 (tt0) REVERT: B 193 LYS cc_start: 0.8276 (tttm) cc_final: 0.8036 (mmpt) REVERT: B 219 HIS cc_start: 0.7009 (m170) cc_final: 0.5433 (t-170) REVERT: B 220 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7898 (mm-30) REVERT: B 232 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7652 (mp0) REVERT: B 310 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6393 (ttm) REVERT: B 576 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6832 (tpp) outliers start: 24 outliers final: 11 residues processed: 102 average time/residue: 1.3687 time to fit residues: 147.9062 Evaluate side-chains 104 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.878 ------------------------------------------------------------------------------- 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 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 63 optimal weight: 3.9990 chunk 27 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.201077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.148311 restraints weight = 7803.927| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.57 r_work: 0.3573 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8296 Z= 0.186 Angle : 0.601 9.465 11238 Z= 0.295 Chirality : 0.042 0.144 1328 Planarity : 0.004 0.045 1378 Dihedral : 4.743 23.726 1128 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 1.93 % Allowed : 17.57 % Favored : 80.50 % 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: -1.83 (0.26), residues: 1026 helix: -0.74 (0.21), residues: 626 sheet: -2.09 (0.62), residues: 60 loop : -1.70 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 425 HIS 0.003 0.001 HIS A 484 PHE 0.016 0.001 PHE B 406 TYR 0.009 0.001 TYR B 649 ARG 0.004 0.000 ARG A 205 *********************** 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 108 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.902 Fit side-chains REVERT: A 90 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.5660 (mpp) REVERT: A 95 GLU cc_start: 0.5891 (mt-10) cc_final: 0.4565 (mp0) REVERT: A 219 HIS cc_start: 0.7089 (m170) cc_final: 0.5719 (t70) REVERT: A 220 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7731 (mm-30) REVERT: A 274 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5944 (mtm) REVERT: A 293 ARG cc_start: 0.6217 (mmt180) cc_final: 0.5802 (ttp80) REVERT: A 546 LYS cc_start: 0.7528 (tttm) cc_final: 0.7264 (ttpt) REVERT: B 40 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.6080 (tp) REVERT: B 95 GLU cc_start: 0.5702 (mt-10) cc_final: 0.4486 (mp0) REVERT: B 188 GLU cc_start: 0.6658 (tt0) cc_final: 0.6353 (tt0) REVERT: B 219 HIS cc_start: 0.7127 (m170) cc_final: 0.5753 (t70) REVERT: B 220 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7650 (mm-30) REVERT: B 232 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7807 (mp0) REVERT: B 310 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.6197 (ttm) REVERT: B 576 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6787 (tpp) outliers start: 17 outliers final: 9 residues processed: 99 average time/residue: 1.3845 time to fit residues: 144.8583 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 : 0.903 ------------------------------------------------------------------------------- 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 274 MET 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 75 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 40 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** 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 = 0.4346 r_free = 0.4346 target = 0.202784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.147545 restraints weight = 7642.650| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.05 r_work: 0.3599 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3816 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= 0.197 Angle : 0.606 9.327 11238 Z= 0.295 Chirality : 0.042 0.146 1328 Planarity : 0.004 0.044 1378 Dihedral : 4.682 23.848 1128 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.60 % Favored : 92.20 % Rotamer: Outliers : 1.70 % Allowed : 18.14 % 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: -1.62 (0.26), residues: 1026 helix: -0.49 (0.21), residues: 614 sheet: -2.04 (0.64), residues: 60 loop : -1.75 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 425 HIS 0.003 0.001 HIS B 484 PHE 0.020 0.001 PHE A 406 TYR 0.008 0.001 TYR A 649 ARG 0.004 0.000 ARG A 205 ********************** 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 107 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.5683 (mpp) REVERT: A 95 GLU cc_start: 0.5890 (mt-10) cc_final: 0.4537 (mp0) REVERT: A 219 HIS cc_start: 0.6895 (m170) cc_final: 0.5687 (t-170) REVERT: A 220 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 274 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5915 (mtm) REVERT: A 293 ARG cc_start: 0.6136 (mmt180) cc_final: 0.5730 (ttp80) REVERT: B 40 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6090 (tp) REVERT: B 95 GLU cc_start: 0.5690 (mt-10) cc_final: 0.4581 (mp0) REVERT: B 188 GLU cc_start: 0.6824 (tt0) cc_final: 0.6506 (tt0) REVERT: B 219 HIS cc_start: 0.7039 (m170) cc_final: 0.5727 (t70) REVERT: B 220 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 232 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7777 (mp0) REVERT: B 310 MET cc_start: 0.6532 (OUTLIER) cc_final: 0.6184 (ttm) REVERT: B 546 LYS cc_start: 0.7468 (tttm) cc_final: 0.7248 (ttmt) REVERT: B 576 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.6728 (tpp) outliers start: 15 outliers final: 9 residues processed: 100 average time/residue: 1.3231 time to fit residues: 140.1160 Evaluate side-chains 103 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 274 MET 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 12 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 7 optimal weight: 0.2980 chunk 85 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ** 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 = 0.4287 r_free = 0.4287 target = 0.200472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.148453 restraints weight = 7787.070| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.61 r_work: 0.3527 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8296 Z= 0.150 Angle : 0.578 8.856 11238 Z= 0.281 Chirality : 0.041 0.148 1328 Planarity : 0.004 0.045 1378 Dihedral : 4.485 24.157 1128 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.73 % Favored : 93.08 % Rotamer: Outliers : 1.47 % Allowed : 18.48 % Favored : 80.05 % 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: -1.19 (0.27), residues: 1026 helix: -0.13 (0.21), residues: 612 sheet: -1.94 (0.65), residues: 60 loop : -1.60 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 425 HIS 0.003 0.001 HIS B 434 PHE 0.025 0.001 PHE A 406 TYR 0.007 0.001 TYR A 649 ARG 0.004 0.000 ARG A 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6146.70 seconds wall clock time: 108 minutes 58.08 seconds (6538.08 seconds total)