Starting phenix.real_space_refine on Sun Aug 24 02:16:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pcz_17596/08_2025/8pcz_17596.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pcz_17596/08_2025/8pcz_17596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pcz_17596/08_2025/8pcz_17596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pcz_17596/08_2025/8pcz_17596.map" model { file = "/net/cci-nas-00/data/ceres_data/8pcz_17596/08_2025/8pcz_17596.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pcz_17596/08_2025/8pcz_17596.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 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 84 5.16 5 C 10574 2.51 5 N 2686 2.21 5 O 2832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16176 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8088 Classifications: {'peptide': 1023} Link IDs: {'PTRANS': 30, 'TRANS': 992} Chain breaks: 5 Restraints were copied for chains: B Time building chain proxies: 6.29, per 1000 atoms: 0.39 Number of scatterers: 16176 At special positions: 0 Unit cell: (112.86, 152.988, 122.892, 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 84 16.00 O 2832 8.00 N 2686 7.00 C 10574 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: 1.35 Conformation dependent library (CDL) restraints added in 624.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 8 sheets defined 78.2% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.565A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.986A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.644A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 153 Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 162 Processing helix chain 'A' and resid 162 through 188 removed outlier: 3.574A pdb=" N GLY A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.564A pdb=" N ALA A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 removed outlier: 3.924A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.566A pdb=" N GLY A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 273 through 291 Processing helix chain 'A' and resid 296 through 317 Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 376 removed outlier: 3.637A pdb=" N ARG A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 380 Processing helix chain 'A' and resid 381 through 412 removed outlier: 3.835A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Proline residue: A 408 - end of helix removed outlier: 3.997A pdb=" N ARG A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 Processing helix chain 'A' and resid 449 through 469 removed outlier: 4.242A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 481 removed outlier: 4.985A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.881A pdb=" N ALA A 519 " --> pdb=" O ARG A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 571 through 600 Processing helix chain 'A' and resid 604 through 619 Processing helix chain 'A' and resid 627 through 633 removed outlier: 3.964A pdb=" N LEU A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 Processing helix chain 'A' and resid 653 through 657 removed outlier: 4.504A pdb=" N LYS A 656 " --> pdb=" O SER A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 676 Processing helix chain 'A' and resid 677 through 703 removed outlier: 3.942A pdb=" N GLU A 681 " --> pdb=" O HIS A 677 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix removed outlier: 4.093A pdb=" N PHE A 699 " --> pdb=" O ILE A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 755 removed outlier: 3.657A pdb=" N ALA A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 4.063A pdb=" N ILE A 759 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 780 Processing helix chain 'A' and resid 797 through 811 removed outlier: 3.676A pdb=" N ARG A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG A 806 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 854 Proline residue: A 819 - end of helix removed outlier: 3.643A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 857 No H-bonds generated for 'chain 'A' and resid 855 through 857' Processing helix chain 'A' and resid 860 through 889 Processing helix chain 'A' and resid 889 through 919 Processing helix chain 'A' and resid 923 through 942 removed outlier: 3.644A pdb=" N MET A 942 " --> pdb=" O MET A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.525A pdb=" N ALA A 964 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 977 Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1108 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1123 Processing helix chain 'A' and resid 1179 through 1183 Processing helix chain 'B' and resid 76 through 95 removed outlier: 3.566A pdb=" N PHE B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 3.986A pdb=" N VAL B 105 " --> pdb=" O PRO B 101 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN B 119 " --> pdb=" O VAL B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 4.644A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 153 Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 162 through 188 removed outlier: 3.574A pdb=" N GLY B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 207 removed outlier: 3.564A pdb=" N ALA B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 removed outlier: 3.924A pdb=" N LEU B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 removed outlier: 3.566A pdb=" N GLY B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 273 Processing helix chain 'B' and resid 273 through 291 Processing helix chain 'B' and resid 296 through 317 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 342 through 376 removed outlier: 3.637A pdb=" N ARG B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 380 Processing helix chain 'B' and resid 381 through 412 removed outlier: 3.835A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Proline residue: B 408 - end of helix removed outlier: 3.997A pdb=" N ARG B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 Processing helix chain 'B' and resid 449 through 469 removed outlier: 4.242A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 481 removed outlier: 4.986A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.880A pdb=" N ALA B 519 " --> pdb=" O ARG B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 531 Processing helix chain 'B' and resid 571 through 600 Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 627 through 633 removed outlier: 3.964A pdb=" N LEU B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 652 Processing helix chain 'B' and resid 653 through 657 removed outlier: 4.504A pdb=" N LYS B 656 " --> pdb=" O SER B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 Processing helix chain 'B' and resid 677 through 703 removed outlier: 3.942A pdb=" N GLU B 681 " --> pdb=" O HIS B 677 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix removed outlier: 4.093A pdb=" N PHE B 699 " --> pdb=" O ILE B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 755 removed outlier: 3.657A pdb=" N ALA B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 760 removed outlier: 4.062A pdb=" N ILE B 759 " --> pdb=" O ARG B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 780 Processing helix chain 'B' and resid 797 through 811 removed outlier: 3.676A pdb=" N ARG B 803 " --> pdb=" O VAL B 799 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG B 806 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 854 Proline residue: B 819 - end of helix removed outlier: 3.643A pdb=" N LYS B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 855 through 857 No H-bonds generated for 'chain 'B' and resid 855 through 857' Processing helix chain 'B' and resid 860 through 889 Processing helix chain 'B' and resid 889 through 919 Processing helix chain 'B' and resid 923 through 942 removed outlier: 3.643A pdb=" N MET B 942 " --> pdb=" O MET B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 959 Processing helix chain 'B' and resid 960 through 964 removed outlier: 3.525A pdb=" N ALA B 964 " --> pdb=" O SER B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 977 Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1070 through 1080 Processing helix chain 'B' and resid 1085 through 1108 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1123 Processing helix chain 'B' and resid 1179 through 1183 Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.366A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.718A pdb=" N VAL A 987 " --> pdb=" O CYS A1059 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N CYS A1059 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL A 989 " --> pdb=" O VAL A1057 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1127 removed outlier: 4.771A pdb=" N LEU A1186 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1134 through 1136 removed outlier: 3.644A pdb=" N ALA A1152 " --> pdb=" O ILE A1161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.366A pdb=" N GLN B1064 " --> pdb=" O VAL B1002 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 987 through 989 removed outlier: 6.718A pdb=" N VAL B 987 " --> pdb=" O CYS B1059 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N CYS B1059 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 989 " --> pdb=" O VAL B1057 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1125 through 1127 removed outlier: 4.770A pdb=" N LEU B1186 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1134 through 1136 removed outlier: 3.644A pdb=" N ALA B1152 " --> pdb=" O ILE B1161 " (cutoff:3.500A) 1208 hydrogen bonds defined for protein. 3534 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: 2.67 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4054 1.33 - 1.46: 3362 1.46 - 1.58: 8922 1.58 - 1.70: 0 1.70 - 1.83: 154 Bond restraints: 16492 Sorted by residual: bond pdb=" C GLN B 624 " pdb=" O GLN B 624 " ideal model delta sigma weight residual 1.235 1.210 0.025 1.19e-02 7.06e+03 4.50e+00 bond pdb=" N ALA B 619 " pdb=" CA ALA B 619 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.35e-02 5.49e+03 4.36e+00 bond pdb=" C GLN A 624 " pdb=" O GLN A 624 " ideal model delta sigma weight residual 1.235 1.211 0.025 1.19e-02 7.06e+03 4.33e+00 bond pdb=" N ALA A 619 " pdb=" CA ALA A 619 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.35e-02 5.49e+03 4.23e+00 bond pdb=" N ASP A 623 " pdb=" CA ASP A 623 " ideal model delta sigma weight residual 1.457 1.483 -0.025 1.29e-02 6.01e+03 3.84e+00 ... (remaining 16487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 21940 1.69 - 3.37: 357 3.37 - 5.06: 55 5.06 - 6.74: 8 6.74 - 8.43: 4 Bond angle restraints: 22364 Sorted by residual: angle pdb=" CA GLN A 624 " pdb=" C GLN A 624 " pdb=" O GLN A 624 " ideal model delta sigma weight residual 120.54 116.32 4.22 1.04e+00 9.25e-01 1.65e+01 angle pdb=" CA GLN B 624 " pdb=" C GLN B 624 " pdb=" O GLN B 624 " ideal model delta sigma weight residual 120.54 116.33 4.21 1.04e+00 9.25e-01 1.64e+01 angle pdb=" CA ASP B 620 " pdb=" C ASP B 620 " pdb=" O ASP B 620 " ideal model delta sigma weight residual 121.32 117.13 4.19 1.16e+00 7.43e-01 1.30e+01 angle pdb=" CA ASP A 620 " pdb=" C ASP A 620 " pdb=" O ASP A 620 " ideal model delta sigma weight residual 121.32 117.16 4.16 1.16e+00 7.43e-01 1.28e+01 angle pdb=" CG MET B1073 " pdb=" SD MET B1073 " pdb=" CE MET B1073 " ideal model delta sigma weight residual 100.90 108.24 -7.34 2.20e+00 2.07e-01 1.11e+01 ... (remaining 22359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 8989 16.44 - 32.88: 649 32.88 - 49.31: 168 49.31 - 65.75: 24 65.75 - 82.19: 18 Dihedral angle restraints: 9848 sinusoidal: 3896 harmonic: 5952 Sorted by residual: dihedral pdb=" CA PRO A 210 " pdb=" C PRO A 210 " pdb=" N VAL A 211 " pdb=" CA VAL A 211 " ideal model delta harmonic sigma weight residual 180.00 -159.80 -20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA PRO B 210 " pdb=" C PRO B 210 " pdb=" N VAL B 211 " pdb=" CA VAL B 211 " ideal model delta harmonic sigma weight residual 180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA MET A 154 " pdb=" C MET A 154 " pdb=" N ASP A 155 " pdb=" CA ASP A 155 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 9845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1649 0.027 - 0.055: 583 0.055 - 0.082: 305 0.082 - 0.109: 121 0.109 - 0.136: 30 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA ILE A 948 " pdb=" N ILE A 948 " pdb=" C ILE A 948 " pdb=" CB ILE A 948 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE B 948 " pdb=" N ILE B 948 " pdb=" C ILE B 948 " pdb=" CB ILE B 948 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.54e-01 chirality pdb=" CA ILE B1068 " pdb=" N ILE B1068 " pdb=" C ILE B1068 " pdb=" CB ILE B1068 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 2685 not shown) Planarity restraints: 2750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 571 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO A 572 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 572 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 572 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 571 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO B 572 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 572 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 572 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 275 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 276 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " -0.024 5.00e-02 4.00e+02 ... (remaining 2747 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2207 2.75 - 3.29: 17035 3.29 - 3.83: 26404 3.83 - 4.36: 30483 4.36 - 4.90: 54307 Nonbonded interactions: 130436 Sorted by model distance: nonbonded pdb=" OD1 ASP A 923 " pdb=" N GLU A 924 " model vdw 2.216 3.120 nonbonded pdb=" OD1 ASP B 923 " pdb=" N GLU B 924 " model vdw 2.217 3.120 nonbonded pdb=" O ALA A1140 " pdb=" OG1 THR A1141 " model vdw 2.273 3.040 nonbonded pdb=" O ALA B1140 " pdb=" OG1 THR B1141 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASN B 237 " pdb=" N ASP B 238 " model vdw 2.306 3.120 ... (remaining 130431 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: 0.03 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: 1.710 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.280 Find NCS groups from input model: 0.110 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 : 0.003 0.037 16492 Z= 0.153 Angle : 0.559 8.429 22364 Z= 0.314 Chirality : 0.039 0.136 2688 Planarity : 0.004 0.050 2750 Dihedral : 12.911 82.188 5988 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.23 % Allowed : 5.23 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.19), residues: 2022 helix: 1.85 (0.14), residues: 1442 sheet: 0.17 (0.61), residues: 76 loop : -0.34 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 573 TYR 0.014 0.001 TYR A 737 PHE 0.012 0.001 PHE A 769 TRP 0.014 0.001 TRP A 419 HIS 0.005 0.001 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00320 (16492) covalent geometry : angle 0.55945 (22364) hydrogen bonds : bond 0.11144 ( 1208) hydrogen bonds : angle 5.16122 ( 3534) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 529 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7528 (ttpt) REVERT: A 132 HIS cc_start: 0.7080 (m-70) cc_final: 0.6727 (m-70) REVERT: A 160 MET cc_start: 0.7337 (mmt) cc_final: 0.6957 (mmm) REVERT: A 163 PHE cc_start: 0.7576 (t80) cc_final: 0.7260 (t80) REVERT: A 164 SER cc_start: 0.7963 (m) cc_final: 0.7696 (p) REVERT: A 233 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7098 (tt0) REVERT: A 250 LYS cc_start: 0.7397 (mttt) cc_final: 0.7149 (mttt) REVERT: A 300 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7625 (mt-10) REVERT: A 316 ASP cc_start: 0.7776 (t0) cc_final: 0.7424 (m-30) REVERT: A 319 LEU cc_start: 0.8222 (mt) cc_final: 0.7981 (mp) REVERT: A 320 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7337 (mt-10) REVERT: A 337 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7190 (mm-30) REVERT: A 375 LYS cc_start: 0.7867 (mttt) cc_final: 0.7474 (mttt) REVERT: A 383 MET cc_start: 0.7343 (tpp) cc_final: 0.6656 (mmm) REVERT: A 485 ASP cc_start: 0.7454 (m-30) cc_final: 0.7228 (p0) REVERT: A 511 MET cc_start: 0.7165 (tmm) cc_final: 0.6732 (ttp) REVERT: A 516 ARG cc_start: 0.8065 (ptm160) cc_final: 0.7853 (ptm160) REVERT: A 580 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6456 (tp30) REVERT: A 633 LYS cc_start: 0.8021 (mtmm) cc_final: 0.7458 (mtmm) REVERT: A 640 ILE cc_start: 0.7070 (mt) cc_final: 0.6416 (tt) REVERT: A 644 LEU cc_start: 0.7025 (mt) cc_final: 0.6559 (mp) REVERT: A 648 LEU cc_start: 0.6689 (mt) cc_final: 0.6487 (mp) REVERT: A 777 ASP cc_start: 0.3050 (m-30) cc_final: 0.2629 (t70) REVERT: A 810 MET cc_start: 0.4995 (ptp) cc_final: 0.4572 (ptp) REVERT: A 837 TYR cc_start: 0.7784 (m-80) cc_final: 0.7553 (m-80) REVERT: A 847 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6624 (mm-30) REVERT: A 877 GLN cc_start: 0.7549 (tt0) cc_final: 0.7141 (tt0) REVERT: A 903 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7250 (ttm-80) REVERT: A 925 MET cc_start: 0.6125 (ppp) cc_final: 0.5886 (ppp) REVERT: A 939 LYS cc_start: 0.7799 (tttt) cc_final: 0.7562 (tttt) REVERT: A 966 ASP cc_start: 0.7729 (t0) cc_final: 0.7289 (t0) REVERT: A 994 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7175 (mt-10) REVERT: A 1003 SER cc_start: 0.7831 (t) cc_final: 0.7501 (t) REVERT: A 1007 LYS cc_start: 0.7572 (tttt) cc_final: 0.7054 (tttp) REVERT: A 1033 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7078 (mt-10) REVERT: A 1037 THR cc_start: 0.7705 (t) cc_final: 0.7491 (m) REVERT: A 1044 GLU cc_start: 0.5881 (mt-10) cc_final: 0.5393 (mt-10) REVERT: A 1051 LYS cc_start: 0.8520 (mttm) cc_final: 0.7998 (mttm) REVERT: A 1054 ASN cc_start: 0.8297 (t0) cc_final: 0.7708 (t0) REVERT: A 1073 MET cc_start: 0.7226 (mmp) cc_final: 0.7024 (mmm) REVERT: A 1107 MET cc_start: 0.5770 (mtt) cc_final: 0.5531 (mpp) REVERT: A 1122 GLU cc_start: 0.7528 (tp30) cc_final: 0.7316 (tp30) REVERT: A 1123 ARG cc_start: 0.7644 (ttm170) cc_final: 0.7076 (ttp80) REVERT: A 1125 TYR cc_start: 0.6141 (p90) cc_final: 0.5810 (p90) REVERT: A 1191 ASN cc_start: 0.7343 (t0) cc_final: 0.7137 (p0) REVERT: B 91 SER cc_start: 0.7829 (m) cc_final: 0.7429 (p) REVERT: B 96 LYS cc_start: 0.7867 (ttpt) cc_final: 0.7551 (ttpt) REVERT: B 97 LYS cc_start: 0.7935 (ptmt) cc_final: 0.7673 (ptmt) REVERT: B 149 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7317 (tm-30) REVERT: B 150 SER cc_start: 0.7821 (t) cc_final: 0.7472 (m) REVERT: B 160 MET cc_start: 0.7593 (mmt) cc_final: 0.7257 (mmm) REVERT: B 161 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.7181 (mtm-85) REVERT: B 164 SER cc_start: 0.7832 (m) cc_final: 0.7618 (p) REVERT: B 250 LYS cc_start: 0.7401 (mttt) cc_final: 0.7043 (mttp) REVERT: B 259 SER cc_start: 0.8037 (m) cc_final: 0.7799 (t) REVERT: B 300 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7650 (mt-10) REVERT: B 320 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7394 (mt-10) REVERT: B 337 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7210 (mm-30) REVERT: B 355 MET cc_start: 0.7787 (tmm) cc_final: 0.7451 (ttp) REVERT: B 383 MET cc_start: 0.7264 (tpp) cc_final: 0.6519 (mmm) REVERT: B 387 TYR cc_start: 0.7641 (m-10) cc_final: 0.7425 (m-10) REVERT: B 443 GLU cc_start: 0.7549 (tm-30) cc_final: 0.7173 (tm-30) REVERT: B 475 GLN cc_start: 0.7628 (tp40) cc_final: 0.7418 (tt0) REVERT: B 486 ILE cc_start: 0.8220 (mp) cc_final: 0.7955 (mm) REVERT: B 580 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6296 (tp30) REVERT: B 591 LYS cc_start: 0.7236 (mtmt) cc_final: 0.6969 (mtpp) REVERT: B 621 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6044 (mt-10) REVERT: B 632 LYS cc_start: 0.7338 (ttmm) cc_final: 0.7098 (ttmm) REVERT: B 633 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7547 (mmtm) REVERT: B 634 SER cc_start: 0.8444 (m) cc_final: 0.8001 (t) REVERT: B 635 TRP cc_start: 0.7385 (p90) cc_final: 0.7021 (p90) REVERT: B 678 MET cc_start: 0.7041 (mmm) cc_final: 0.6839 (mmm) REVERT: B 697 MET cc_start: 0.6135 (ttt) cc_final: 0.5865 (ttt) REVERT: B 777 ASP cc_start: 0.3459 (m-30) cc_final: 0.2637 (t70) REVERT: B 810 MET cc_start: 0.5081 (ptp) cc_final: 0.4529 (ptp) REVERT: B 847 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6719 (mm-30) REVERT: B 877 GLN cc_start: 0.7585 (tt0) cc_final: 0.7095 (tt0) REVERT: B 880 LYS cc_start: 0.7226 (ttpp) cc_final: 0.6938 (tttp) REVERT: B 903 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.7085 (ttm-80) REVERT: B 966 ASP cc_start: 0.7552 (t0) cc_final: 0.7193 (t0) REVERT: B 990 ARG cc_start: 0.7182 (mtt-85) cc_final: 0.6898 (mtp85) REVERT: B 994 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7124 (mt-10) REVERT: B 1003 SER cc_start: 0.7835 (t) cc_final: 0.7448 (t) REVERT: B 1007 LYS cc_start: 0.7545 (tttt) cc_final: 0.7235 (tttp) REVERT: B 1037 THR cc_start: 0.7762 (t) cc_final: 0.7543 (m) REVERT: B 1051 LYS cc_start: 0.8442 (mttm) cc_final: 0.7938 (mttm) REVERT: B 1054 ASN cc_start: 0.8457 (t0) cc_final: 0.7991 (t0) REVERT: B 1064 GLN cc_start: 0.7620 (mt0) cc_final: 0.7362 (mt0) REVERT: B 1115 GLU cc_start: 0.7495 (tt0) cc_final: 0.7237 (tt0) REVERT: B 1123 ARG cc_start: 0.7721 (ttm170) cc_final: 0.7380 (ttp80) REVERT: B 1125 TYR cc_start: 0.6110 (p90) cc_final: 0.5885 (p90) REVERT: B 1191 ASN cc_start: 0.7324 (t0) cc_final: 0.7112 (p0) outliers start: 4 outliers final: 3 residues processed: 533 average time/residue: 0.1309 time to fit residues: 98.6837 Evaluate side-chains 450 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 447 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain B residue 622 LYS Chi-restraints excluded: chain B residue 1134 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 ASN ** A 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 GLN A 981 HIS ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN ** B 444 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 GLN B 914 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.155255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.130952 restraints weight = 21994.893| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.63 r_work: 0.3480 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16492 Z= 0.146 Angle : 0.544 7.804 22364 Z= 0.292 Chirality : 0.042 0.160 2688 Planarity : 0.004 0.047 2750 Dihedral : 4.306 38.547 2194 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.82 % Allowed : 11.02 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.19), residues: 2022 helix: 2.05 (0.13), residues: 1460 sheet: 0.07 (0.53), residues: 96 loop : -0.04 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 351 TYR 0.018 0.001 TYR A 984 PHE 0.023 0.002 PHE B 769 TRP 0.014 0.001 TRP A 962 HIS 0.006 0.001 HIS B1120 Details of bonding type rmsd covalent geometry : bond 0.00325 (16492) covalent geometry : angle 0.54435 (22364) hydrogen bonds : bond 0.04722 ( 1208) hydrogen bonds : angle 4.27361 ( 3534) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 465 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8233 (ttpt) cc_final: 0.8005 (ttpt) REVERT: A 154 MET cc_start: 0.8392 (mmm) cc_final: 0.7971 (mmm) REVERT: A 163 PHE cc_start: 0.8257 (t80) cc_final: 0.7917 (t80) REVERT: A 250 LYS cc_start: 0.8597 (mttt) cc_final: 0.8311 (mttm) REVERT: A 289 PHE cc_start: 0.8268 (m-80) cc_final: 0.8027 (m-80) REVERT: A 300 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 383 MET cc_start: 0.8324 (tpp) cc_final: 0.7968 (mmm) REVERT: A 580 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7461 (tp30) REVERT: A 591 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8224 (mtpp) REVERT: A 608 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7913 (tp) REVERT: A 621 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7272 (mt-10) REVERT: A 622 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7416 (mtpm) REVERT: A 628 VAL cc_start: 0.8522 (p) cc_final: 0.7938 (p) REVERT: A 633 LYS cc_start: 0.8338 (mtmm) cc_final: 0.8073 (mtmm) REVERT: A 640 ILE cc_start: 0.8123 (mt) cc_final: 0.7514 (tt) REVERT: A 644 LEU cc_start: 0.8274 (mt) cc_final: 0.7905 (mp) REVERT: A 678 MET cc_start: 0.7174 (mmm) cc_final: 0.6529 (tmm) REVERT: A 777 ASP cc_start: 0.4742 (m-30) cc_final: 0.3446 (t70) REVERT: A 810 MET cc_start: 0.5613 (ptp) cc_final: 0.5147 (ptp) REVERT: A 828 LYS cc_start: 0.8401 (mttt) cc_final: 0.8058 (mmmm) REVERT: A 847 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7374 (mm-30) REVERT: A 877 GLN cc_start: 0.8399 (tt0) cc_final: 0.8014 (tt0) REVERT: A 1003 SER cc_start: 0.8636 (t) cc_final: 0.8379 (t) REVERT: A 1007 LYS cc_start: 0.8540 (tttt) cc_final: 0.8078 (tttp) REVERT: A 1033 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 1037 THR cc_start: 0.8436 (t) cc_final: 0.8138 (m) REVERT: A 1044 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6994 (mt-10) REVERT: A 1054 ASN cc_start: 0.8331 (t0) cc_final: 0.7933 (t0) REVERT: A 1134 PHE cc_start: 0.6630 (OUTLIER) cc_final: 0.6331 (p90) REVERT: B 96 LYS cc_start: 0.8274 (ttpt) cc_final: 0.8030 (ttpt) REVERT: B 150 SER cc_start: 0.8301 (t) cc_final: 0.7795 (m) REVERT: B 154 MET cc_start: 0.8314 (mmm) cc_final: 0.7779 (tpp) REVERT: B 160 MET cc_start: 0.7832 (mmt) cc_final: 0.7599 (mmm) REVERT: B 205 MET cc_start: 0.8086 (mmm) cc_final: 0.7660 (mmm) REVERT: B 250 LYS cc_start: 0.8662 (mttt) cc_final: 0.8361 (mttm) REVERT: B 300 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7637 (mt-10) REVERT: B 355 MET cc_start: 0.8370 (tmm) cc_final: 0.7798 (ttp) REVERT: B 383 MET cc_start: 0.8303 (tpp) cc_final: 0.7688 (mmm) REVERT: B 387 TYR cc_start: 0.8462 (m-10) cc_final: 0.8123 (m-10) REVERT: B 580 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7321 (tp30) REVERT: B 590 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7810 (mt-10) REVERT: B 621 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7304 (mt-10) REVERT: B 628 VAL cc_start: 0.8627 (p) cc_final: 0.8156 (p) REVERT: B 632 LYS cc_start: 0.8424 (ttmm) cc_final: 0.7982 (ttmm) REVERT: B 633 LYS cc_start: 0.8391 (mtmm) cc_final: 0.8116 (mmtm) REVERT: B 634 SER cc_start: 0.8690 (m) cc_final: 0.8288 (t) REVERT: B 635 TRP cc_start: 0.8575 (p90) cc_final: 0.8066 (p90) REVERT: B 640 ILE cc_start: 0.8261 (mt) cc_final: 0.8014 (tt) REVERT: B 697 MET cc_start: 0.5828 (ttt) cc_final: 0.5521 (ttt) REVERT: B 810 MET cc_start: 0.5642 (ptp) cc_final: 0.5034 (ptp) REVERT: B 847 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7365 (mm-30) REVERT: B 877 GLN cc_start: 0.8427 (tt0) cc_final: 0.8028 (tt0) REVERT: B 881 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7438 (mt-10) REVERT: B 967 MET cc_start: 0.7780 (mmm) cc_final: 0.7562 (mmm) REVERT: B 969 LEU cc_start: 0.7959 (tp) cc_final: 0.7742 (tp) REVERT: B 994 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7765 (mt-10) REVERT: B 1003 SER cc_start: 0.8657 (t) cc_final: 0.8418 (t) REVERT: B 1007 LYS cc_start: 0.8600 (tttt) cc_final: 0.8060 (tttp) REVERT: B 1033 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7593 (mt-10) REVERT: B 1037 THR cc_start: 0.8440 (t) cc_final: 0.8142 (m) REVERT: B 1044 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6952 (mt-10) REVERT: B 1054 ASN cc_start: 0.8399 (t0) cc_final: 0.8012 (t0) REVERT: B 1058 THR cc_start: 0.8463 (m) cc_final: 0.8239 (p) REVERT: B 1060 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7566 (mm-30) REVERT: B 1122 GLU cc_start: 0.7672 (tp30) cc_final: 0.7229 (tp30) REVERT: B 1134 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.6135 (p90) outliers start: 32 outliers final: 12 residues processed: 477 average time/residue: 0.1311 time to fit residues: 90.2922 Evaluate side-chains 441 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 425 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 622 LYS Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1134 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 171 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 160 optimal weight: 20.0000 chunk 137 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.155135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.130990 restraints weight = 22352.007| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.64 r_work: 0.3477 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16492 Z= 0.138 Angle : 0.516 8.113 22364 Z= 0.277 Chirality : 0.041 0.152 2688 Planarity : 0.004 0.065 2750 Dihedral : 4.098 38.977 2190 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.61 % Allowed : 13.24 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.27 (0.19), residues: 2022 helix: 2.05 (0.13), residues: 1462 sheet: 0.82 (0.59), residues: 82 loop : 0.00 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 887 TYR 0.015 0.001 TYR B1009 PHE 0.022 0.001 PHE B 769 TRP 0.012 0.001 TRP A 278 HIS 0.005 0.001 HIS B1120 Details of bonding type rmsd covalent geometry : bond 0.00307 (16492) covalent geometry : angle 0.51603 (22364) hydrogen bonds : bond 0.04433 ( 1208) hydrogen bonds : angle 4.10679 ( 3534) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 430 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 LYS cc_start: 0.8230 (ttpt) cc_final: 0.7995 (ttpt) REVERT: A 154 MET cc_start: 0.8443 (mmm) cc_final: 0.8012 (mmm) REVERT: A 163 PHE cc_start: 0.8150 (t80) cc_final: 0.7783 (t80) REVERT: A 205 MET cc_start: 0.7970 (mmm) cc_final: 0.7536 (mmm) REVERT: A 300 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7683 (mt-10) REVERT: A 383 MET cc_start: 0.8282 (tpp) cc_final: 0.8001 (mmm) REVERT: A 499 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7593 (ttm170) REVERT: A 511 MET cc_start: 0.8210 (tmm) cc_final: 0.7707 (ttp) REVERT: A 580 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7531 (tp30) REVERT: A 590 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 591 LYS cc_start: 0.8502 (mtmt) cc_final: 0.8237 (mtpp) REVERT: A 608 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7960 (tp) REVERT: A 621 GLU cc_start: 0.7633 (mt-10) cc_final: 0.7355 (mt-10) REVERT: A 623 ASP cc_start: 0.7493 (t0) cc_final: 0.7266 (t0) REVERT: A 628 VAL cc_start: 0.8484 (p) cc_final: 0.7824 (p) REVERT: A 633 LYS cc_start: 0.8359 (mtmm) cc_final: 0.8062 (mtmm) REVERT: A 640 ILE cc_start: 0.8100 (mt) cc_final: 0.7624 (tt) REVERT: A 644 LEU cc_start: 0.8280 (mt) cc_final: 0.7994 (mp) REVERT: A 645 LYS cc_start: 0.8067 (tttm) cc_final: 0.7865 (tttm) REVERT: A 678 MET cc_start: 0.7148 (mmm) cc_final: 0.6527 (tmm) REVERT: A 777 ASP cc_start: 0.4715 (m-30) cc_final: 0.3470 (t70) REVERT: A 810 MET cc_start: 0.5514 (ptp) cc_final: 0.5141 (ptp) REVERT: A 828 LYS cc_start: 0.8417 (mttt) cc_final: 0.8089 (mmmm) REVERT: A 847 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 877 GLN cc_start: 0.8473 (tt0) cc_final: 0.8084 (tt0) REVERT: A 963 LEU cc_start: 0.8239 (mt) cc_final: 0.8018 (mt) REVERT: A 1003 SER cc_start: 0.8699 (t) cc_final: 0.8287 (m) REVERT: A 1007 LYS cc_start: 0.8564 (tttt) cc_final: 0.8195 (tttp) REVERT: A 1033 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 1037 THR cc_start: 0.8382 (t) cc_final: 0.8141 (m) REVERT: A 1044 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6819 (mt-10) REVERT: A 1054 ASN cc_start: 0.8299 (t0) cc_final: 0.8082 (t0) REVERT: A 1107 MET cc_start: 0.6931 (mpp) cc_final: 0.6700 (mpp) REVERT: A 1134 PHE cc_start: 0.6589 (OUTLIER) cc_final: 0.6295 (p90) REVERT: B 96 LYS cc_start: 0.8304 (ttpt) cc_final: 0.8047 (ttpt) REVERT: B 150 SER cc_start: 0.8313 (t) cc_final: 0.7836 (m) REVERT: B 154 MET cc_start: 0.8411 (mmm) cc_final: 0.7868 (tpp) REVERT: B 160 MET cc_start: 0.7847 (mmt) cc_final: 0.7603 (mmm) REVERT: B 250 LYS cc_start: 0.8660 (mttt) cc_final: 0.8355 (mttm) REVERT: B 355 MET cc_start: 0.8418 (tmm) cc_final: 0.7880 (ttp) REVERT: B 383 MET cc_start: 0.8311 (tpp) cc_final: 0.7718 (mmm) REVERT: B 387 TYR cc_start: 0.8484 (m-10) cc_final: 0.8077 (m-10) REVERT: B 580 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7372 (tp30) REVERT: B 590 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7819 (mt-10) REVERT: B 621 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7376 (mt-10) REVERT: B 628 VAL cc_start: 0.8597 (p) cc_final: 0.8000 (p) REVERT: B 632 LYS cc_start: 0.8419 (ttmm) cc_final: 0.7901 (ttmm) REVERT: B 633 LYS cc_start: 0.8421 (mtmm) cc_final: 0.8158 (mmtp) REVERT: B 634 SER cc_start: 0.8715 (m) cc_final: 0.8300 (t) REVERT: B 697 MET cc_start: 0.5818 (ttt) cc_final: 0.5509 (ttt) REVERT: B 810 MET cc_start: 0.5520 (ptp) cc_final: 0.4993 (ptp) REVERT: B 847 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7437 (mm-30) REVERT: B 877 GLN cc_start: 0.8518 (tt0) cc_final: 0.8037 (tt0) REVERT: B 967 MET cc_start: 0.7645 (mmm) cc_final: 0.7370 (mmm) REVERT: B 987 VAL cc_start: 0.8871 (t) cc_final: 0.8579 (m) REVERT: B 1003 SER cc_start: 0.8754 (t) cc_final: 0.8510 (t) REVERT: B 1007 LYS cc_start: 0.8689 (tttt) cc_final: 0.8151 (tttm) REVERT: B 1033 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7632 (mt-10) REVERT: B 1037 THR cc_start: 0.8383 (t) cc_final: 0.8131 (m) REVERT: B 1044 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7153 (mt-10) REVERT: B 1054 ASN cc_start: 0.8382 (t0) cc_final: 0.8157 (t0) REVERT: B 1058 THR cc_start: 0.8427 (m) cc_final: 0.8210 (p) REVERT: B 1060 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7859 (mm-30) REVERT: B 1104 MET cc_start: 0.7437 (mtp) cc_final: 0.7210 (ttm) REVERT: B 1134 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.6121 (p90) outliers start: 46 outliers final: 27 residues processed: 447 average time/residue: 0.1288 time to fit residues: 83.5412 Evaluate side-chains 441 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 411 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 627 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 852 LYS Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 1062 THR Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 185 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 195 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 193 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.155292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130894 restraints weight = 22081.720| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.64 r_work: 0.3476 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16492 Z= 0.132 Angle : 0.505 8.615 22364 Z= 0.269 Chirality : 0.040 0.145 2688 Planarity : 0.004 0.065 2750 Dihedral : 3.914 38.229 2186 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.56 % Allowed : 14.49 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.26 (0.19), residues: 2022 helix: 2.07 (0.13), residues: 1468 sheet: 1.00 (0.61), residues: 82 loop : -0.17 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 887 TYR 0.014 0.001 TYR B1009 PHE 0.024 0.001 PHE B 769 TRP 0.011 0.001 TRP A 278 HIS 0.005 0.001 HIS B1120 Details of bonding type rmsd covalent geometry : bond 0.00296 (16492) covalent geometry : angle 0.50503 (22364) hydrogen bonds : bond 0.04268 ( 1208) hydrogen bonds : angle 4.00967 ( 3534) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 411 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8425 (mmm) cc_final: 0.8009 (mmm) REVERT: A 205 MET cc_start: 0.7830 (mmm) cc_final: 0.7258 (mmt) REVERT: A 289 PHE cc_start: 0.8297 (m-80) cc_final: 0.8084 (m-80) REVERT: A 300 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7680 (mt-10) REVERT: A 383 MET cc_start: 0.8302 (tpp) cc_final: 0.7992 (mmm) REVERT: A 475 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7968 (mm-40) REVERT: A 499 ARG cc_start: 0.7744 (ttm170) cc_final: 0.7544 (ttm170) REVERT: A 511 MET cc_start: 0.8182 (tmm) cc_final: 0.7663 (ttp) REVERT: A 580 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7338 (tp30) REVERT: A 590 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 591 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8231 (mtpp) REVERT: A 608 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7980 (tp) REVERT: A 621 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7395 (mt-10) REVERT: A 623 ASP cc_start: 0.7524 (t0) cc_final: 0.7286 (t0) REVERT: A 628 VAL cc_start: 0.8424 (p) cc_final: 0.7585 (p) REVERT: A 633 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8080 (mtmm) REVERT: A 640 ILE cc_start: 0.8102 (mt) cc_final: 0.7713 (tt) REVERT: A 644 LEU cc_start: 0.8280 (mt) cc_final: 0.8030 (mp) REVERT: A 678 MET cc_start: 0.7171 (mmm) cc_final: 0.6806 (tmm) REVERT: A 810 MET cc_start: 0.5454 (ptp) cc_final: 0.5078 (ptp) REVERT: A 828 LYS cc_start: 0.8384 (mttt) cc_final: 0.8069 (mmmm) REVERT: A 847 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7318 (mm-30) REVERT: A 877 GLN cc_start: 0.8474 (tt0) cc_final: 0.8059 (tt0) REVERT: A 989 VAL cc_start: 0.8990 (p) cc_final: 0.8614 (m) REVERT: A 1003 SER cc_start: 0.8693 (t) cc_final: 0.8286 (m) REVERT: A 1007 LYS cc_start: 0.8593 (tttt) cc_final: 0.8248 (tttp) REVERT: A 1033 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 1037 THR cc_start: 0.8386 (t) cc_final: 0.8149 (m) REVERT: A 1044 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7079 (mt-10) REVERT: A 1054 ASN cc_start: 0.8297 (t0) cc_final: 0.8089 (t0) REVERT: A 1112 TRP cc_start: 0.5227 (OUTLIER) cc_final: 0.4793 (m-10) REVERT: A 1134 PHE cc_start: 0.6578 (OUTLIER) cc_final: 0.6293 (p90) REVERT: B 96 LYS cc_start: 0.8288 (ttpt) cc_final: 0.8034 (ttpt) REVERT: B 150 SER cc_start: 0.8315 (t) cc_final: 0.8108 (m) REVERT: B 160 MET cc_start: 0.7811 (mmt) cc_final: 0.7566 (mmm) REVERT: B 233 GLU cc_start: 0.7843 (tt0) cc_final: 0.7620 (tt0) REVERT: B 250 LYS cc_start: 0.8641 (mttt) cc_final: 0.8342 (mttm) REVERT: B 355 MET cc_start: 0.8439 (tmm) cc_final: 0.7880 (ttp) REVERT: B 383 MET cc_start: 0.8334 (tpp) cc_final: 0.7875 (mmm) REVERT: B 387 TYR cc_start: 0.8493 (m-10) cc_final: 0.8119 (m-10) REVERT: B 419 TRP cc_start: 0.8625 (p-90) cc_final: 0.8399 (p-90) REVERT: B 580 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7421 (tp30) REVERT: B 621 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7361 (mt-10) REVERT: B 628 VAL cc_start: 0.8546 (p) cc_final: 0.7888 (p) REVERT: B 632 LYS cc_start: 0.8422 (ttmm) cc_final: 0.7892 (ttmm) REVERT: B 633 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8180 (mmtp) REVERT: B 634 SER cc_start: 0.8696 (m) cc_final: 0.8310 (t) REVERT: B 697 MET cc_start: 0.5840 (ttt) cc_final: 0.5534 (ttt) REVERT: B 810 MET cc_start: 0.5472 (ptp) cc_final: 0.5017 (ptp) REVERT: B 847 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7462 (mm-30) REVERT: B 877 GLN cc_start: 0.8499 (tt0) cc_final: 0.8049 (tt0) REVERT: B 967 MET cc_start: 0.7558 (mmm) cc_final: 0.7304 (mmm) REVERT: B 987 VAL cc_start: 0.8838 (t) cc_final: 0.8566 (m) REVERT: B 1007 LYS cc_start: 0.8685 (tttt) cc_final: 0.8177 (tttp) REVERT: B 1033 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 1037 THR cc_start: 0.8360 (t) cc_final: 0.8109 (m) REVERT: B 1044 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7127 (mt-10) REVERT: B 1054 ASN cc_start: 0.8378 (t0) cc_final: 0.8164 (t0) REVERT: B 1058 THR cc_start: 0.8419 (m) cc_final: 0.8200 (p) REVERT: B 1060 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7833 (mm-30) REVERT: B 1075 ILE cc_start: 0.8728 (mm) cc_final: 0.8437 (mt) REVERT: B 1134 PHE cc_start: 0.6693 (OUTLIER) cc_final: 0.6101 (p90) outliers start: 45 outliers final: 28 residues processed: 434 average time/residue: 0.1340 time to fit residues: 84.5201 Evaluate side-chains 436 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 404 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1191 ASN Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1189 VAL Chi-restraints excluded: chain B residue 1191 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 69 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 145 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 908 HIS A 981 HIS ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.154643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130396 restraints weight = 21986.976| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 1.62 r_work: 0.3472 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16492 Z= 0.140 Angle : 0.506 9.479 22364 Z= 0.267 Chirality : 0.040 0.144 2688 Planarity : 0.004 0.062 2750 Dihedral : 3.879 38.302 2186 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.61 % Allowed : 15.80 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.19), residues: 2022 helix: 2.10 (0.13), residues: 1468 sheet: 1.08 (0.60), residues: 82 loop : -0.20 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 887 TYR 0.013 0.001 TYR B1009 PHE 0.027 0.001 PHE B 769 TRP 0.010 0.001 TRP A 278 HIS 0.005 0.001 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00319 (16492) covalent geometry : angle 0.50578 (22364) hydrogen bonds : bond 0.04263 ( 1208) hydrogen bonds : angle 4.00277 ( 3534) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 420 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8404 (mmm) cc_final: 0.7976 (mmm) REVERT: A 197 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7522 (mt-10) REVERT: A 205 MET cc_start: 0.7760 (mmm) cc_final: 0.7213 (mmt) REVERT: A 250 LYS cc_start: 0.8502 (mttt) cc_final: 0.8294 (mttp) REVERT: A 252 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8578 (t) REVERT: A 300 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7693 (mt-10) REVERT: A 383 MET cc_start: 0.8312 (tpp) cc_final: 0.8021 (mmm) REVERT: A 419 TRP cc_start: 0.8591 (p-90) cc_final: 0.8391 (p-90) REVERT: A 475 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7961 (mm-40) REVERT: A 499 ARG cc_start: 0.7739 (ttm170) cc_final: 0.7537 (ttm170) REVERT: A 511 MET cc_start: 0.8221 (tmm) cc_final: 0.7958 (ttp) REVERT: A 580 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7558 (tp30) REVERT: A 591 LYS cc_start: 0.8491 (mtmt) cc_final: 0.8225 (mtpp) REVERT: A 608 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8006 (tp) REVERT: A 621 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7414 (mt-10) REVERT: A 623 ASP cc_start: 0.7525 (t0) cc_final: 0.7317 (t0) REVERT: A 628 VAL cc_start: 0.8394 (p) cc_final: 0.7559 (p) REVERT: A 633 LYS cc_start: 0.8362 (mtmm) cc_final: 0.8080 (mtmm) REVERT: A 640 ILE cc_start: 0.8115 (mt) cc_final: 0.7754 (tt) REVERT: A 644 LEU cc_start: 0.8276 (mt) cc_final: 0.8050 (mp) REVERT: A 678 MET cc_start: 0.7132 (mmm) cc_final: 0.6498 (tmm) REVERT: A 740 PHE cc_start: 0.5590 (t80) cc_final: 0.5162 (t80) REVERT: A 810 MET cc_start: 0.5454 (ptp) cc_final: 0.5071 (ptp) REVERT: A 828 LYS cc_start: 0.8390 (mttt) cc_final: 0.8072 (mmmm) REVERT: A 847 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7333 (mm-30) REVERT: A 877 GLN cc_start: 0.8505 (tt0) cc_final: 0.8068 (tt0) REVERT: A 989 VAL cc_start: 0.8986 (p) cc_final: 0.8636 (m) REVERT: A 1003 SER cc_start: 0.8693 (t) cc_final: 0.8296 (m) REVERT: A 1007 LYS cc_start: 0.8595 (tttt) cc_final: 0.7981 (tttp) REVERT: A 1033 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7556 (mt-10) REVERT: A 1037 THR cc_start: 0.8393 (t) cc_final: 0.8146 (m) REVERT: A 1044 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7008 (mt-10) REVERT: A 1112 TRP cc_start: 0.5279 (OUTLIER) cc_final: 0.4884 (m-10) REVERT: A 1134 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.6256 (p90) REVERT: B 96 LYS cc_start: 0.8255 (ttpt) cc_final: 0.7998 (ttpt) REVERT: B 160 MET cc_start: 0.7784 (mmt) cc_final: 0.7532 (mmm) REVERT: B 250 LYS cc_start: 0.8637 (mttt) cc_final: 0.8333 (mttm) REVERT: B 339 THR cc_start: 0.8623 (m) cc_final: 0.8374 (p) REVERT: B 355 MET cc_start: 0.8454 (tmm) cc_final: 0.7860 (ttp) REVERT: B 383 MET cc_start: 0.8354 (tpp) cc_final: 0.7993 (mmm) REVERT: B 580 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7402 (tp30) REVERT: B 621 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 628 VAL cc_start: 0.8534 (p) cc_final: 0.8128 (p) REVERT: B 632 LYS cc_start: 0.8409 (ttmm) cc_final: 0.7850 (ttmm) REVERT: B 633 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8189 (mmtp) REVERT: B 634 SER cc_start: 0.8706 (m) cc_final: 0.8327 (t) REVERT: B 697 MET cc_start: 0.5842 (ttt) cc_final: 0.5501 (ttt) REVERT: B 810 MET cc_start: 0.5441 (ptp) cc_final: 0.4974 (ptp) REVERT: B 847 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7454 (mm-30) REVERT: B 877 GLN cc_start: 0.8517 (tt0) cc_final: 0.8120 (tt0) REVERT: B 967 MET cc_start: 0.7546 (mmm) cc_final: 0.7257 (mmm) REVERT: B 987 VAL cc_start: 0.8824 (t) cc_final: 0.8557 (m) REVERT: B 1007 LYS cc_start: 0.8706 (tttt) cc_final: 0.8195 (tttp) REVERT: B 1033 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7662 (mt-10) REVERT: B 1037 THR cc_start: 0.8366 (t) cc_final: 0.8122 (m) REVERT: B 1044 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7255 (mt-10) REVERT: B 1054 ASN cc_start: 0.8351 (t0) cc_final: 0.8137 (t0) REVERT: B 1058 THR cc_start: 0.8389 (m) cc_final: 0.8152 (p) REVERT: B 1060 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7765 (mt-10) REVERT: B 1073 MET cc_start: 0.8419 (mmm) cc_final: 0.8093 (mmp) REVERT: B 1075 ILE cc_start: 0.8720 (mm) cc_final: 0.8417 (mt) REVERT: B 1123 ARG cc_start: 0.8356 (ttp80) cc_final: 0.8109 (ttp80) REVERT: B 1134 PHE cc_start: 0.6676 (OUTLIER) cc_final: 0.6098 (p90) outliers start: 46 outliers final: 31 residues processed: 439 average time/residue: 0.1314 time to fit residues: 83.9855 Evaluate side-chains 440 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 404 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1191 ASN Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 852 LYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1189 VAL Chi-restraints excluded: chain B residue 1191 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 77 optimal weight: 0.1980 chunk 196 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 73 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS A1114 GLN ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.155690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.131472 restraints weight = 22152.510| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.62 r_work: 0.3490 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16492 Z= 0.118 Angle : 0.488 9.849 22364 Z= 0.258 Chirality : 0.040 0.139 2688 Planarity : 0.004 0.065 2750 Dihedral : 3.786 38.164 2186 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.50 % Allowed : 16.19 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.19), residues: 2022 helix: 2.21 (0.13), residues: 1468 sheet: 1.11 (0.60), residues: 82 loop : -0.18 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 887 TYR 0.014 0.001 TYR B1009 PHE 0.027 0.001 PHE B 769 TRP 0.010 0.001 TRP A 278 HIS 0.004 0.001 HIS B 676 Details of bonding type rmsd covalent geometry : bond 0.00259 (16492) covalent geometry : angle 0.48772 (22364) hydrogen bonds : bond 0.04021 ( 1208) hydrogen bonds : angle 3.90106 ( 3534) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 422 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 MET cc_start: 0.7869 (mmt) cc_final: 0.7586 (mmm) REVERT: A 187 ASN cc_start: 0.8487 (m-40) cc_final: 0.8166 (m-40) REVERT: A 197 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7455 (mt-10) REVERT: A 252 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8570 (t) REVERT: A 289 PHE cc_start: 0.8306 (m-80) cc_final: 0.8067 (m-80) REVERT: A 300 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7677 (mt-10) REVERT: A 383 MET cc_start: 0.8290 (tpp) cc_final: 0.8031 (mmm) REVERT: A 475 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7994 (mm-40) REVERT: A 499 ARG cc_start: 0.7705 (ttm170) cc_final: 0.7505 (ttm170) REVERT: A 511 MET cc_start: 0.8201 (tmm) cc_final: 0.7931 (ttp) REVERT: A 580 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7563 (tp30) REVERT: A 591 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8235 (mtpp) REVERT: A 608 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7993 (tp) REVERT: A 610 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8035 (mp) REVERT: A 621 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7383 (mt-10) REVERT: A 623 ASP cc_start: 0.7577 (t0) cc_final: 0.7350 (t0) REVERT: A 628 VAL cc_start: 0.8336 (p) cc_final: 0.7453 (p) REVERT: A 633 LYS cc_start: 0.8348 (mtmm) cc_final: 0.8071 (mtmm) REVERT: A 640 ILE cc_start: 0.8077 (mt) cc_final: 0.7765 (tt) REVERT: A 644 LEU cc_start: 0.8259 (mt) cc_final: 0.8020 (mp) REVERT: A 678 MET cc_start: 0.7004 (mmm) cc_final: 0.6344 (tmm) REVERT: A 810 MET cc_start: 0.5384 (ptp) cc_final: 0.5000 (ptp) REVERT: A 828 LYS cc_start: 0.8365 (mttt) cc_final: 0.8046 (mmmm) REVERT: A 847 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7276 (mm-30) REVERT: A 877 GLN cc_start: 0.8497 (tt0) cc_final: 0.8045 (tt0) REVERT: A 989 VAL cc_start: 0.8970 (p) cc_final: 0.8605 (m) REVERT: A 1003 SER cc_start: 0.8693 (t) cc_final: 0.8304 (m) REVERT: A 1007 LYS cc_start: 0.8596 (tttt) cc_final: 0.8217 (tttp) REVERT: A 1033 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7564 (mt-10) REVERT: A 1037 THR cc_start: 0.8371 (t) cc_final: 0.8137 (m) REVERT: A 1044 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7017 (mt-10) REVERT: A 1104 MET cc_start: 0.7764 (mmm) cc_final: 0.7303 (mmm) REVERT: A 1112 TRP cc_start: 0.5312 (OUTLIER) cc_final: 0.4875 (m-10) REVERT: A 1134 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.6259 (p90) REVERT: B 96 LYS cc_start: 0.8265 (ttpt) cc_final: 0.8005 (ttpt) REVERT: B 154 MET cc_start: 0.8271 (tpp) cc_final: 0.8004 (mmm) REVERT: B 160 MET cc_start: 0.7799 (mmt) cc_final: 0.7556 (mmm) REVERT: B 214 VAL cc_start: 0.8572 (p) cc_final: 0.8349 (m) REVERT: B 250 LYS cc_start: 0.8588 (mttt) cc_final: 0.8272 (mttm) REVERT: B 300 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7583 (mt-10) REVERT: B 322 SER cc_start: 0.8210 (t) cc_final: 0.7664 (p) REVERT: B 355 MET cc_start: 0.8403 (tmm) cc_final: 0.7815 (ttp) REVERT: B 383 MET cc_start: 0.8329 (tpp) cc_final: 0.7977 (mmm) REVERT: B 419 TRP cc_start: 0.8648 (p-90) cc_final: 0.8442 (p-90) REVERT: B 580 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7388 (tp30) REVERT: B 621 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7363 (mt-10) REVERT: B 632 LYS cc_start: 0.8373 (ttmm) cc_final: 0.7823 (ttmm) REVERT: B 633 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8192 (mmtp) REVERT: B 697 MET cc_start: 0.5882 (ttt) cc_final: 0.5622 (ttt) REVERT: B 847 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7521 (mm-30) REVERT: B 877 GLN cc_start: 0.8550 (tt0) cc_final: 0.8145 (tt0) REVERT: B 987 VAL cc_start: 0.8810 (t) cc_final: 0.8559 (m) REVERT: B 999 PHE cc_start: 0.7877 (m-80) cc_final: 0.7465 (m-80) REVERT: B 1007 LYS cc_start: 0.8703 (tttt) cc_final: 0.8441 (tttp) REVERT: B 1033 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7620 (mt-10) REVERT: B 1037 THR cc_start: 0.8364 (t) cc_final: 0.8108 (m) REVERT: B 1044 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7297 (mt-10) REVERT: B 1054 ASN cc_start: 0.8324 (t0) cc_final: 0.8086 (t0) REVERT: B 1058 THR cc_start: 0.8390 (m) cc_final: 0.8174 (p) REVERT: B 1060 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7801 (mt-10) REVERT: B 1123 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8055 (ttp80) REVERT: B 1134 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.6068 (p90) outliers start: 44 outliers final: 27 residues processed: 443 average time/residue: 0.1460 time to fit residues: 93.5402 Evaluate side-chains 440 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 407 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1191 ASN Chi-restraints excluded: chain B residue 200 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 852 LYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 47 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 199 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN B 502 HIS B 981 HIS B1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.154826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.130414 restraints weight = 22118.184| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.63 r_work: 0.3476 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16492 Z= 0.145 Angle : 0.521 10.841 22364 Z= 0.270 Chirality : 0.041 0.143 2688 Planarity : 0.004 0.092 2750 Dihedral : 3.788 37.959 2186 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.73 % Allowed : 16.82 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.39 (0.19), residues: 2022 helix: 2.18 (0.13), residues: 1468 sheet: 1.16 (0.60), residues: 82 loop : -0.21 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 887 TYR 0.014 0.001 TYR B1009 PHE 0.028 0.001 PHE B 769 TRP 0.009 0.001 TRP B 419 HIS 0.005 0.001 HIS B1120 Details of bonding type rmsd covalent geometry : bond 0.00337 (16492) covalent geometry : angle 0.52122 (22364) hydrogen bonds : bond 0.04198 ( 1208) hydrogen bonds : angle 3.93951 ( 3534) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 425 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8448 (tpp) cc_final: 0.8179 (tpp) REVERT: A 197 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7458 (mt-10) REVERT: A 249 MET cc_start: 0.8315 (ttp) cc_final: 0.8001 (ttp) REVERT: A 252 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8620 (t) REVERT: A 289 PHE cc_start: 0.8337 (m-80) cc_final: 0.8055 (m-80) REVERT: A 383 MET cc_start: 0.8296 (tpp) cc_final: 0.8047 (mmm) REVERT: A 499 ARG cc_start: 0.7753 (ttm170) cc_final: 0.7551 (ttm170) REVERT: A 511 MET cc_start: 0.8229 (tmm) cc_final: 0.7985 (ttp) REVERT: A 580 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7526 (tp30) REVERT: A 591 LYS cc_start: 0.8494 (mtmt) cc_final: 0.8260 (mtpp) REVERT: A 608 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8029 (tp) REVERT: A 610 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 621 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7413 (mt-10) REVERT: A 628 VAL cc_start: 0.8336 (p) cc_final: 0.7893 (p) REVERT: A 633 LYS cc_start: 0.8369 (mtmm) cc_final: 0.8089 (mtmm) REVERT: A 640 ILE cc_start: 0.8095 (mt) cc_final: 0.7801 (tt) REVERT: A 644 LEU cc_start: 0.8286 (mt) cc_final: 0.8075 (mp) REVERT: A 678 MET cc_start: 0.6969 (mmm) cc_final: 0.6284 (tmm) REVERT: A 740 PHE cc_start: 0.5674 (t80) cc_final: 0.5198 (t80) REVERT: A 810 MET cc_start: 0.5383 (ptp) cc_final: 0.4983 (ptp) REVERT: A 828 LYS cc_start: 0.8379 (mttt) cc_final: 0.8055 (mmmm) REVERT: A 847 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7328 (mm-30) REVERT: A 877 GLN cc_start: 0.8496 (tt0) cc_final: 0.8114 (tt0) REVERT: A 989 VAL cc_start: 0.8988 (p) cc_final: 0.8627 (m) REVERT: A 1003 SER cc_start: 0.8703 (t) cc_final: 0.8302 (m) REVERT: A 1007 LYS cc_start: 0.8608 (tttt) cc_final: 0.7976 (tttp) REVERT: A 1033 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7583 (mt-10) REVERT: A 1037 THR cc_start: 0.8361 (t) cc_final: 0.8137 (m) REVERT: A 1044 GLU cc_start: 0.7615 (mt-10) cc_final: 0.6961 (mt-10) REVERT: A 1072 ASP cc_start: 0.7728 (t0) cc_final: 0.7498 (t0) REVERT: A 1104 MET cc_start: 0.7813 (mmm) cc_final: 0.7326 (mmm) REVERT: A 1112 TRP cc_start: 0.5325 (OUTLIER) cc_final: 0.4953 (m-10) REVERT: A 1134 PHE cc_start: 0.6566 (OUTLIER) cc_final: 0.6264 (p90) REVERT: A 1139 ASP cc_start: 0.7849 (m-30) cc_final: 0.6131 (m-30) REVERT: B 96 LYS cc_start: 0.8279 (ttpt) cc_final: 0.8009 (ttpt) REVERT: B 160 MET cc_start: 0.7818 (mmt) cc_final: 0.7584 (mmm) REVERT: B 214 VAL cc_start: 0.8567 (p) cc_final: 0.8356 (m) REVERT: B 250 LYS cc_start: 0.8565 (mttt) cc_final: 0.8304 (mttp) REVERT: B 322 SER cc_start: 0.8220 (t) cc_final: 0.7676 (p) REVERT: B 355 MET cc_start: 0.8405 (tmm) cc_final: 0.7833 (ttp) REVERT: B 383 MET cc_start: 0.8313 (tpp) cc_final: 0.7951 (mmm) REVERT: B 419 TRP cc_start: 0.8663 (p-90) cc_final: 0.8462 (p-90) REVERT: B 580 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7367 (tp30) REVERT: B 621 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7409 (mt-10) REVERT: B 632 LYS cc_start: 0.8386 (ttmm) cc_final: 0.7854 (ttmm) REVERT: B 633 LYS cc_start: 0.8494 (mtmm) cc_final: 0.8217 (mmtm) REVERT: B 697 MET cc_start: 0.5911 (ttt) cc_final: 0.5645 (ttt) REVERT: B 810 MET cc_start: 0.5370 (ptp) cc_final: 0.4930 (ptt) REVERT: B 847 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7461 (mm-30) REVERT: B 877 GLN cc_start: 0.8528 (tt0) cc_final: 0.8124 (tt0) REVERT: B 961 SER cc_start: 0.8253 (m) cc_final: 0.8051 (p) REVERT: B 987 VAL cc_start: 0.8814 (t) cc_final: 0.8561 (m) REVERT: B 989 VAL cc_start: 0.8839 (p) cc_final: 0.8526 (m) REVERT: B 999 PHE cc_start: 0.7899 (m-80) cc_final: 0.7511 (m-80) REVERT: B 1007 LYS cc_start: 0.8700 (tttt) cc_final: 0.8429 (tttp) REVERT: B 1033 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7634 (mt-10) REVERT: B 1037 THR cc_start: 0.8382 (t) cc_final: 0.8114 (m) REVERT: B 1044 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7359 (mt-10) REVERT: B 1054 ASN cc_start: 0.8328 (t0) cc_final: 0.8095 (t0) REVERT: B 1058 THR cc_start: 0.8411 (m) cc_final: 0.8177 (p) REVERT: B 1060 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7807 (mt-10) REVERT: B 1075 ILE cc_start: 0.8677 (mm) cc_final: 0.8369 (mt) REVERT: B 1123 ARG cc_start: 0.8357 (ttp80) cc_final: 0.8044 (ttp80) REVERT: B 1134 PHE cc_start: 0.6630 (OUTLIER) cc_final: 0.6068 (p90) outliers start: 48 outliers final: 33 residues processed: 445 average time/residue: 0.1221 time to fit residues: 79.3633 Evaluate side-chains 450 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 411 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 848 GLU Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1112 TRP Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1146 ILE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1191 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 852 LYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 911 GLU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1122 GLU Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 0.0170 chunk 17 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 170 optimal weight: 0.7980 chunk 145 optimal weight: 0.5980 chunk 166 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS B1106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.154651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.129913 restraints weight = 22180.746| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.69 r_work: 0.3447 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16492 Z= 0.127 Angle : 0.510 11.645 22364 Z= 0.265 Chirality : 0.040 0.140 2688 Planarity : 0.004 0.081 2750 Dihedral : 3.770 37.795 2186 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.44 % Allowed : 17.90 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.19), residues: 2022 helix: 2.21 (0.13), residues: 1468 sheet: 1.20 (0.60), residues: 82 loop : -0.14 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 887 TYR 0.014 0.001 TYR B1009 PHE 0.030 0.001 PHE B 769 TRP 0.009 0.001 TRP B 278 HIS 0.004 0.001 HIS B 676 Details of bonding type rmsd covalent geometry : bond 0.00286 (16492) covalent geometry : angle 0.51010 (22364) hydrogen bonds : bond 0.04076 ( 1208) hydrogen bonds : angle 3.90440 ( 3534) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 417 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8423 (tpp) cc_final: 0.8165 (tpp) REVERT: A 197 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 208 THR cc_start: 0.7964 (m) cc_final: 0.7698 (m) REVERT: A 249 MET cc_start: 0.8337 (ttp) cc_final: 0.8025 (ttp) REVERT: A 252 VAL cc_start: 0.8854 (OUTLIER) cc_final: 0.8643 (t) REVERT: A 289 PHE cc_start: 0.8340 (m-80) cc_final: 0.8065 (m-80) REVERT: A 383 MET cc_start: 0.8310 (tpp) cc_final: 0.8017 (mmm) REVERT: A 499 ARG cc_start: 0.7681 (ttm170) cc_final: 0.7479 (ttm170) REVERT: A 511 MET cc_start: 0.8230 (tmm) cc_final: 0.8003 (ttp) REVERT: A 580 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7537 (tp30) REVERT: A 591 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8237 (mtpp) REVERT: A 608 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7995 (tp) REVERT: A 610 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8003 (mp) REVERT: A 621 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7383 (mt-10) REVERT: A 628 VAL cc_start: 0.8282 (p) cc_final: 0.7369 (p) REVERT: A 633 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8053 (mtmm) REVERT: A 640 ILE cc_start: 0.8069 (mt) cc_final: 0.7792 (tt) REVERT: A 644 LEU cc_start: 0.8212 (mt) cc_final: 0.8010 (mp) REVERT: A 678 MET cc_start: 0.6859 (mmm) cc_final: 0.6579 (tmm) REVERT: A 740 PHE cc_start: 0.5581 (t80) cc_final: 0.5124 (t80) REVERT: A 810 MET cc_start: 0.5406 (ptp) cc_final: 0.4885 (ptp) REVERT: A 828 LYS cc_start: 0.8373 (mttt) cc_final: 0.8029 (mmmm) REVERT: A 847 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 877 GLN cc_start: 0.8550 (tt0) cc_final: 0.8077 (tt0) REVERT: A 938 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.8311 (mtp) REVERT: A 989 VAL cc_start: 0.8949 (p) cc_final: 0.8595 (m) REVERT: A 1003 SER cc_start: 0.8725 (t) cc_final: 0.8306 (m) REVERT: A 1007 LYS cc_start: 0.8595 (tttt) cc_final: 0.7909 (tttp) REVERT: A 1033 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7467 (mt-10) REVERT: A 1037 THR cc_start: 0.8373 (t) cc_final: 0.8132 (m) REVERT: A 1044 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7001 (mt-10) REVERT: A 1060 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7739 (mt-10) REVERT: A 1072 ASP cc_start: 0.7733 (t0) cc_final: 0.7517 (t0) REVERT: A 1104 MET cc_start: 0.7825 (mmm) cc_final: 0.7391 (mmm) REVERT: A 1134 PHE cc_start: 0.6627 (OUTLIER) cc_final: 0.6310 (p90) REVERT: B 96 LYS cc_start: 0.8244 (ttpt) cc_final: 0.7959 (ttpt) REVERT: B 160 MET cc_start: 0.7907 (mmt) cc_final: 0.7665 (mmm) REVERT: B 214 VAL cc_start: 0.8527 (p) cc_final: 0.8318 (m) REVERT: B 250 LYS cc_start: 0.8519 (mttt) cc_final: 0.8230 (mttp) REVERT: B 322 SER cc_start: 0.8233 (t) cc_final: 0.7670 (p) REVERT: B 355 MET cc_start: 0.8376 (tmm) cc_final: 0.7802 (ttp) REVERT: B 383 MET cc_start: 0.8306 (tpp) cc_final: 0.7961 (mmm) REVERT: B 451 ILE cc_start: 0.8074 (mm) cc_final: 0.7673 (tt) REVERT: B 580 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7404 (tp30) REVERT: B 610 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8102 (mp) REVERT: B 621 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7414 (mt-10) REVERT: B 633 LYS cc_start: 0.8473 (mtmm) cc_final: 0.8162 (mmtm) REVERT: B 697 MET cc_start: 0.5871 (ttt) cc_final: 0.5582 (ttt) REVERT: B 810 MET cc_start: 0.5380 (ptp) cc_final: 0.4926 (ptt) REVERT: B 847 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7531 (mm-30) REVERT: B 877 GLN cc_start: 0.8569 (tt0) cc_final: 0.8211 (tt0) REVERT: B 961 SER cc_start: 0.8284 (m) cc_final: 0.8079 (p) REVERT: B 987 VAL cc_start: 0.8811 (t) cc_final: 0.8554 (m) REVERT: B 989 VAL cc_start: 0.8815 (p) cc_final: 0.8494 (m) REVERT: B 999 PHE cc_start: 0.7912 (m-80) cc_final: 0.7546 (m-80) REVERT: B 1007 LYS cc_start: 0.8705 (tttt) cc_final: 0.8415 (tttp) REVERT: B 1033 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7582 (mt-10) REVERT: B 1037 THR cc_start: 0.8391 (t) cc_final: 0.8101 (m) REVERT: B 1044 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7351 (mt-10) REVERT: B 1054 ASN cc_start: 0.8315 (t0) cc_final: 0.8066 (t0) REVERT: B 1058 THR cc_start: 0.8397 (m) cc_final: 0.8144 (p) REVERT: B 1060 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7775 (mt-10) REVERT: B 1075 ILE cc_start: 0.8638 (mm) cc_final: 0.8340 (mt) REVERT: B 1123 ARG cc_start: 0.8317 (ttp80) cc_final: 0.7926 (ttp80) REVERT: B 1134 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.6105 (p90) outliers start: 43 outliers final: 28 residues processed: 438 average time/residue: 0.1306 time to fit residues: 82.7779 Evaluate side-chains 446 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 411 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 938 MET Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1191 ASN Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 852 LYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 55 optimal weight: 0.0980 chunk 142 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.154555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.130054 restraints weight = 22039.349| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.66 r_work: 0.3450 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16492 Z= 0.131 Angle : 0.521 11.590 22364 Z= 0.269 Chirality : 0.040 0.249 2688 Planarity : 0.004 0.069 2750 Dihedral : 3.743 37.473 2186 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.22 % Allowed : 18.58 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.19), residues: 2022 helix: 2.22 (0.13), residues: 1466 sheet: 1.27 (0.60), residues: 82 loop : -0.14 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 887 TYR 0.014 0.001 TYR B1009 PHE 0.031 0.001 PHE B 769 TRP 0.013 0.001 TRP A 962 HIS 0.004 0.001 HIS A1120 Details of bonding type rmsd covalent geometry : bond 0.00295 (16492) covalent geometry : angle 0.52138 (22364) hydrogen bonds : bond 0.04081 ( 1208) hydrogen bonds : angle 3.90573 ( 3534) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 423 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7496 (mt-10) REVERT: A 208 THR cc_start: 0.7971 (m) cc_final: 0.7696 (m) REVERT: A 249 MET cc_start: 0.8337 (ttp) cc_final: 0.8033 (ttp) REVERT: A 252 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8632 (t) REVERT: A 289 PHE cc_start: 0.8359 (m-80) cc_final: 0.8069 (m-80) REVERT: A 383 MET cc_start: 0.8309 (tpp) cc_final: 0.8021 (mmm) REVERT: A 511 MET cc_start: 0.8222 (tmm) cc_final: 0.7985 (ttp) REVERT: A 580 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7512 (tp30) REVERT: A 587 LEU cc_start: 0.8460 (mm) cc_final: 0.8251 (mp) REVERT: A 591 LYS cc_start: 0.8499 (mtmt) cc_final: 0.8235 (mtpp) REVERT: A 608 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8003 (tp) REVERT: A 610 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8011 (mp) REVERT: A 621 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 628 VAL cc_start: 0.8277 (p) cc_final: 0.7340 (p) REVERT: A 633 LYS cc_start: 0.8374 (mtmm) cc_final: 0.8063 (mtmm) REVERT: A 640 ILE cc_start: 0.8052 (mt) cc_final: 0.7794 (tt) REVERT: A 678 MET cc_start: 0.6841 (mmm) cc_final: 0.6568 (tmm) REVERT: A 740 PHE cc_start: 0.5561 (t80) cc_final: 0.5112 (t80) REVERT: A 810 MET cc_start: 0.5426 (ptp) cc_final: 0.4890 (ptp) REVERT: A 828 LYS cc_start: 0.8400 (mttt) cc_final: 0.8065 (mmmm) REVERT: A 847 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7360 (mm-30) REVERT: A 877 GLN cc_start: 0.8543 (tt0) cc_final: 0.8079 (tt0) REVERT: A 989 VAL cc_start: 0.8949 (p) cc_final: 0.8601 (m) REVERT: A 1003 SER cc_start: 0.8719 (t) cc_final: 0.8302 (m) REVERT: A 1007 LYS cc_start: 0.8576 (tttt) cc_final: 0.7854 (tttp) REVERT: A 1033 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7328 (mt-10) REVERT: A 1037 THR cc_start: 0.8365 (t) cc_final: 0.8106 (m) REVERT: A 1044 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7033 (mt-10) REVERT: A 1060 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7670 (mt-10) REVERT: A 1072 ASP cc_start: 0.7719 (t0) cc_final: 0.7473 (t0) REVERT: A 1104 MET cc_start: 0.7802 (mmm) cc_final: 0.7441 (mmm) REVERT: A 1134 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.6340 (p90) REVERT: A 1169 ARG cc_start: 0.6573 (mtt180) cc_final: 0.6316 (mtt180) REVERT: B 96 LYS cc_start: 0.8245 (ttpt) cc_final: 0.7952 (ttpt) REVERT: B 160 MET cc_start: 0.7901 (mmt) cc_final: 0.7654 (mmm) REVERT: B 250 LYS cc_start: 0.8508 (mttt) cc_final: 0.8213 (mttp) REVERT: B 322 SER cc_start: 0.8271 (t) cc_final: 0.7711 (p) REVERT: B 355 MET cc_start: 0.8372 (tmm) cc_final: 0.7792 (ttp) REVERT: B 383 MET cc_start: 0.8298 (tpp) cc_final: 0.7948 (mmm) REVERT: B 610 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8105 (mp) REVERT: B 621 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7489 (mt-10) REVERT: B 632 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8206 (ttmm) REVERT: B 633 LYS cc_start: 0.8494 (mtmm) cc_final: 0.8167 (mmtm) REVERT: B 678 MET cc_start: 0.6253 (OUTLIER) cc_final: 0.5972 (mmm) REVERT: B 697 MET cc_start: 0.5920 (ttt) cc_final: 0.5634 (ttt) REVERT: B 810 MET cc_start: 0.5424 (ptp) cc_final: 0.4960 (ptt) REVERT: B 847 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7509 (mm-30) REVERT: B 877 GLN cc_start: 0.8561 (tt0) cc_final: 0.8189 (tt0) REVERT: B 929 LYS cc_start: 0.7825 (mtpt) cc_final: 0.7614 (mttt) REVERT: B 987 VAL cc_start: 0.8801 (t) cc_final: 0.8553 (m) REVERT: B 989 VAL cc_start: 0.8797 (p) cc_final: 0.8473 (m) REVERT: B 999 PHE cc_start: 0.7904 (m-80) cc_final: 0.7545 (m-80) REVERT: B 1007 LYS cc_start: 0.8706 (tttt) cc_final: 0.8227 (tttp) REVERT: B 1033 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7444 (mt-10) REVERT: B 1037 THR cc_start: 0.8391 (t) cc_final: 0.8093 (m) REVERT: B 1044 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7260 (mt-10) REVERT: B 1054 ASN cc_start: 0.8271 (t0) cc_final: 0.8030 (t0) REVERT: B 1058 THR cc_start: 0.8369 (m) cc_final: 0.8098 (p) REVERT: B 1075 ILE cc_start: 0.8675 (mm) cc_final: 0.8365 (mt) REVERT: B 1134 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.6102 (p90) outliers start: 39 outliers final: 29 residues processed: 440 average time/residue: 0.1140 time to fit residues: 72.5682 Evaluate side-chains 451 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 415 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 852 LYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1191 ASN Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 852 LYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 110 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 155 optimal weight: 0.0040 chunk 128 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS B 981 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.155069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.130505 restraints weight = 22170.342| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 1.69 r_work: 0.3454 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16492 Z= 0.123 Angle : 0.529 12.186 22364 Z= 0.272 Chirality : 0.041 0.261 2688 Planarity : 0.004 0.068 2750 Dihedral : 3.710 37.125 2186 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.99 % Allowed : 18.86 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.19), residues: 2022 helix: 2.24 (0.13), residues: 1460 sheet: 1.33 (0.60), residues: 82 loop : -0.12 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 887 TYR 0.014 0.001 TYR B1009 PHE 0.031 0.001 PHE B 769 TRP 0.012 0.001 TRP A 962 HIS 0.004 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00274 (16492) covalent geometry : angle 0.52884 (22364) hydrogen bonds : bond 0.03973 ( 1208) hydrogen bonds : angle 3.88534 ( 3534) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 422 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7463 (mt-10) REVERT: A 208 THR cc_start: 0.7952 (m) cc_final: 0.7687 (m) REVERT: A 249 MET cc_start: 0.8344 (ttp) cc_final: 0.8040 (ttp) REVERT: A 252 VAL cc_start: 0.8840 (OUTLIER) cc_final: 0.8630 (t) REVERT: A 289 PHE cc_start: 0.8374 (m-80) cc_final: 0.8069 (m-80) REVERT: A 383 MET cc_start: 0.8300 (tpp) cc_final: 0.8024 (mmm) REVERT: A 511 MET cc_start: 0.8206 (tmm) cc_final: 0.7964 (ttp) REVERT: A 580 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7437 (tp30) REVERT: A 591 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8225 (mtpp) REVERT: A 608 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7997 (tp) REVERT: A 610 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8003 (mp) REVERT: A 621 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7405 (mt-10) REVERT: A 633 LYS cc_start: 0.8389 (mtmm) cc_final: 0.8073 (mtmm) REVERT: A 644 LEU cc_start: 0.8110 (mp) cc_final: 0.7898 (mt) REVERT: A 678 MET cc_start: 0.6786 (mmm) cc_final: 0.6536 (tmm) REVERT: A 740 PHE cc_start: 0.5558 (t80) cc_final: 0.5100 (t80) REVERT: A 810 MET cc_start: 0.5409 (ptp) cc_final: 0.4865 (ptp) REVERT: A 828 LYS cc_start: 0.8409 (mttt) cc_final: 0.8061 (mmmm) REVERT: A 847 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7376 (mm-30) REVERT: A 877 GLN cc_start: 0.8537 (tt0) cc_final: 0.8143 (tt0) REVERT: A 989 VAL cc_start: 0.8940 (p) cc_final: 0.8595 (m) REVERT: A 1003 SER cc_start: 0.8710 (t) cc_final: 0.8285 (m) REVERT: A 1007 LYS cc_start: 0.8568 (tttt) cc_final: 0.7864 (tttp) REVERT: A 1033 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7322 (mt-10) REVERT: A 1037 THR cc_start: 0.8362 (t) cc_final: 0.8084 (m) REVERT: A 1044 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7047 (mt-10) REVERT: A 1060 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7695 (mt-10) REVERT: A 1104 MET cc_start: 0.7748 (mmm) cc_final: 0.7360 (mmm) REVERT: A 1134 PHE cc_start: 0.6591 (OUTLIER) cc_final: 0.6296 (p90) REVERT: A 1169 ARG cc_start: 0.6603 (mtt180) cc_final: 0.6333 (mtt180) REVERT: B 96 LYS cc_start: 0.8258 (ttpt) cc_final: 0.7956 (ttpt) REVERT: B 160 MET cc_start: 0.7894 (mmt) cc_final: 0.7640 (mmm) REVERT: B 214 VAL cc_start: 0.8471 (m) cc_final: 0.8242 (t) REVERT: B 250 LYS cc_start: 0.8510 (mttt) cc_final: 0.8217 (mttp) REVERT: B 322 SER cc_start: 0.8259 (t) cc_final: 0.7707 (p) REVERT: B 355 MET cc_start: 0.8355 (tmm) cc_final: 0.7790 (ttp) REVERT: B 383 MET cc_start: 0.8289 (tpp) cc_final: 0.7956 (mmm) REVERT: B 610 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8094 (mp) REVERT: B 621 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7502 (mt-10) REVERT: B 632 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8067 (ttmm) REVERT: B 633 LYS cc_start: 0.8479 (mtmm) cc_final: 0.8155 (mmtm) REVERT: B 678 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5885 (mmm) REVERT: B 697 MET cc_start: 0.5917 (ttt) cc_final: 0.5630 (ttt) REVERT: B 810 MET cc_start: 0.5440 (ptp) cc_final: 0.5212 (ptp) REVERT: B 847 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7498 (mm-30) REVERT: B 877 GLN cc_start: 0.8589 (tt0) cc_final: 0.8304 (tt0) REVERT: B 881 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7749 (mt-10) REVERT: B 929 LYS cc_start: 0.7818 (mtpt) cc_final: 0.7611 (mttt) REVERT: B 987 VAL cc_start: 0.8803 (t) cc_final: 0.8548 (m) REVERT: B 989 VAL cc_start: 0.8773 (p) cc_final: 0.8436 (m) REVERT: B 1007 LYS cc_start: 0.8729 (tttt) cc_final: 0.8396 (tttp) REVERT: B 1033 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7406 (mt-10) REVERT: B 1037 THR cc_start: 0.8380 (t) cc_final: 0.8086 (m) REVERT: B 1044 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7209 (mt-10) REVERT: B 1054 ASN cc_start: 0.8287 (t0) cc_final: 0.8045 (t0) REVERT: B 1058 THR cc_start: 0.8370 (m) cc_final: 0.8105 (p) REVERT: B 1075 ILE cc_start: 0.8623 (mm) cc_final: 0.8317 (mt) REVERT: B 1134 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.6450 (p90) outliers start: 35 outliers final: 25 residues processed: 439 average time/residue: 0.1399 time to fit residues: 88.9803 Evaluate side-chains 448 residues out of total 1760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 416 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 970 ILE Chi-restraints excluded: chain A residue 1062 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1134 PHE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1191 ASN Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 606 GLU Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 678 MET Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 852 LYS Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 926 GLU Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 1134 PHE Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 77 optimal weight: 0.1980 chunk 96 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 83 optimal weight: 0.0070 chunk 110 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 34 optimal weight: 0.0670 chunk 61 optimal weight: 9.9990 chunk 31 optimal weight: 0.0670 chunk 149 optimal weight: 3.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 981 HIS ** A1154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.156422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.131721 restraints weight = 22043.870| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.69 r_work: 0.3477 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16492 Z= 0.107 Angle : 0.511 11.336 22364 Z= 0.264 Chirality : 0.040 0.245 2688 Planarity : 0.004 0.065 2750 Dihedral : 3.650 36.608 2186 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.53 % Allowed : 19.15 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.58 (0.19), residues: 2022 helix: 2.29 (0.13), residues: 1464 sheet: 1.21 (0.60), residues: 82 loop : -0.00 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 887 TYR 0.014 0.001 TYR B1009 PHE 0.031 0.001 PHE B 769 TRP 0.011 0.001 TRP B 278 HIS 0.004 0.001 HIS B 676 Details of bonding type rmsd covalent geometry : bond 0.00218 (16492) covalent geometry : angle 0.51111 (22364) hydrogen bonds : bond 0.03706 ( 1208) hydrogen bonds : angle 3.81293 ( 3534) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4083.28 seconds wall clock time: 70 minutes 33.54 seconds (4233.54 seconds total)