Starting phenix.real_space_refine on Wed Mar 4 05:31:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bsq_30164/03_2026/7bsq_30164_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bsq_30164/03_2026/7bsq_30164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bsq_30164/03_2026/7bsq_30164_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bsq_30164/03_2026/7bsq_30164_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bsq_30164/03_2026/7bsq_30164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bsq_30164/03_2026/7bsq_30164.map" } resolution = 3.2 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= 0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 2 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 7117 2.51 5 N 1807 2.21 5 O 2033 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11024 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8311 Classifications: {'peptide': 1028} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 1002} Chain breaks: 3 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2613 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 25, 'TRANS': 298} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.16, per 1000 atoms: 0.20 Number of scatterers: 11024 At special positions: 0 Unit cell: (106.24, 87.15, 161.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 58 16.00 P 2 15.00 Al 1 13.00 Mg 2 11.99 F 4 9.00 O 2033 8.00 N 1807 7.00 C 7117 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 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=2, symmetry=0 Links applied ALPHA1-3 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 404 " - " ASN C 294 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 398.7 milliseconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 11 sheets defined 45.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 55 through 64 removed outlier: 4.104A pdb=" N PHE A 61 " --> pdb=" O PRO A 57 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.500A pdb=" N TYR A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 121 Proline residue: A 94 - end of helix removed outlier: 3.630A pdb=" N VAL A 98 " --> pdb=" O PRO A 94 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.394A pdb=" N ALA A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 Processing helix chain 'A' and resid 286 through 312 removed outlier: 3.575A pdb=" N THR A 301 " --> pdb=" O PHE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 320 removed outlier: 3.933A pdb=" N ASP A 320 " --> pdb=" O PRO A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 335 through 349 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.598A pdb=" N ILE A 354 " --> pdb=" O PHE A 351 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ILE A 355 " --> pdb=" O ASN A 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 355' Processing helix chain 'A' and resid 358 through 371 removed outlier: 3.586A pdb=" N LYS A 367 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 395 through 400 removed outlier: 4.462A pdb=" N GLU A 398 " --> pdb=" O ASP A 395 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 400 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.852A pdb=" N THR A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 495 through 508 removed outlier: 3.581A pdb=" N ILE A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 500 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 577 through 591 removed outlier: 4.628A pdb=" N VAL A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 620 removed outlier: 3.652A pdb=" N ARG A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 634 removed outlier: 3.859A pdb=" N VAL A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 666 removed outlier: 3.613A pdb=" N ALA A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 688 Processing helix chain 'A' and resid 709 through 721 removed outlier: 3.592A pdb=" N ASP A 713 " --> pdb=" O GLU A 709 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 721 " --> pdb=" O GLU A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 761 Processing helix chain 'A' and resid 770 through 781 removed outlier: 3.783A pdb=" N LYS A 781 " --> pdb=" O GLN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 805 removed outlier: 3.826A pdb=" N VAL A 799 " --> pdb=" O LYS A 795 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 804 " --> pdb=" O ARG A 800 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 805 " --> pdb=" O MET A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 821 removed outlier: 3.548A pdb=" N VAL A 821 " --> pdb=" O ALA A 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 818 through 821' Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 840 through 845 removed outlier: 3.782A pdb=" N ASN A 844 " --> pdb=" O GLN A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 891 removed outlier: 4.214A pdb=" N LYS A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N HIS A 864 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU A 865 " --> pdb=" O ALA A 861 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 870 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR A 876 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 878 " --> pdb=" O VAL A 874 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Proline residue: A 887 - end of helix Processing helix chain 'A' and resid 904 through 914 removed outlier: 3.506A pdb=" N LEU A 908 " --> pdb=" O ASP A 904 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 926 removed outlier: 4.658A pdb=" N ILE A 920 " --> pdb=" O THR A 916 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 948 through 951 Processing helix chain 'A' and resid 952 through 978 removed outlier: 3.894A pdb=" N PHE A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1013 Processing helix chain 'A' and resid 1019 through 1042 removed outlier: 3.709A pdb=" N PHE A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1061 Processing helix chain 'A' and resid 1063 through 1090 Proline residue: A1080 - end of helix removed outlier: 4.087A pdb=" N LEU A1084 " --> pdb=" O PRO A1080 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL A1086 " --> pdb=" O ILE A1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 74 Proline residue: C 52 - end of helix Proline residue: C 63 - end of helix removed outlier: 3.898A pdb=" N PHE C 69 " --> pdb=" O GLY C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 removed outlier: 4.219A pdb=" N LYS C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 146 through 151 removed outlier: 3.853A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 222 through 227 removed outlier: 3.896A pdb=" N ARG C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 227' Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.558A pdb=" N MET C 242 " --> pdb=" O PRO C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 250 removed outlier: 3.775A pdb=" N ASN C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 262 removed outlier: 3.539A pdb=" N ARG C 262 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 350 removed outlier: 3.873A pdb=" N PHE C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 22 Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 128 removed outlier: 3.608A pdb=" N LYS A 136 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 6.868A pdb=" N LYS A 256 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N SER A 164 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR A 258 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.906A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 250 " --> pdb=" O THR A 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 381 through 382 removed outlier: 3.612A pdb=" N GLU A 387 " --> pdb=" O ASP A 382 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 390 through 391 removed outlier: 6.807A pdb=" N THR A 811 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N ILE A 831 " --> pdb=" O THR A 811 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N SER A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 833 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY A 815 " --> pdb=" O ILE A 833 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL A 406 " --> pdb=" O TRP A 671 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 673 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N THR A 408 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL A 670 " --> pdb=" O VAL A 785 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N CYS A 787 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 672 " --> pdb=" O CYS A 787 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA A 784 " --> pdb=" O TYR A 747 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 420 through 426 removed outlier: 3.686A pdb=" N ALA A 647 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N CYS A 424 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA A 645 " --> pdb=" O CYS A 424 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ILE A 426 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ILE A 643 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LEU A 642 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N PHE A 600 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 603 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE A 558 " --> pdb=" O ILE A 603 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS A 536 " --> pdb=" O ILE A 550 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS A 552 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU A 534 " --> pdb=" O LYS A 552 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 511 through 512 Processing sheet with id=AA9, first strand: chain 'C' and resid 78 through 81 removed outlier: 3.676A pdb=" N ARG C 309 " --> pdb=" O GLY C 123 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 104 through 110 removed outlier: 4.770A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 163 434 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1916 1.32 - 1.45: 3064 1.45 - 1.57: 6205 1.57 - 1.70: 3 1.70 - 1.83: 91 Bond restraints: 11279 Sorted by residual: bond pdb=" CA PHE A 64 " pdb=" C PHE A 64 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.34e-02 5.57e+03 4.01e+01 bond pdb=" C4 ADP A1102 " pdb=" C5 ADP A1102 " ideal model delta sigma weight residual 1.490 1.378 0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.797 -0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.790 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.49e+01 ... (remaining 11274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 13.90: 15286 13.90 - 27.79: 4 27.79 - 41.69: 0 41.69 - 55.59: 0 55.59 - 69.49: 2 Bond angle restraints: 15292 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 178.17 -69.49 3.00e+00 1.11e-01 5.36e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 178.91 -69.28 3.00e+00 1.11e-01 5.33e+02 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 88.55 21.66 3.00e+00 1.11e-01 5.22e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.02 89.82 19.20 3.00e+00 1.11e-01 4.09e+01 angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.69 90.79 18.90 3.00e+00 1.11e-01 3.97e+01 ... (remaining 15287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.97: 6216 23.97 - 47.95: 474 47.95 - 71.92: 64 71.92 - 95.90: 11 95.90 - 119.87: 2 Dihedral angle restraints: 6767 sinusoidal: 2798 harmonic: 3969 Sorted by residual: dihedral pdb=" CB CYS C 94 " pdb=" SG CYS C 94 " pdb=" SG CYS C 102 " pdb=" CB CYS C 102 " ideal model delta sinusoidal sigma weight residual -86.00 -20.89 -65.11 1 1.00e+01 1.00e-02 5.56e+01 dihedral pdb=" O2A ADP A1102 " pdb=" O3A ADP A1102 " pdb=" PA ADP A1102 " pdb=" PB ADP A1102 " ideal model delta sinusoidal sigma weight residual -60.00 59.87 -119.87 1 2.00e+01 2.50e-03 3.60e+01 dihedral pdb=" C5' ADP A1102 " pdb=" O5' ADP A1102 " pdb=" PA ADP A1102 " pdb=" O2A ADP A1102 " ideal model delta sinusoidal sigma weight residual -60.00 -174.15 114.15 1 2.00e+01 2.50e-03 3.38e+01 ... (remaining 6764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1672 0.125 - 0.250: 50 0.250 - 0.376: 3 0.376 - 0.501: 1 0.501 - 0.626: 1 Chirality restraints: 1727 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.82e+01 chirality pdb=" C1 MAN B 3 " pdb=" O3 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.27 0.13 2.00e-02 2.50e+03 4.07e+01 chirality pdb=" C1 NAG C 404 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 404 " pdb=" O5 NAG C 404 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 9.80e+00 ... (remaining 1724 not shown) Planarity restraints: 1921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 404 " -0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG C 404 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C 404 " -0.097 2.00e-02 2.50e+03 pdb=" N2 NAG C 404 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG C 404 " -0.177 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 405 " -0.293 2.00e-02 2.50e+03 2.54e-01 8.09e+02 pdb=" C7 NAG C 405 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG C 405 " -0.008 2.00e-02 2.50e+03 pdb=" N2 NAG C 405 " 0.441 2.00e-02 2.50e+03 pdb=" O7 NAG C 405 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.077 2.00e-02 2.50e+03 6.50e-02 5.28e+01 pdb=" C7 NAG B 2 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.023 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.104 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.062 2.00e-02 2.50e+03 ... (remaining 1918 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 103 2.45 - 3.06: 8277 3.06 - 3.68: 15344 3.68 - 4.29: 25700 4.29 - 4.90: 43629 Nonbonded interactions: 93053 Sorted by model distance: nonbonded pdb=" O2A ADP A1102 " pdb="MG MG A1104 " model vdw 1.841 2.170 nonbonded pdb=" F4 ALF A1101 " pdb=" O1B ADP A1102 " model vdw 1.866 2.990 nonbonded pdb=" CA GLY A 815 " pdb="MG MG A1103 " model vdw 1.878 2.570 nonbonded pdb=" O ILE A 225 " pdb=" CB ALA A 236 " model vdw 1.895 3.460 nonbonded pdb=" OG SER A 813 " pdb=" OG SER A 827 " model vdw 1.897 3.040 ... (remaining 93048 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.090 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.080 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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: 0.020 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 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 : 0.016 0.820 11288 Z= 0.971 Angle : 1.307 69.486 15310 Z= 0.597 Chirality : 0.061 0.626 1727 Planarity : 0.011 0.306 1919 Dihedral : 16.724 119.870 4196 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 35.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 15.95 % Favored : 83.98 % Rotamer: Outliers : 6.31 % Allowed : 17.28 % Favored : 76.41 % Cbeta Deviations : 0.16 % 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 are not related in a simple way. whole: -5.29 (0.18), residues: 1342 helix: -3.17 (0.16), residues: 568 sheet: -2.32 (0.34), residues: 203 loop : -4.30 (0.20), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 544 TYR 0.032 0.003 TYR C 297 PHE 0.034 0.003 PHE A 971 TRP 0.025 0.004 TRP C 260 HIS 0.006 0.002 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.01398 (11279) covalent geometry : angle 1.30082 (15292) SS BOND : bond 0.00145 ( 3) SS BOND : angle 1.66555 ( 6) hydrogen bonds : bond 0.13349 ( 434) hydrogen bonds : angle 7.05072 ( 1236) Misc. bond : bond 0.57952 ( 2) link_ALPHA1-3 : bond 0.00329 ( 1) link_ALPHA1-3 : angle 4.25085 ( 3) link_BETA1-4 : bond 0.00097 ( 1) link_BETA1-4 : angle 1.77252 ( 3) link_NAG-ASN : bond 0.01230 ( 2) link_NAG-ASN : angle 5.91195 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 176 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.6854 (OUTLIER) cc_final: 0.6605 (p90) REVERT: A 135 ARG cc_start: 0.7455 (ptm-80) cc_final: 0.7198 (ttp80) REVERT: A 181 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6787 (mt-10) REVERT: A 292 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8249 (mp) REVERT: A 330 LYS cc_start: 0.8254 (tttt) cc_final: 0.8017 (tttm) REVERT: A 340 MET cc_start: 0.7631 (mtp) cc_final: 0.7417 (mtt) REVERT: A 492 ILE cc_start: 0.8530 (pt) cc_final: 0.8170 (pt) REVERT: A 521 ARG cc_start: 0.5989 (mtt180) cc_final: 0.5585 (mtp85) REVERT: A 628 LYS cc_start: 0.8423 (ttmt) cc_final: 0.7430 (tptt) REVERT: A 943 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.4847 (tpt) REVERT: C 69 PHE cc_start: 0.8634 (t80) cc_final: 0.8410 (t80) REVERT: C 210 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8287 (tttp) outliers start: 76 outliers final: 56 residues processed: 239 average time/residue: 0.1133 time to fit residues: 37.5667 Evaluate side-chains 220 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 160 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 323 TRP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 352 ASN Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 633 PHE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 846 ASP Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 944 LYS Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 210 LYS Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 ASN A 59 ASN A 63 GLN A 106 GLN A 114 HIS A 326 GLN A 329 GLN A 392 ASN A 397 ASN A 524 ASN A 539 ASN A 574 GLN A 744 HIS A 840 GLN A 864 HIS A 888 GLN A1050 GLN C 152 ASN C 347 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.166413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.123751 restraints weight = 11317.161| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.33 r_work: 0.3023 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11288 Z= 0.167 Angle : 0.919 30.435 15310 Z= 0.415 Chirality : 0.048 0.551 1727 Planarity : 0.005 0.045 1919 Dihedral : 10.682 125.451 1688 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.49 % Allowed : 19.35 % Favored : 76.16 % 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 are not related in a simple way. whole: -3.41 (0.21), residues: 1342 helix: -1.54 (0.20), residues: 577 sheet: -1.80 (0.37), residues: 191 loop : -3.16 (0.22), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 723 TYR 0.018 0.002 TYR A 747 PHE 0.023 0.002 PHE A 971 TRP 0.015 0.001 TRP A 323 HIS 0.004 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00387 (11279) covalent geometry : angle 0.90508 (15292) SS BOND : bond 0.00372 ( 3) SS BOND : angle 2.11459 ( 6) hydrogen bonds : bond 0.04320 ( 434) hydrogen bonds : angle 5.26511 ( 1236) Misc. bond : bond 0.00074 ( 2) link_ALPHA1-3 : bond 0.01758 ( 1) link_ALPHA1-3 : angle 4.94612 ( 3) link_BETA1-4 : bond 0.00199 ( 1) link_BETA1-4 : angle 2.78452 ( 3) link_NAG-ASN : bond 0.01195 ( 2) link_NAG-ASN : angle 6.79036 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 183 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 27 HIS cc_start: 0.6676 (OUTLIER) cc_final: 0.6459 (p-80) REVERT: A 181 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7084 (mt-10) REVERT: A 212 GLU cc_start: 0.7245 (tp30) cc_final: 0.6906 (tp30) REVERT: A 330 LYS cc_start: 0.8102 (tttt) cc_final: 0.7885 (tttm) REVERT: A 340 MET cc_start: 0.7977 (mtp) cc_final: 0.7771 (mtt) REVERT: A 367 LYS cc_start: 0.8352 (mttt) cc_final: 0.7889 (mtmt) REVERT: A 628 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7346 (tptt) REVERT: A 941 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5972 (tt) REVERT: A 1055 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.8157 (t80) REVERT: A 1075 PHE cc_start: 0.8488 (t80) cc_final: 0.7535 (m-80) REVERT: C 69 PHE cc_start: 0.8542 (t80) cc_final: 0.8317 (t80) REVERT: C 152 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7909 (t0) REVERT: C 162 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7578 (ttm110) REVERT: C 275 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8262 (pp) outliers start: 54 outliers final: 31 residues processed: 222 average time/residue: 0.1110 time to fit residues: 34.0415 Evaluate side-chains 195 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 326 GLN Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 1043 ILE Chi-restraints excluded: chain A residue 1053 MET Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 88 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN A 777 GLN C 152 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.163652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.122040 restraints weight = 11480.975| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.33 r_work: 0.2989 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 11288 Z= 0.272 Angle : 0.936 30.866 15310 Z= 0.426 Chirality : 0.051 0.560 1727 Planarity : 0.005 0.045 1919 Dihedral : 9.851 129.994 1623 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 5.07 % Allowed : 19.85 % Favored : 75.08 % 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 are not related in a simple way. whole: -2.86 (0.22), residues: 1342 helix: -1.11 (0.21), residues: 583 sheet: -1.42 (0.38), residues: 198 loop : -2.89 (0.24), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 613 TYR 0.021 0.002 TYR C 297 PHE 0.026 0.002 PHE A 971 TRP 0.016 0.002 TRP C 260 HIS 0.005 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00666 (11279) covalent geometry : angle 0.92256 (15292) SS BOND : bond 0.00313 ( 3) SS BOND : angle 1.80222 ( 6) hydrogen bonds : bond 0.04640 ( 434) hydrogen bonds : angle 5.19809 ( 1236) Misc. bond : bond 0.00181 ( 2) link_ALPHA1-3 : bond 0.01722 ( 1) link_ALPHA1-3 : angle 5.05017 ( 3) link_BETA1-4 : bond 0.00068 ( 1) link_BETA1-4 : angle 2.58943 ( 3) link_NAG-ASN : bond 0.01519 ( 2) link_NAG-ASN : angle 6.72364 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.6668 (OUTLIER) cc_final: 0.6411 (p-80) REVERT: A 181 GLU cc_start: 0.7303 (mt-10) cc_final: 0.7035 (mt-10) REVERT: A 212 GLU cc_start: 0.7306 (tp30) cc_final: 0.6991 (tp30) REVERT: A 330 LYS cc_start: 0.8145 (tttt) cc_final: 0.7916 (tttm) REVERT: A 367 LYS cc_start: 0.8433 (mttt) cc_final: 0.7975 (mtmt) REVERT: A 628 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7321 (tptt) REVERT: A 816 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8645 (p0) REVERT: A 843 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7965 (ptm-80) REVERT: A 941 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.6155 (tt) REVERT: C 69 PHE cc_start: 0.8580 (t80) cc_final: 0.8374 (t80) REVERT: C 275 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8315 (pp) outliers start: 61 outliers final: 41 residues processed: 216 average time/residue: 0.1035 time to fit residues: 31.3113 Evaluate side-chains 207 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 714 ARG Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 909 THR Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 84 optimal weight: 0.5980 chunk 97 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 54 ASN A 69 ASN A 828 HIS C 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.170038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.3310 r_free = 0.3310 target = 0.123183 restraints weight = 11329.948| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.33 r_work: 0.3062 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11288 Z= 0.130 Angle : 0.841 31.349 15310 Z= 0.370 Chirality : 0.045 0.452 1727 Planarity : 0.004 0.043 1919 Dihedral : 9.261 126.902 1619 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.82 % Allowed : 21.43 % Favored : 74.75 % 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 are not related in a simple way. whole: -2.13 (0.22), residues: 1342 helix: -0.42 (0.22), residues: 579 sheet: -1.11 (0.38), residues: 199 loop : -2.59 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 613 TYR 0.015 0.001 TYR A 324 PHE 0.020 0.001 PHE A 633 TRP 0.016 0.001 TRP A 323 HIS 0.003 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00296 (11279) covalent geometry : angle 0.83048 (15292) SS BOND : bond 0.00367 ( 3) SS BOND : angle 1.52286 ( 6) hydrogen bonds : bond 0.03773 ( 434) hydrogen bonds : angle 4.81515 ( 1236) Misc. bond : bond 0.00146 ( 2) link_ALPHA1-3 : bond 0.01466 ( 1) link_ALPHA1-3 : angle 4.44340 ( 3) link_BETA1-4 : bond 0.00655 ( 1) link_BETA1-4 : angle 2.66355 ( 3) link_NAG-ASN : bond 0.01095 ( 2) link_NAG-ASN : angle 5.50075 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6968 (mt-10) REVERT: A 212 GLU cc_start: 0.7230 (tp30) cc_final: 0.6934 (tp30) REVERT: A 330 LYS cc_start: 0.8034 (tttt) cc_final: 0.7794 (tttm) REVERT: A 340 MET cc_start: 0.7888 (mtp) cc_final: 0.7628 (mtt) REVERT: A 367 LYS cc_start: 0.8259 (mttt) cc_final: 0.7819 (mtmt) REVERT: A 613 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7808 (mtm-85) REVERT: A 628 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7261 (tptt) REVERT: A 941 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5721 (tt) REVERT: A 1075 PHE cc_start: 0.8385 (t80) cc_final: 0.7491 (m-80) REVERT: C 152 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7820 (t0) REVERT: C 155 LYS cc_start: 0.8085 (pttp) cc_final: 0.7828 (pttt) REVERT: C 161 ARG cc_start: 0.8173 (ttt180) cc_final: 0.7933 (ttp-170) REVERT: C 275 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8217 (pp) outliers start: 46 outliers final: 29 residues processed: 199 average time/residue: 0.1069 time to fit residues: 29.7532 Evaluate side-chains 189 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 128 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 127 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 GLN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.166776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.120204 restraints weight = 11361.026| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.41 r_work: 0.3008 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11288 Z= 0.190 Angle : 0.853 30.882 15310 Z= 0.379 Chirality : 0.047 0.483 1727 Planarity : 0.004 0.043 1919 Dihedral : 8.896 129.021 1604 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 4.73 % Allowed : 20.60 % Favored : 74.67 % 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 are not related in a simple way. whole: -1.96 (0.23), residues: 1342 helix: -0.32 (0.22), residues: 583 sheet: -0.92 (0.39), residues: 199 loop : -2.51 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 613 TYR 0.020 0.002 TYR A 311 PHE 0.022 0.002 PHE A 971 TRP 0.015 0.002 TRP A 323 HIS 0.004 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00463 (11279) covalent geometry : angle 0.84222 (15292) SS BOND : bond 0.00324 ( 3) SS BOND : angle 1.54277 ( 6) hydrogen bonds : bond 0.04035 ( 434) hydrogen bonds : angle 4.81805 ( 1236) Misc. bond : bond 0.00155 ( 2) link_ALPHA1-3 : bond 0.01487 ( 1) link_ALPHA1-3 : angle 4.28350 ( 3) link_BETA1-4 : bond 0.00286 ( 1) link_BETA1-4 : angle 2.42931 ( 3) link_NAG-ASN : bond 0.01271 ( 2) link_NAG-ASN : angle 5.77708 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 172 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7585 (tptp) REVERT: A 181 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7030 (mt-10) REVERT: A 212 GLU cc_start: 0.7199 (tp30) cc_final: 0.6888 (tp30) REVERT: A 330 LYS cc_start: 0.8045 (tttt) cc_final: 0.7787 (tttm) REVERT: A 367 LYS cc_start: 0.8347 (mttt) cc_final: 0.7904 (mtmt) REVERT: A 577 GLU cc_start: 0.6353 (mm-30) cc_final: 0.5704 (pm20) REVERT: A 613 ARG cc_start: 0.8049 (mtm-85) cc_final: 0.7610 (mtm-85) REVERT: A 628 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7322 (tptt) REVERT: A 816 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8570 (p0) REVERT: A 843 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7753 (ptm-80) REVERT: A 941 LEU cc_start: 0.6044 (OUTLIER) cc_final: 0.5778 (tt) REVERT: A 1075 PHE cc_start: 0.8464 (t80) cc_final: 0.7540 (m-80) REVERT: C 275 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8297 (pp) outliers start: 57 outliers final: 42 residues processed: 213 average time/residue: 0.1084 time to fit residues: 32.2181 Evaluate side-chains 214 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 780 MET Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 0.0570 chunk 40 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 overall best weight: 0.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.170027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.123531 restraints weight = 11342.998| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.37 r_work: 0.3058 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11288 Z= 0.132 Angle : 0.823 31.282 15310 Z= 0.361 Chirality : 0.045 0.450 1727 Planarity : 0.004 0.042 1919 Dihedral : 8.561 127.044 1602 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.24 % Allowed : 21.10 % Favored : 74.67 % 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 are not related in a simple way. whole: -1.68 (0.23), residues: 1342 helix: -0.05 (0.22), residues: 578 sheet: -0.75 (0.39), residues: 199 loop : -2.40 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 613 TYR 0.015 0.001 TYR A 311 PHE 0.020 0.001 PHE A 633 TRP 0.017 0.001 TRP A 323 HIS 0.003 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00308 (11279) covalent geometry : angle 0.81335 (15292) SS BOND : bond 0.00350 ( 3) SS BOND : angle 1.42949 ( 6) hydrogen bonds : bond 0.03699 ( 434) hydrogen bonds : angle 4.67167 ( 1236) Misc. bond : bond 0.00138 ( 2) link_ALPHA1-3 : bond 0.01523 ( 1) link_ALPHA1-3 : angle 3.95397 ( 3) link_BETA1-4 : bond 0.00410 ( 1) link_BETA1-4 : angle 2.35765 ( 3) link_NAG-ASN : bond 0.01179 ( 2) link_NAG-ASN : angle 5.52616 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7552 (tptp) REVERT: A 181 GLU cc_start: 0.7312 (mt-10) cc_final: 0.7023 (mt-10) REVERT: A 212 GLU cc_start: 0.7146 (tp30) cc_final: 0.6846 (tp30) REVERT: A 235 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8186 (m) REVERT: A 330 LYS cc_start: 0.7940 (tttt) cc_final: 0.7680 (tttm) REVERT: A 340 MET cc_start: 0.7920 (mtp) cc_final: 0.7705 (mtt) REVERT: A 367 LYS cc_start: 0.8283 (mttt) cc_final: 0.7826 (mtpt) REVERT: A 577 GLU cc_start: 0.6329 (mm-30) cc_final: 0.5683 (pm20) REVERT: A 628 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7296 (tptt) REVERT: A 843 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7582 (ptm-80) REVERT: A 941 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5667 (tt) REVERT: A 1075 PHE cc_start: 0.8449 (t80) cc_final: 0.7544 (m-80) REVERT: C 190 GLN cc_start: 0.6223 (OUTLIER) cc_final: 0.5962 (tt0) REVERT: C 275 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8220 (pp) outliers start: 51 outliers final: 35 residues processed: 217 average time/residue: 0.1095 time to fit residues: 32.7791 Evaluate side-chains 206 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 84 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.166531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.124339 restraints weight = 11310.695| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.32 r_work: 0.3025 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 11288 Z= 0.204 Angle : 0.857 31.148 15310 Z= 0.381 Chirality : 0.047 0.487 1727 Planarity : 0.004 0.043 1919 Dihedral : 8.578 127.563 1602 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 4.90 % Allowed : 20.76 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.23), residues: 1342 helix: -0.11 (0.22), residues: 581 sheet: -0.75 (0.39), residues: 196 loop : -2.36 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 613 TYR 0.019 0.002 TYR A 311 PHE 0.023 0.002 PHE A 971 TRP 0.014 0.002 TRP A 323 HIS 0.004 0.001 HIS C 302 Details of bonding type rmsd covalent geometry : bond 0.00500 (11279) covalent geometry : angle 0.84707 (15292) SS BOND : bond 0.00297 ( 3) SS BOND : angle 1.51006 ( 6) hydrogen bonds : bond 0.04070 ( 434) hydrogen bonds : angle 4.75805 ( 1236) Misc. bond : bond 0.00166 ( 2) link_ALPHA1-3 : bond 0.01330 ( 1) link_ALPHA1-3 : angle 3.98157 ( 3) link_BETA1-4 : bond 0.00310 ( 1) link_BETA1-4 : angle 2.28087 ( 3) link_NAG-ASN : bond 0.01293 ( 2) link_NAG-ASN : angle 5.72892 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 172 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7524 (tptm) REVERT: A 181 GLU cc_start: 0.7335 (mt-10) cc_final: 0.7032 (mt-10) REVERT: A 212 GLU cc_start: 0.7190 (tp30) cc_final: 0.6874 (tp30) REVERT: A 235 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8173 (m) REVERT: A 237 ARG cc_start: 0.7695 (mpt180) cc_final: 0.7477 (mmm160) REVERT: A 330 LYS cc_start: 0.8009 (tttt) cc_final: 0.7750 (tttm) REVERT: A 340 MET cc_start: 0.7951 (mtp) cc_final: 0.7725 (mtt) REVERT: A 367 LYS cc_start: 0.8366 (mttt) cc_final: 0.7922 (mtmt) REVERT: A 430 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8140 (tppt) REVERT: A 577 GLU cc_start: 0.6318 (mm-30) cc_final: 0.5671 (pm20) REVERT: A 628 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7289 (tptt) REVERT: A 816 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8605 (p0) REVERT: A 843 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7659 (ptm-80) REVERT: A 941 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5858 (tt) REVERT: A 1075 PHE cc_start: 0.8488 (t80) cc_final: 0.7581 (m-80) REVERT: C 244 ASP cc_start: 0.8751 (t70) cc_final: 0.8533 (t70) REVERT: C 275 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8310 (pp) outliers start: 59 outliers final: 47 residues processed: 220 average time/residue: 0.1069 time to fit residues: 32.7130 Evaluate side-chains 221 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 58 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 0.0270 chunk 82 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.167898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.125648 restraints weight = 11356.252| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.37 r_work: 0.3034 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11288 Z= 0.166 Angle : 0.842 31.359 15310 Z= 0.372 Chirality : 0.046 0.469 1727 Planarity : 0.004 0.043 1919 Dihedral : 8.476 127.356 1602 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.65 % Allowed : 21.35 % Favored : 74.00 % 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 are not related in a simple way. whole: -1.64 (0.23), residues: 1342 helix: -0.04 (0.22), residues: 585 sheet: -0.74 (0.38), residues: 203 loop : -2.37 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 613 TYR 0.016 0.001 TYR A 311 PHE 0.021 0.002 PHE A 633 TRP 0.016 0.002 TRP A 323 HIS 0.003 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00402 (11279) covalent geometry : angle 0.83184 (15292) SS BOND : bond 0.00350 ( 3) SS BOND : angle 1.45183 ( 6) hydrogen bonds : bond 0.03887 ( 434) hydrogen bonds : angle 4.72202 ( 1236) Misc. bond : bond 0.00160 ( 2) link_ALPHA1-3 : bond 0.01291 ( 1) link_ALPHA1-3 : angle 3.83275 ( 3) link_BETA1-4 : bond 0.00336 ( 1) link_BETA1-4 : angle 2.21504 ( 3) link_NAG-ASN : bond 0.01240 ( 2) link_NAG-ASN : angle 5.65223 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 172 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7530 (tptm) REVERT: A 181 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7065 (mt-10) REVERT: A 212 GLU cc_start: 0.7163 (tp30) cc_final: 0.6850 (tp30) REVERT: A 235 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8189 (m) REVERT: A 237 ARG cc_start: 0.7684 (mpt180) cc_final: 0.7480 (mmm160) REVERT: A 330 LYS cc_start: 0.7967 (tttt) cc_final: 0.7701 (tttm) REVERT: A 340 MET cc_start: 0.7966 (mtp) cc_final: 0.7729 (mtt) REVERT: A 367 LYS cc_start: 0.8346 (mttt) cc_final: 0.7905 (mtmt) REVERT: A 577 GLU cc_start: 0.6336 (mm-30) cc_final: 0.5705 (pm20) REVERT: A 628 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7273 (tptt) REVERT: A 843 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7666 (ptm-80) REVERT: A 941 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5833 (tt) REVERT: A 1075 PHE cc_start: 0.8485 (t80) cc_final: 0.7571 (m-80) REVERT: C 190 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5992 (tt0) REVERT: C 244 ASP cc_start: 0.8707 (t70) cc_final: 0.8447 (t70) REVERT: C 275 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8292 (pp) outliers start: 56 outliers final: 44 residues processed: 219 average time/residue: 0.1093 time to fit residues: 33.2172 Evaluate side-chains 213 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 190 GLN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 129 optimal weight: 0.0970 chunk 48 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 116 optimal weight: 0.4980 chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.169619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.135141 restraints weight = 11218.063| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.16 r_work: 0.3009 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11288 Z= 0.130 Angle : 0.822 31.652 15310 Z= 0.360 Chirality : 0.045 0.445 1727 Planarity : 0.004 0.042 1919 Dihedral : 8.232 125.325 1600 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 4.07 % Allowed : 22.18 % Favored : 73.75 % 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 are not related in a simple way. whole: -1.37 (0.23), residues: 1342 helix: 0.18 (0.22), residues: 578 sheet: -0.29 (0.41), residues: 186 loop : -2.29 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 613 TYR 0.014 0.001 TYR A 311 PHE 0.020 0.001 PHE A 633 TRP 0.017 0.001 TRP A 323 HIS 0.003 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00305 (11279) covalent geometry : angle 0.81321 (15292) SS BOND : bond 0.00360 ( 3) SS BOND : angle 1.39091 ( 6) hydrogen bonds : bond 0.03648 ( 434) hydrogen bonds : angle 4.63112 ( 1236) Misc. bond : bond 0.00137 ( 2) link_ALPHA1-3 : bond 0.01255 ( 1) link_ALPHA1-3 : angle 3.53567 ( 3) link_BETA1-4 : bond 0.00393 ( 1) link_BETA1-4 : angle 2.11047 ( 3) link_NAG-ASN : bond 0.01161 ( 2) link_NAG-ASN : angle 5.44117 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7307 (mt-10) cc_final: 0.6976 (mt-10) REVERT: A 212 GLU cc_start: 0.7111 (tp30) cc_final: 0.6818 (tp30) REVERT: A 330 LYS cc_start: 0.7974 (tttt) cc_final: 0.7722 (tttm) REVERT: A 340 MET cc_start: 0.7885 (mtp) cc_final: 0.7615 (mtt) REVERT: A 367 LYS cc_start: 0.8235 (mttt) cc_final: 0.7783 (mtmt) REVERT: A 577 GLU cc_start: 0.6220 (mm-30) cc_final: 0.5628 (pm20) REVERT: A 613 ARG cc_start: 0.7947 (mtm-85) cc_final: 0.7741 (mtm-85) REVERT: A 628 LYS cc_start: 0.7910 (ttmt) cc_final: 0.7060 (tptm) REVERT: A 639 ASN cc_start: 0.8106 (p0) cc_final: 0.7902 (p0) REVERT: A 721 GLU cc_start: 0.4484 (OUTLIER) cc_final: 0.3819 (mp0) REVERT: A 843 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7561 (ptm-80) REVERT: A 941 LEU cc_start: 0.5845 (OUTLIER) cc_final: 0.5570 (tt) REVERT: A 1055 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.8071 (t80) REVERT: A 1075 PHE cc_start: 0.8412 (t80) cc_final: 0.7523 (m-80) REVERT: C 244 ASP cc_start: 0.8641 (t70) cc_final: 0.8435 (t70) REVERT: C 275 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8273 (pp) outliers start: 49 outliers final: 37 residues processed: 207 average time/residue: 0.1018 time to fit residues: 29.7845 Evaluate side-chains 204 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 721 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 899 GLN Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 63 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 828 HIS C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.168818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.134441 restraints weight = 11315.086| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.19 r_work: 0.2949 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11288 Z= 0.151 Angle : 0.833 31.557 15310 Z= 0.365 Chirality : 0.046 0.453 1727 Planarity : 0.004 0.043 1919 Dihedral : 8.180 125.485 1600 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.90 % Allowed : 22.26 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.23), residues: 1342 helix: 0.23 (0.22), residues: 578 sheet: -0.18 (0.41), residues: 186 loop : -2.26 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 613 TYR 0.019 0.001 TYR A 311 PHE 0.023 0.001 PHE A 633 TRP 0.016 0.001 TRP A 323 HIS 0.003 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00361 (11279) covalent geometry : angle 0.82447 (15292) SS BOND : bond 0.00340 ( 3) SS BOND : angle 1.38292 ( 6) hydrogen bonds : bond 0.03747 ( 434) hydrogen bonds : angle 4.64188 ( 1236) Misc. bond : bond 0.00140 ( 2) link_ALPHA1-3 : bond 0.01177 ( 1) link_ALPHA1-3 : angle 3.42218 ( 3) link_BETA1-4 : bond 0.00320 ( 1) link_BETA1-4 : angle 1.99906 ( 3) link_NAG-ASN : bond 0.01187 ( 2) link_NAG-ASN : angle 5.43704 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 181 GLU cc_start: 0.7349 (mt-10) cc_final: 0.7028 (mt-10) REVERT: A 212 GLU cc_start: 0.7128 (tp30) cc_final: 0.6825 (tp30) REVERT: A 252 LYS cc_start: 0.7485 (mmmt) cc_final: 0.7043 (mmtt) REVERT: A 330 LYS cc_start: 0.8016 (tttt) cc_final: 0.7754 (tttm) REVERT: A 367 LYS cc_start: 0.8258 (mttt) cc_final: 0.7807 (mtmt) REVERT: A 430 LYS cc_start: 0.8418 (ttpt) cc_final: 0.8044 (tppp) REVERT: A 577 GLU cc_start: 0.6221 (mm-30) cc_final: 0.5643 (pm20) REVERT: A 628 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7201 (tptm) REVERT: A 639 ASN cc_start: 0.8106 (p0) cc_final: 0.7896 (p0) REVERT: A 721 GLU cc_start: 0.4568 (OUTLIER) cc_final: 0.3936 (mp0) REVERT: A 816 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8554 (p0) REVERT: A 843 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7616 (ptm-80) REVERT: A 941 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5728 (tt) REVERT: A 943 MET cc_start: 0.8178 (tpt) cc_final: 0.4976 (tpt) REVERT: A 1075 PHE cc_start: 0.8449 (t80) cc_final: 0.7551 (m-80) REVERT: C 244 ASP cc_start: 0.8691 (t70) cc_final: 0.8479 (t70) REVERT: C 275 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8285 (pp) REVERT: C 294 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7167 (t0) outliers start: 47 outliers final: 36 residues processed: 199 average time/residue: 0.1054 time to fit residues: 29.3379 Evaluate side-chains 201 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 721 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 816 ASP Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1060 MET Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 102 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 62 optimal weight: 0.0670 chunk 127 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 828 HIS C 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.165925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.126764 restraints weight = 11420.879| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.28 r_work: 0.3037 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11288 Z= 0.236 Angle : 0.881 31.325 15310 Z= 0.393 Chirality : 0.049 0.498 1727 Planarity : 0.004 0.043 1919 Dihedral : 8.354 129.355 1600 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.82 % Allowed : 22.51 % Favored : 73.67 % 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 are not related in a simple way. whole: -1.53 (0.23), residues: 1342 helix: -0.03 (0.22), residues: 581 sheet: -0.48 (0.38), residues: 200 loop : -2.29 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 613 TYR 0.024 0.002 TYR A 311 PHE 0.026 0.002 PHE A 633 TRP 0.016 0.002 TRP C 260 HIS 0.004 0.001 HIS C 131 Details of bonding type rmsd covalent geometry : bond 0.00585 (11279) covalent geometry : angle 0.87151 (15292) SS BOND : bond 0.00318 ( 3) SS BOND : angle 1.53443 ( 6) hydrogen bonds : bond 0.04212 ( 434) hydrogen bonds : angle 4.80795 ( 1236) Misc. bond : bond 0.00183 ( 2) link_ALPHA1-3 : bond 0.01094 ( 1) link_ALPHA1-3 : angle 3.61417 ( 3) link_BETA1-4 : bond 0.00078 ( 1) link_BETA1-4 : angle 2.11926 ( 3) link_NAG-ASN : bond 0.01358 ( 2) link_NAG-ASN : angle 5.80256 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2919.67 seconds wall clock time: 50 minutes 43.75 seconds (3043.75 seconds total)