Starting phenix.real_space_refine on Fri Nov 15 03:19:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i38_35145/11_2024/8i38_35145.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i38_35145/11_2024/8i38_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i38_35145/11_2024/8i38_35145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i38_35145/11_2024/8i38_35145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i38_35145/11_2024/8i38_35145.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i38_35145/11_2024/8i38_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-5513/modules/chem_data/mon_lib" Total number of atoms: 8122 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4061 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 17, 'TRANS': 503} Chain breaks: 3 Restraints were copied for chains: B Time building chain proxies: 7.29, per 1000 atoms: 0.90 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: 2.10 Conformation dependent library (CDL) restraints added in 1.1 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 52.0% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 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: 2.12 Time building geometry restraints manager: 2.25 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: 0.00 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: 1.220 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: 23.130 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.650 ------------------------------------------------------------------------------- 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 : 0.940 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: 1.3192 time to fit residues: 197.4645 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 : 0.884 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 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 : 0.892 Fit side-chains REVERT: A 90 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.4651 (mpp) REVERT: A 219 HIS cc_start: 0.6546 (m170) cc_final: 0.5374 (t70) REVERT: A 220 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7326 (mm-30) REVERT: A 424 MET cc_start: 0.7467 (mmm) cc_final: 0.7246 (mmm) REVERT: A 546 LYS cc_start: 0.7430 (tttm) cc_final: 0.7224 (ttpt) REVERT: B 219 HIS cc_start: 0.6799 (m170) cc_final: 0.5297 (t70) REVERT: B 220 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7350 (mm-30) REVERT: B 232 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7454 (mp0) REVERT: B 244 ARG cc_start: 0.4954 (mtm180) cc_final: 0.4693 (mtm180) REVERT: B 274 MET cc_start: 0.4619 (OUTLIER) cc_final: 0.4305 (mpt) outliers start: 27 outliers final: 8 residues processed: 123 average time/residue: 1.1808 time to fit residues: 155.4031 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 : 0.914 ------------------------------------------------------------------------------- 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 52 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 75 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN B 403 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8296 Z= 0.213 Angle : 0.605 7.999 11238 Z= 0.307 Chirality : 0.041 0.137 1328 Planarity : 0.004 0.046 1378 Dihedral : 5.377 47.659 1130 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.92 % Favored : 92.88 % Rotamer: Outliers : 3.29 % Allowed : 12.70 % Favored : 84.01 % 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: -3.35 (0.24), residues: 1026 helix: -1.98 (0.19), residues: 624 sheet: -2.53 (0.59), residues: 70 loop : -2.24 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 426 HIS 0.004 0.001 HIS B 484 PHE 0.011 0.001 PHE B 387 TYR 0.018 0.002 TYR A 649 ARG 0.003 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 131 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.964 Fit side-chains REVERT: A 90 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.4771 (mpp) REVERT: A 219 HIS cc_start: 0.6531 (m170) cc_final: 0.5246 (t70) REVERT: A 220 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7382 (mm-30) REVERT: B 117 ARG cc_start: 0.5890 (mmm-85) cc_final: 0.5186 (mmm-85) REVERT: B 219 HIS cc_start: 0.6727 (m170) cc_final: 0.5238 (t70) REVERT: B 220 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7404 (mm-30) REVERT: B 232 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7510 (mp0) REVERT: B 274 MET cc_start: 0.4785 (OUTLIER) cc_final: 0.4536 (mmt) REVERT: B 293 ARG cc_start: 0.6308 (ttp80) cc_final: 0.6039 (ttp80) outliers start: 29 outliers final: 8 residues processed: 115 average time/residue: 1.3171 time to fit residues: 160.5705 Evaluate side-chains 102 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 174 THR Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 49 optimal weight: 0.0040 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.0470 chunk 63 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.6094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN B 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8296 Z= 0.169 Angle : 0.555 6.637 11238 Z= 0.282 Chirality : 0.040 0.147 1328 Planarity : 0.004 0.046 1378 Dihedral : 4.862 24.253 1128 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.41 % Favored : 92.40 % Rotamer: Outliers : 2.72 % Allowed : 15.08 % Favored : 82.20 % 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: -2.57 (0.26), residues: 1026 helix: -1.32 (0.20), residues: 620 sheet: -2.36 (0.60), residues: 70 loop : -1.99 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 425 HIS 0.003 0.001 HIS A 484 PHE 0.013 0.001 PHE A 406 TYR 0.010 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 124 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.6129 (OUTLIER) cc_final: 0.5012 (mpp) REVERT: A 97 MET cc_start: 0.6268 (OUTLIER) cc_final: 0.5807 (tpt) REVERT: A 220 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7378 (mm-30) REVERT: B 117 ARG cc_start: 0.5796 (mmm-85) cc_final: 0.5178 (mmm-85) REVERT: B 205 ARG cc_start: 0.7861 (mmm-85) cc_final: 0.7565 (mmm-85) REVERT: B 219 HIS cc_start: 0.6622 (m170) cc_final: 0.5224 (t70) REVERT: B 220 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7370 (mm-30) REVERT: B 232 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7493 (mp0) REVERT: B 274 MET cc_start: 0.4819 (OUTLIER) cc_final: 0.4571 (mmt) outliers start: 24 outliers final: 12 residues processed: 112 average time/residue: 1.2561 time to fit residues: 149.6683 Evaluate side-chains 110 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 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 57 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8296 Z= 0.311 Angle : 0.630 6.040 11238 Z= 0.317 Chirality : 0.044 0.145 1328 Planarity : 0.004 0.046 1378 Dihedral : 5.117 22.628 1128 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.99 % Favored : 91.81 % Rotamer: Outliers : 2.72 % Allowed : 16.44 % Favored : 80.84 % 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: -2.57 (0.25), residues: 1026 helix: -1.38 (0.20), residues: 618 sheet: -2.50 (0.60), residues: 70 loop : -1.80 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 425 HIS 0.005 0.001 HIS A 484 PHE 0.012 0.001 PHE B 387 TYR 0.014 0.002 TYR A 649 ARG 0.005 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: 24 poor density : 97 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.6378 (OUTLIER) cc_final: 0.5535 (mpp) REVERT: A 95 GLU cc_start: 0.5879 (mt-10) cc_final: 0.4477 (mp0) REVERT: A 205 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7676 (mmm-85) REVERT: A 219 HIS cc_start: 0.6773 (m170) cc_final: 0.5327 (t-170) REVERT: A 220 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 193 LYS cc_start: 0.8375 (tttm) cc_final: 0.7920 (mmpt) REVERT: B 219 HIS cc_start: 0.6753 (m170) cc_final: 0.5286 (t-170) REVERT: B 220 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7650 (mm-30) REVERT: B 232 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7542 (mp0) REVERT: B 477 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6795 (tp) REVERT: B 576 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6609 (tpp) outliers start: 24 outliers final: 10 residues processed: 109 average time/residue: 1.2982 time to fit residues: 150.5267 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 : 0.903 ------------------------------------------------------------------------------- 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 B residue 97 MET Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 477 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 90 optimal weight: 0.9990 chunk 19 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 83 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 97 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8296 Z= 0.227 Angle : 0.588 6.424 11238 Z= 0.295 Chirality : 0.042 0.142 1328 Planarity : 0.004 0.044 1378 Dihedral : 4.913 23.476 1128 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 2.83 % Allowed : 16.78 % Favored : 80.39 % 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: -2.21 (0.26), residues: 1026 helix: -1.11 (0.20), residues: 624 sheet: -1.99 (0.65), residues: 60 loop : -1.74 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 425 HIS 0.004 0.001 HIS A 484 PHE 0.010 0.001 PHE A 387 TYR 0.011 0.001 TYR B 649 ARG 0.003 0.000 ARG B 410 *********************** 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: 25 poor density : 95 time to evaluate : 0.873 Fit side-chains REVERT: A 90 MET cc_start: 0.6379 (OUTLIER) cc_final: 0.5605 (mpp) REVERT: A 95 GLU cc_start: 0.5893 (mt-10) cc_final: 0.4489 (mp0) REVERT: A 205 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7638 (mmm-85) REVERT: A 219 HIS cc_start: 0.6741 (m170) cc_final: 0.5309 (t-170) REVERT: A 220 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7528 (mm-30) REVERT: B 40 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.5996 (tp) REVERT: B 95 GLU cc_start: 0.5652 (mt-10) cc_final: 0.4458 (mp0) REVERT: B 193 LYS cc_start: 0.8358 (tttm) cc_final: 0.7910 (mmpt) REVERT: B 205 ARG cc_start: 0.7739 (mmm-85) cc_final: 0.7512 (mmm-85) REVERT: B 219 HIS cc_start: 0.6679 (m170) cc_final: 0.5268 (t-170) REVERT: B 220 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7491 (mm-30) REVERT: B 232 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7533 (mp0) REVERT: B 274 MET cc_start: 0.4833 (OUTLIER) cc_final: 0.4580 (mmt) REVERT: B 310 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.6394 (ttm) REVERT: B 576 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6557 (tpp) outliers start: 25 outliers final: 11 residues processed: 108 average time/residue: 1.2809 time to fit residues: 147.2043 Evaluate side-chains 104 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 174 THR Chi-restraints excluded: chain B residue 258 LYS 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 Chi-restraints excluded: chain B residue 632 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.0570 chunk 57 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 100 optimal weight: 0.0670 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.3563 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= 0.153 Angle : 0.546 7.209 11238 Z= 0.273 Chirality : 0.040 0.143 1328 Planarity : 0.003 0.046 1378 Dihedral : 4.627 23.602 1128 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.31 % Favored : 92.50 % Rotamer: Outliers : 2.95 % Allowed : 17.12 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.27), residues: 1026 helix: -0.62 (0.21), residues: 612 sheet: -1.82 (0.66), residues: 60 loop : -1.70 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 425 HIS 0.003 0.001 HIS A 484 PHE 0.016 0.001 PHE B 406 TYR 0.007 0.001 TYR A 649 ARG 0.006 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 121 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.880 Fit side-chains REVERT: A 90 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.5629 (mpp) REVERT: A 95 GLU cc_start: 0.5816 (mt-10) cc_final: 0.4483 (mp0) REVERT: A 97 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.5862 (tpt) REVERT: A 193 LYS cc_start: 0.8351 (ttpp) cc_final: 0.7982 (mmpt) REVERT: A 205 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7662 (mmm-85) REVERT: A 219 HIS cc_start: 0.6592 (m170) cc_final: 0.5299 (t70) REVERT: A 220 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7527 (mm-30) REVERT: A 280 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5525 (mt) REVERT: A 545 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7692 (mptp) REVERT: B 40 LEU cc_start: 0.6346 (OUTLIER) cc_final: 0.6051 (tp) REVERT: B 95 GLU cc_start: 0.5604 (mt-10) cc_final: 0.4426 (mp0) REVERT: B 188 GLU cc_start: 0.6534 (tt0) cc_final: 0.6288 (tt0) REVERT: B 219 HIS cc_start: 0.6603 (m170) cc_final: 0.5311 (t70) REVERT: B 220 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7405 (mm-30) REVERT: B 274 MET cc_start: 0.4743 (OUTLIER) cc_final: 0.4518 (mmt) REVERT: B 310 MET cc_start: 0.6496 (OUTLIER) cc_final: 0.6184 (ttm) REVERT: B 576 MET cc_start: 0.6805 (OUTLIER) cc_final: 0.6503 (tpp) outliers start: 26 outliers final: 11 residues processed: 111 average time/residue: 1.2414 time to fit residues: 146.9125 Evaluate side-chains 109 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 545 LYS 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 258 LYS 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 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 30 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.3633 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= 0.188 Angle : 0.584 9.374 11238 Z= 0.286 Chirality : 0.042 0.142 1328 Planarity : 0.004 0.044 1378 Dihedral : 4.614 24.037 1128 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.21 % Favored : 92.59 % Rotamer: Outliers : 2.83 % Allowed : 17.01 % 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: -1.49 (0.26), residues: 1026 helix: -0.43 (0.21), residues: 608 sheet: -1.72 (0.67), residues: 60 loop : -1.63 (0.33), residues: 358 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 0.008 0.001 PHE B 387 TYR 0.007 0.001 TYR A 649 ARG 0.003 0.000 ARG A 293 *********************** 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 111 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.868 Fit side-chains REVERT: A 90 MET cc_start: 0.6381 (OUTLIER) cc_final: 0.5618 (mpp) REVERT: A 95 GLU cc_start: 0.5855 (mt-10) cc_final: 0.4502 (mp0) REVERT: A 97 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.5779 (tpt) REVERT: A 193 LYS cc_start: 0.8348 (ttpp) cc_final: 0.7991 (mmpt) REVERT: A 205 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7631 (mmm-85) REVERT: A 219 HIS cc_start: 0.6592 (m170) cc_final: 0.5298 (t-170) REVERT: A 220 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 280 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5532 (mt) REVERT: A 545 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7604 (mptp) REVERT: B 40 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6023 (tp) REVERT: B 95 GLU cc_start: 0.5584 (mt-10) cc_final: 0.4405 (mp0) REVERT: B 188 GLU cc_start: 0.6527 (tt0) cc_final: 0.6276 (tt0) REVERT: B 219 HIS cc_start: 0.6596 (m170) cc_final: 0.5349 (t70) REVERT: B 220 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7429 (mm-30) REVERT: B 232 GLU cc_start: 0.8173 (mp0) cc_final: 0.7908 (mp0) REVERT: B 310 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6229 (ttm) REVERT: B 576 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6524 (tpp) outliers start: 25 outliers final: 12 residues processed: 102 average time/residue: 1.3844 time to fit residues: 149.4852 Evaluate side-chains 105 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 97 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 546 LYS 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 258 LYS 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 546 LYS 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 96 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8296 Z= 0.190 Angle : 0.594 9.199 11238 Z= 0.289 Chirality : 0.042 0.144 1328 Planarity : 0.004 0.045 1378 Dihedral : 4.598 23.754 1128 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.98 % Rotamer: Outliers : 2.49 % Allowed : 17.69 % Favored : 79.82 % 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: -1.36 (0.26), residues: 1026 helix: -0.30 (0.21), residues: 608 sheet: -1.88 (0.64), residues: 60 loop : -1.58 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 425 HIS 0.003 0.001 HIS A 484 PHE 0.019 0.001 PHE B 406 TYR 0.007 0.001 TYR A 649 ARG 0.004 0.000 ARG B 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: 22 poor density : 86 time to evaluate : 0.915 Fit side-chains REVERT: A 90 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.5688 (mpp) REVERT: A 95 GLU cc_start: 0.5854 (mt-10) cc_final: 0.4506 (mp0) REVERT: A 97 MET cc_start: 0.6189 (OUTLIER) cc_final: 0.5798 (tpt) REVERT: A 158 ARG cc_start: 0.5560 (ttm170) cc_final: 0.5299 (ttm110) REVERT: A 205 ARG cc_start: 0.7920 (mmm-85) cc_final: 0.7614 (mmm-85) REVERT: A 219 HIS cc_start: 0.6560 (m170) cc_final: 0.5288 (t-170) REVERT: A 220 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7558 (mm-30) REVERT: A 280 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.5297 (mt) REVERT: A 293 ARG cc_start: 0.6207 (mmt180) cc_final: 0.5733 (ttp80) REVERT: A 310 MET cc_start: 0.6192 (ttm) cc_final: 0.5937 (ttm) REVERT: B 95 GLU cc_start: 0.5577 (mt-10) cc_final: 0.4409 (mp0) REVERT: B 219 HIS cc_start: 0.6580 (m170) cc_final: 0.5327 (t70) REVERT: B 220 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7427 (mm-30) REVERT: B 232 GLU cc_start: 0.8162 (mp0) cc_final: 0.7910 (mp0) REVERT: B 310 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6216 (ttm) REVERT: B 576 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6503 (tpp) outliers start: 22 outliers final: 13 residues processed: 98 average time/residue: 1.3643 time to fit residues: 141.8752 Evaluate side-chains 102 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 97 MET Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 258 LYS 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 546 LYS 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 46 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.3822 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= 0.232 Angle : 0.611 9.021 11238 Z= 0.299 Chirality : 0.043 0.141 1328 Planarity : 0.004 0.044 1378 Dihedral : 4.708 23.919 1128 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.31 % Favored : 92.50 % Rotamer: Outliers : 1.93 % Allowed : 18.71 % Favored : 79.37 % 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: -1.46 (0.26), residues: 1026 helix: -0.46 (0.21), residues: 624 sheet: -1.89 (0.65), residues: 60 loop : -1.53 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 425 HIS 0.004 0.001 HIS A 484 PHE 0.027 0.001 PHE A 406 TYR 0.008 0.001 TYR A 649 ARG 0.004 0.000 ARG B 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 105 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.791 Fit side-chains REVERT: A 90 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.5722 (mpp) REVERT: A 95 GLU cc_start: 0.5897 (mt-10) cc_final: 0.4500 (mp0) REVERT: A 158 ARG cc_start: 0.5513 (ttm170) cc_final: 0.5248 (ttm110) REVERT: A 205 ARG cc_start: 0.7937 (mmm-85) cc_final: 0.7634 (mmm-85) REVERT: A 219 HIS cc_start: 0.6645 (m170) cc_final: 0.5305 (t-170) REVERT: A 220 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7585 (mm-30) REVERT: A 280 LEU cc_start: 0.5901 (OUTLIER) cc_final: 0.5297 (mt) REVERT: A 310 MET cc_start: 0.6097 (ttm) cc_final: 0.5869 (ttm) REVERT: B 95 GLU cc_start: 0.5578 (mt-10) cc_final: 0.4388 (mp0) REVERT: B 219 HIS cc_start: 0.6574 (m170) cc_final: 0.5269 (t70) REVERT: B 220 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7493 (mm-30) REVERT: B 232 GLU cc_start: 0.8203 (mp0) cc_final: 0.7934 (mp0) REVERT: B 310 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.6097 (ttm) REVERT: B 576 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6510 (tpp) outliers start: 17 outliers final: 11 residues processed: 98 average time/residue: 1.3253 time to fit residues: 138.1756 Evaluate side-chains 99 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.869 ------------------------------------------------------------------------------- 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 280 LEU Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 546 LYS 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 546 LYS 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 76 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 59 optimal weight: 0.0870 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 = 0.4361 r_free = 0.4361 target = 0.204246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.148184 restraints weight = 7624.298| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 1.91 r_work: 0.3628 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8296 Z= 0.192 Angle : 0.598 9.062 11238 Z= 0.291 Chirality : 0.042 0.145 1328 Planarity : 0.004 0.045 1378 Dihedral : 4.606 23.836 1128 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.92 % Favored : 92.88 % Rotamer: Outliers : 1.81 % Allowed : 18.93 % Favored : 79.25 % 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: -1.27 (0.27), residues: 1026 helix: -0.23 (0.21), residues: 612 sheet: -1.92 (0.64), residues: 60 loop : -1.56 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 425 HIS 0.003 0.001 HIS A 484 PHE 0.028 0.001 PHE A 406 TYR 0.007 0.001 TYR A 649 ARG 0.004 0.000 ARG B 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3169.21 seconds wall clock time: 57 minutes 36.52 seconds (3456.52 seconds total)