Starting phenix.real_space_refine on Tue Jul 29 08:53:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bsq_30164/07_2025/7bsq_30164_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bsq_30164/07_2025/7bsq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7bsq_30164/07_2025/7bsq_30164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bsq_30164/07_2025/7bsq_30164.map" model { file = "/net/cci-nas-00/data/ceres_data/7bsq_30164/07_2025/7bsq_30164_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bsq_30164/07_2025/7bsq_30164_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.33, per 1000 atoms: 0.66 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: 3.77 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.31 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: 4.24 Time building geometry restraints manager: 3.68 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: 1.000 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 30.320 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.280 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.025 0.004 TRP C 260 HIS 0.006 0.002 HIS C 131 PHE 0.034 0.003 PHE A 971 TYR 0.032 0.003 TYR C 297 ARG 0.004 0.001 ARG A 544 Details of bonding type rmsd link_NAG-ASN : bond 0.01230 ( 2) link_NAG-ASN : angle 5.91195 ( 6) link_BETA1-4 : bond 0.00097 ( 1) link_BETA1-4 : angle 1.77252 ( 3) link_ALPHA1-3 : bond 0.00329 ( 1) link_ALPHA1-3 : angle 4.25085 ( 3) hydrogen bonds : bond 0.13349 ( 434) hydrogen bonds : angle 7.05072 ( 1236) SS BOND : bond 0.00145 ( 3) SS BOND : angle 1.66555 ( 6) covalent geometry : bond 0.01398 (11279) covalent geometry : angle 1.30082 (15292) Misc. bond : bond 0.57952 ( 2) *********************** 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 : 1.128 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: 0.8288 (tttp) outliers start: 76 outliers final: 56 residues processed: 239 average time/residue: 0.2676 time to fit residues: 87.6094 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 : 1.180 ------------------------------------------------------------------------------- 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 113 optimal weight: 0.6980 chunk 101 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 59 ASN A 63 GLN A 69 ASN A 106 GLN A 114 HIS A 326 GLN A 329 GLN A 392 ASN A 397 ASN A 524 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.169211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.124140 restraints weight = 11184.993| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.38 r_work: 0.3028 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11288 Z= 0.154 Angle : 0.919 29.259 15310 Z= 0.414 Chirality : 0.048 0.559 1727 Planarity : 0.005 0.045 1919 Dihedral : 10.602 123.319 1688 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.99 % Allowed : 18.94 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.21), residues: 1342 helix: -1.43 (0.20), residues: 577 sheet: -1.78 (0.37), residues: 191 loop : -3.10 (0.22), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.004 0.001 HIS A 470 PHE 0.024 0.002 PHE A 633 TYR 0.018 0.002 TYR A 747 ARG 0.004 0.001 ARG A 594 Details of bonding type rmsd link_NAG-ASN : bond 0.01348 ( 2) link_NAG-ASN : angle 6.84492 ( 6) link_BETA1-4 : bond 0.00402 ( 1) link_BETA1-4 : angle 2.76508 ( 3) link_ALPHA1-3 : bond 0.01989 ( 1) link_ALPHA1-3 : angle 4.89035 ( 3) hydrogen bonds : bond 0.04206 ( 434) hydrogen bonds : angle 5.23436 ( 1236) SS BOND : bond 0.00412 ( 3) SS BOND : angle 2.09819 ( 6) covalent geometry : bond 0.00349 (11279) covalent geometry : angle 0.90509 (15292) Misc. bond : bond 0.00127 ( 2) *********************** 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 228 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 180 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.6666 (OUTLIER) cc_final: 0.6455 (p-80) REVERT: A 135 ARG cc_start: 0.7524 (ptm-80) cc_final: 0.7204 (ttp80) REVERT: A 212 GLU cc_start: 0.7247 (tp30) cc_final: 0.6920 (tp30) REVERT: A 330 LYS cc_start: 0.8077 (tttt) cc_final: 0.7862 (tttm) REVERT: A 340 MET cc_start: 0.7938 (mtp) cc_final: 0.7727 (mtt) REVERT: A 367 LYS cc_start: 0.8312 (mttt) cc_final: 0.7847 (mtmt) REVERT: A 628 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7276 (tptt) REVERT: A 780 MET cc_start: 0.7401 (mmp) cc_final: 0.6265 (mtp) REVERT: A 941 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5929 (tt) REVERT: A 1055 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.8122 (t80) REVERT: A 1075 PHE cc_start: 0.8465 (t80) cc_final: 0.7548 (m-80) REVERT: C 69 PHE cc_start: 0.8516 (t80) cc_final: 0.8280 (t80) REVERT: C 152 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7908 (t0) REVERT: C 162 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7589 (ttm110) REVERT: C 275 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8260 (pp) outliers start: 48 outliers final: 30 residues processed: 217 average time/residue: 0.2809 time to fit residues: 83.3816 Evaluate side-chains 196 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 1.325 ------------------------------------------------------------------------------- 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 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 83 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 777 GLN A 828 HIS C 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.168369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.125906 restraints weight = 11342.554| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.35 r_work: 0.3039 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11288 Z= 0.151 Angle : 0.860 30.856 15310 Z= 0.382 Chirality : 0.046 0.495 1727 Planarity : 0.004 0.042 1919 Dihedral : 9.355 123.840 1622 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.16 % Allowed : 20.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.22), residues: 1342 helix: -0.74 (0.21), residues: 579 sheet: -1.24 (0.38), residues: 195 loop : -2.73 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 323 HIS 0.004 0.001 HIS C 131 PHE 0.022 0.001 PHE A 633 TYR 0.016 0.001 TYR A 876 ARG 0.005 0.000 ARG A 613 Details of bonding type rmsd link_NAG-ASN : bond 0.01305 ( 2) link_NAG-ASN : angle 6.16415 ( 6) link_BETA1-4 : bond 0.00262 ( 1) link_BETA1-4 : angle 2.48940 ( 3) link_ALPHA1-3 : bond 0.01787 ( 1) link_ALPHA1-3 : angle 4.37658 ( 3) hydrogen bonds : bond 0.03935 ( 434) hydrogen bonds : angle 4.93229 ( 1236) SS BOND : bond 0.00346 ( 3) SS BOND : angle 1.60460 ( 6) covalent geometry : bond 0.00350 (11279) covalent geometry : angle 0.84808 (15292) Misc. bond : bond 0.00180 ( 2) *********************** 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 214 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7459 (ptm-80) cc_final: 0.7197 (ttp80) REVERT: A 181 GLU cc_start: 0.7364 (mt-10) cc_final: 0.7071 (mt-10) REVERT: A 212 GLU cc_start: 0.7202 (tp30) cc_final: 0.6896 (tp30) REVERT: A 330 LYS cc_start: 0.8097 (tttt) cc_final: 0.7881 (tttm) REVERT: A 367 LYS cc_start: 0.8301 (mttt) cc_final: 0.7867 (mtmt) REVERT: A 430 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8010 (tppp) REVERT: A 507 ARG cc_start: 0.7851 (mtp180) cc_final: 0.7568 (ttm170) REVERT: A 628 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7298 (tptt) REVERT: A 941 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5639 (tt) REVERT: A 1075 PHE cc_start: 0.8499 (t80) cc_final: 0.7603 (m-80) REVERT: C 69 PHE cc_start: 0.8502 (t80) cc_final: 0.8296 (t80) REVERT: C 275 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8229 (pp) outliers start: 38 outliers final: 25 residues processed: 204 average time/residue: 0.3481 time to fit residues: 96.1911 Evaluate side-chains 191 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 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 714 ARG Chi-restraints excluded: chain A residue 751 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 C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU 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 338 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 13 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 74 optimal weight: 0.1980 chunk 42 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 213 GLN A 777 GLN C 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.169131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.123055 restraints weight = 11185.458| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.38 r_work: 0.3047 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11288 Z= 0.146 Angle : 0.842 30.989 15310 Z= 0.369 Chirality : 0.046 0.498 1727 Planarity : 0.004 0.041 1919 Dihedral : 8.910 124.224 1608 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.65 % Allowed : 20.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.23), residues: 1342 helix: -0.30 (0.22), residues: 580 sheet: -0.94 (0.39), residues: 195 loop : -2.56 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.003 0.001 HIS C 131 PHE 0.023 0.001 PHE A 633 TYR 0.015 0.001 TYR A 876 ARG 0.011 0.000 ARG A 613 Details of bonding type rmsd link_NAG-ASN : bond 0.01226 ( 2) link_NAG-ASN : angle 5.93750 ( 6) link_BETA1-4 : bond 0.00271 ( 1) link_BETA1-4 : angle 2.36476 ( 3) link_ALPHA1-3 : bond 0.01491 ( 1) link_ALPHA1-3 : angle 4.14160 ( 3) hydrogen bonds : bond 0.03827 ( 434) hydrogen bonds : angle 4.75141 ( 1236) SS BOND : bond 0.00308 ( 3) SS BOND : angle 1.41205 ( 6) covalent geometry : bond 0.00346 (11279) covalent geometry : angle 0.83081 (15292) Misc. bond : bond 0.00146 ( 2) *********************** 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 232 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 176 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7606 (tptp) REVERT: A 135 ARG cc_start: 0.7428 (ptm-80) cc_final: 0.7206 (ttp80) REVERT: A 181 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7002 (mt-10) REVERT: A 212 GLU cc_start: 0.7149 (tp30) cc_final: 0.6847 (tp30) REVERT: A 330 LYS cc_start: 0.8024 (tttt) cc_final: 0.7773 (tttm) REVERT: A 340 MET cc_start: 0.7905 (mtp) cc_final: 0.7649 (mtt) REVERT: A 367 LYS cc_start: 0.8291 (mttt) cc_final: 0.7843 (mtmt) REVERT: A 628 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7267 (tptt) REVERT: A 816 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8538 (p0) REVERT: A 843 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7696 (ptm-80) REVERT: A 941 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.5768 (tt) REVERT: A 1075 PHE cc_start: 0.8425 (t80) cc_final: 0.7552 (m-80) REVERT: C 152 ASN cc_start: 0.8287 (OUTLIER) cc_final: 0.8045 (p0) REVERT: C 275 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8238 (pp) outliers start: 56 outliers final: 37 residues processed: 217 average time/residue: 0.2617 time to fit residues: 78.4200 Evaluate side-chains 208 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 162 LEU Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 292 LEU 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 474 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 843 ARG 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.168484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.122406 restraints weight = 11246.787| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.36 r_work: 0.3035 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11288 Z= 0.164 Angle : 0.840 30.769 15310 Z= 0.371 Chirality : 0.046 0.500 1727 Planarity : 0.004 0.043 1919 Dihedral : 8.701 124.916 1604 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 4.82 % Allowed : 19.85 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.23), residues: 1342 helix: -0.13 (0.22), residues: 581 sheet: -0.77 (0.39), residues: 195 loop : -2.48 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 323 HIS 0.003 0.001 HIS C 131 PHE 0.023 0.001 PHE A 633 TYR 0.019 0.001 TYR A 311 ARG 0.014 0.000 ARG A 613 Details of bonding type rmsd link_NAG-ASN : bond 0.01279 ( 2) link_NAG-ASN : angle 5.90384 ( 6) link_BETA1-4 : bond 0.00335 ( 1) link_BETA1-4 : angle 2.35086 ( 3) link_ALPHA1-3 : bond 0.01407 ( 1) link_ALPHA1-3 : angle 4.00435 ( 3) hydrogen bonds : bond 0.03891 ( 434) hydrogen bonds : angle 4.72767 ( 1236) SS BOND : bond 0.00313 ( 3) SS BOND : angle 1.43518 ( 6) covalent geometry : bond 0.00395 (11279) covalent geometry : angle 0.82924 (15292) Misc. bond : bond 0.00149 ( 2) *********************** 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 232 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 174 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7585 (tptp) REVERT: A 135 ARG cc_start: 0.7431 (ptm-80) cc_final: 0.7227 (ttp80) REVERT: A 181 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7037 (mt-10) REVERT: A 212 GLU cc_start: 0.7139 (tp30) cc_final: 0.6826 (tp30) REVERT: A 330 LYS cc_start: 0.8020 (tttt) cc_final: 0.7762 (tttm) REVERT: A 340 MET cc_start: 0.7977 (mtp) cc_final: 0.7772 (mtt) REVERT: A 367 LYS cc_start: 0.8293 (mttt) cc_final: 0.7860 (mtmt) REVERT: A 420 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6940 (tm-30) REVERT: A 577 GLU cc_start: 0.6332 (mm-30) cc_final: 0.5690 (pm20) REVERT: A 628 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7284 (tptt) REVERT: A 816 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8540 (p0) REVERT: A 843 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7660 (ptm-80) REVERT: A 941 LEU cc_start: 0.5966 (OUTLIER) cc_final: 0.5730 (tt) REVERT: A 1075 PHE cc_start: 0.8456 (t80) cc_final: 0.7580 (m-80) REVERT: C 161 ARG cc_start: 0.8262 (ttt180) cc_final: 0.8007 (ttp-170) REVERT: C 275 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8232 (pp) outliers start: 58 outliers final: 38 residues processed: 218 average time/residue: 0.3111 time to fit residues: 93.8860 Evaluate side-chains 213 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 292 LEU 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 420 GLU Chi-restraints excluded: chain A residue 472 VAL 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 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 821 VAL Chi-restraints excluded: chain A residue 843 ARG 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 124 LEU Chi-restraints excluded: chain C residue 200 LYS 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 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 63 optimal weight: 5.9990 chunk 133 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.168384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.126517 restraints weight = 11340.377| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.34 r_work: 0.3049 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11288 Z= 0.152 Angle : 0.836 30.525 15310 Z= 0.365 Chirality : 0.046 0.493 1727 Planarity : 0.004 0.043 1919 Dihedral : 8.598 125.401 1604 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 5.07 % Allowed : 20.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.23), residues: 1342 helix: 0.01 (0.22), residues: 579 sheet: -0.83 (0.38), residues: 206 loop : -2.40 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.003 0.001 HIS C 302 PHE 0.022 0.001 PHE A 633 TYR 0.016 0.001 TYR A 311 ARG 0.008 0.000 ARG A 613 Details of bonding type rmsd link_NAG-ASN : bond 0.01204 ( 2) link_NAG-ASN : angle 5.75438 ( 6) link_BETA1-4 : bond 0.00382 ( 1) link_BETA1-4 : angle 2.22923 ( 3) link_ALPHA1-3 : bond 0.01388 ( 1) link_ALPHA1-3 : angle 3.81647 ( 3) hydrogen bonds : bond 0.03822 ( 434) hydrogen bonds : angle 4.66781 ( 1236) SS BOND : bond 0.00321 ( 3) SS BOND : angle 1.38506 ( 6) covalent geometry : bond 0.00363 (11279) covalent geometry : angle 0.82559 (15292) Misc. bond : bond 0.00145 ( 2) *********************** 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 238 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 177 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7594 (tptp) REVERT: A 212 GLU cc_start: 0.7120 (tp30) cc_final: 0.6806 (tp30) REVERT: A 330 LYS cc_start: 0.7977 (tttt) cc_final: 0.7711 (tttm) REVERT: A 340 MET cc_start: 0.7979 (mtp) cc_final: 0.7764 (mtt) REVERT: A 367 LYS cc_start: 0.8290 (mttt) cc_final: 0.7854 (mtmt) REVERT: A 430 LYS cc_start: 0.8451 (ttpt) cc_final: 0.8005 (tppp) REVERT: A 577 GLU cc_start: 0.6356 (mm-30) cc_final: 0.5696 (pm20) REVERT: A 628 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7277 (tptt) REVERT: A 816 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8570 (p0) REVERT: A 843 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7658 (ptm-80) REVERT: A 941 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5656 (tt) REVERT: A 1075 PHE cc_start: 0.8424 (t80) cc_final: 0.7563 (m-80) REVERT: C 161 ARG cc_start: 0.8256 (ttt180) cc_final: 0.8022 (ttp-170) REVERT: C 190 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.5986 (tt0) REVERT: C 275 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8231 (pp) REVERT: C 294 ASN cc_start: 0.7783 (OUTLIER) cc_final: 0.7202 (t0) outliers start: 61 outliers final: 38 residues processed: 227 average time/residue: 0.3443 time to fit residues: 108.7605 Evaluate side-chains 212 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 1.856 ------------------------------------------------------------------------------- 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 292 LEU 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 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 690 LEU Chi-restraints excluded: chain A residue 696 GLU 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 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 124 LEU 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 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 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 118 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.164764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.120904 restraints weight = 11544.797| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.42 r_work: 0.2961 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 11288 Z= 0.278 Angle : 0.905 30.781 15310 Z= 0.407 Chirality : 0.051 0.556 1727 Planarity : 0.005 0.044 1919 Dihedral : 8.782 130.079 1602 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.65 % Allowed : 20.85 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.22), residues: 1342 helix: -0.31 (0.21), residues: 587 sheet: -0.85 (0.37), residues: 203 loop : -2.49 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 260 HIS 0.005 0.001 HIS C 131 PHE 0.025 0.002 PHE A 971 TYR 0.021 0.002 TYR C 297 ARG 0.008 0.001 ARG A 613 Details of bonding type rmsd link_NAG-ASN : bond 0.01480 ( 2) link_NAG-ASN : angle 6.26643 ( 6) link_BETA1-4 : bond 0.00010 ( 1) link_BETA1-4 : angle 2.16843 ( 3) link_ALPHA1-3 : bond 0.01347 ( 1) link_ALPHA1-3 : angle 4.12497 ( 3) hydrogen bonds : bond 0.04508 ( 434) hydrogen bonds : angle 4.90982 ( 1236) SS BOND : bond 0.00291 ( 3) SS BOND : angle 1.62539 ( 6) covalent geometry : bond 0.00685 (11279) covalent geometry : angle 0.89444 (15292) Misc. bond : bond 0.00195 ( 2) *********************** 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 223 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 3.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7699 (tptp) REVERT: A 212 GLU cc_start: 0.7233 (tp30) cc_final: 0.6903 (tp30) REVERT: A 237 ARG cc_start: 0.7741 (mpt180) cc_final: 0.7521 (mmm160) REVERT: A 330 LYS cc_start: 0.8026 (tttt) cc_final: 0.7768 (tttm) REVERT: A 367 LYS cc_start: 0.8448 (mttt) cc_final: 0.7994 (mtpt) REVERT: A 420 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: A 468 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6873 (mp) REVERT: A 507 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7562 (ttm170) REVERT: A 577 GLU cc_start: 0.6377 (mm-30) cc_final: 0.5707 (pm20) REVERT: A 628 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7225 (tptt) REVERT: A 843 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7889 (ptm-80) REVERT: A 941 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6189 (tt) REVERT: A 1075 PHE cc_start: 0.8571 (t80) cc_final: 0.7663 (m-80) REVERT: C 161 ARG cc_start: 0.8367 (ttt180) cc_final: 0.8095 (ttp-170) REVERT: C 275 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8340 (pp) REVERT: C 294 ASN cc_start: 0.7952 (OUTLIER) cc_final: 0.7232 (t0) outliers start: 56 outliers final: 36 residues processed: 215 average time/residue: 0.3616 time to fit residues: 110.3770 Evaluate side-chains 206 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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 384 GLU Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 472 VAL 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 690 LEU Chi-restraints excluded: chain A residue 696 GLU 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 843 ARG 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 124 LEU Chi-restraints excluded: chain C residue 191 ASP 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 102 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.169418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.131090 restraints weight = 11240.922| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.17 r_work: 0.3030 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11288 Z= 0.138 Angle : 0.831 30.274 15310 Z= 0.364 Chirality : 0.046 0.482 1727 Planarity : 0.004 0.043 1919 Dihedral : 8.493 127.949 1602 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.41 % Allowed : 22.09 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.23), residues: 1342 helix: 0.03 (0.22), residues: 586 sheet: -0.77 (0.38), residues: 203 loop : -2.31 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.003 0.001 HIS C 131 PHE 0.023 0.001 PHE A 633 TYR 0.014 0.001 TYR A 311 ARG 0.007 0.000 ARG A 613 Details of bonding type rmsd link_NAG-ASN : bond 0.01175 ( 2) link_NAG-ASN : angle 5.66901 ( 6) link_BETA1-4 : bond 0.00359 ( 1) link_BETA1-4 : angle 2.13975 ( 3) link_ALPHA1-3 : bond 0.01321 ( 1) link_ALPHA1-3 : angle 3.68720 ( 3) hydrogen bonds : bond 0.03724 ( 434) hydrogen bonds : angle 4.69885 ( 1236) SS BOND : bond 0.00372 ( 3) SS BOND : angle 1.35502 ( 6) covalent geometry : bond 0.00325 (11279) covalent geometry : angle 0.82090 (15292) Misc. bond : bond 0.00149 ( 2) *********************** 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 208 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7631 (tptm) REVERT: A 212 GLU cc_start: 0.7240 (tp30) cc_final: 0.6953 (tp30) REVERT: A 330 LYS cc_start: 0.7967 (tttt) cc_final: 0.7717 (tttm) REVERT: A 340 MET cc_start: 0.7965 (mtp) cc_final: 0.7754 (mtt) REVERT: A 367 LYS cc_start: 0.8287 (mttt) cc_final: 0.7815 (mtmt) REVERT: A 468 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6722 (mp) REVERT: A 577 GLU cc_start: 0.6267 (mm-30) cc_final: 0.5630 (pm20) REVERT: A 628 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7067 (tptm) REVERT: A 721 GLU cc_start: 0.4557 (OUTLIER) cc_final: 0.3864 (mp0) REVERT: A 843 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7632 (ptm-80) REVERT: A 941 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5886 (tt) REVERT: A 1075 PHE cc_start: 0.8513 (t80) cc_final: 0.7560 (m-80) REVERT: C 161 ARG cc_start: 0.8318 (ttt180) cc_final: 0.8078 (ttp-170) REVERT: C 275 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8293 (pp) REVERT: C 294 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7286 (t0) outliers start: 41 outliers final: 28 residues processed: 202 average time/residue: 0.2960 time to fit residues: 83.1744 Evaluate side-chains 193 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 337 VAL Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 431 TYR Chi-restraints excluded: chain A residue 468 LEU 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 690 LEU 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 843 ARG 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 191 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU 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 83 optimal weight: 0.0970 chunk 81 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 44 optimal weight: 0.0170 chunk 6 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 HIS A 862 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.172672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.138543 restraints weight = 11301.499| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.14 r_work: 0.3059 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11288 Z= 0.112 Angle : 0.819 30.879 15310 Z= 0.352 Chirality : 0.044 0.433 1727 Planarity : 0.004 0.043 1919 Dihedral : 8.038 121.599 1600 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.74 % Allowed : 23.17 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.23), residues: 1342 helix: 0.35 (0.22), residues: 582 sheet: -0.24 (0.40), residues: 193 loop : -2.23 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 323 HIS 0.003 0.001 HIS A 576 PHE 0.022 0.001 PHE A 633 TYR 0.011 0.001 TYR A 876 ARG 0.008 0.000 ARG A 613 Details of bonding type rmsd link_NAG-ASN : bond 0.01063 ( 2) link_NAG-ASN : angle 5.19416 ( 6) link_BETA1-4 : bond 0.00459 ( 1) link_BETA1-4 : angle 1.83096 ( 3) link_ALPHA1-3 : bond 0.01066 ( 1) link_ALPHA1-3 : angle 3.00323 ( 3) hydrogen bonds : bond 0.03428 ( 434) hydrogen bonds : angle 4.53761 ( 1236) SS BOND : bond 0.00354 ( 3) SS BOND : angle 1.24925 ( 6) covalent geometry : bond 0.00255 (11279) covalent geometry : angle 0.81079 (15292) Misc. bond : bond 0.00121 ( 2) *********************** 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 205 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 212 GLU cc_start: 0.7031 (tp30) cc_final: 0.6751 (tp30) REVERT: A 252 LYS cc_start: 0.7408 (mmmt) cc_final: 0.7011 (mmtt) REVERT: A 330 LYS cc_start: 0.7920 (tttt) cc_final: 0.7665 (tttm) REVERT: A 367 LYS cc_start: 0.8111 (mttt) cc_final: 0.7651 (mtmt) REVERT: A 468 LEU cc_start: 0.6923 (OUTLIER) cc_final: 0.6715 (mp) REVERT: A 577 GLU cc_start: 0.6186 (mm-30) cc_final: 0.5603 (pm20) REVERT: A 628 LYS cc_start: 0.7777 (ttmt) cc_final: 0.6988 (tptm) REVERT: A 721 GLU cc_start: 0.4514 (OUTLIER) cc_final: 0.3870 (mp0) REVERT: A 780 MET cc_start: 0.7227 (mmp) cc_final: 0.6182 (mtt) REVERT: A 843 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7453 (ptm-80) REVERT: A 941 LEU cc_start: 0.5855 (OUTLIER) cc_final: 0.5571 (tt) REVERT: A 1055 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7989 (t80) REVERT: A 1075 PHE cc_start: 0.8340 (t80) cc_final: 0.7487 (m-80) REVERT: C 155 LYS cc_start: 0.7952 (pttp) cc_final: 0.7704 (pttt) REVERT: C 161 ARG cc_start: 0.8159 (ttt180) cc_final: 0.7942 (ttp-170) REVERT: C 275 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8215 (pp) REVERT: C 294 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7282 (t0) outliers start: 33 outliers final: 22 residues processed: 199 average time/residue: 0.2531 time to fit residues: 70.0673 Evaluate side-chains 192 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 472 VAL 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 690 LEU 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 843 ARG 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 230 THR 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 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 76 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 828 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.165963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.127538 restraints weight = 11278.521| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.39 r_work: 0.2900 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11288 Z= 0.253 Angle : 0.893 30.864 15310 Z= 0.400 Chirality : 0.050 0.527 1727 Planarity : 0.005 0.044 1919 Dihedral : 8.357 129.508 1600 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.99 % Allowed : 22.59 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.23), residues: 1342 helix: 0.01 (0.22), residues: 588 sheet: -0.27 (0.39), residues: 193 loop : -2.28 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 260 HIS 0.004 0.001 HIS C 302 PHE 0.027 0.002 PHE A 633 TYR 0.021 0.002 TYR A 324 ARG 0.012 0.001 ARG A 613 Details of bonding type rmsd link_NAG-ASN : bond 0.01430 ( 2) link_NAG-ASN : angle 5.95743 ( 6) link_BETA1-4 : bond 0.00072 ( 1) link_BETA1-4 : angle 1.98567 ( 3) link_ALPHA1-3 : bond 0.00987 ( 1) link_ALPHA1-3 : angle 3.44299 ( 3) hydrogen bonds : bond 0.04350 ( 434) hydrogen bonds : angle 4.82165 ( 1236) SS BOND : bond 0.00307 ( 3) SS BOND : angle 1.54702 ( 6) covalent geometry : bond 0.00620 (11279) covalent geometry : angle 0.88374 (15292) Misc. bond : bond 0.00188 ( 2) ********************** 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 199 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.7171 (tp30) cc_final: 0.6870 (tp30) REVERT: A 252 LYS cc_start: 0.7365 (mmmt) cc_final: 0.6933 (mmtt) REVERT: A 330 LYS cc_start: 0.8016 (tttt) cc_final: 0.7751 (tttm) REVERT: A 367 LYS cc_start: 0.8337 (mttt) cc_final: 0.7869 (mtpt) REVERT: A 468 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6630 (mp) REVERT: A 507 ARG cc_start: 0.7711 (mtp180) cc_final: 0.7418 (ttm170) REVERT: A 577 GLU cc_start: 0.6222 (mm-30) cc_final: 0.5605 (pm20) REVERT: A 613 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7695 (mtm-85) REVERT: A 628 LYS cc_start: 0.7744 (ttmt) cc_final: 0.6960 (tptt) REVERT: A 721 GLU cc_start: 0.4623 (OUTLIER) cc_final: 0.4009 (mp0) REVERT: A 843 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7719 (ptm-80) REVERT: A 941 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5936 (tt) REVERT: A 943 MET cc_start: 0.8183 (tpt) cc_final: 0.5011 (tpt) REVERT: A 1075 PHE cc_start: 0.8496 (t80) cc_final: 0.7565 (m-80) REVERT: C 161 ARG cc_start: 0.8272 (ttt180) cc_final: 0.8011 (ttp-170) REVERT: C 275 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8344 (pp) REVERT: C 294 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7193 (t0) outliers start: 36 outliers final: 27 residues processed: 194 average time/residue: 0.2862 time to fit residues: 76.4628 Evaluate side-chains 195 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG 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 468 LEU Chi-restraints excluded: chain A residue 472 VAL 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 690 LEU 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 843 ARG 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 124 LEU Chi-restraints excluded: chain C residue 230 THR 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 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 60 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.170710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.133696 restraints weight = 11244.584| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.17 r_work: 0.2994 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11288 Z= 0.125 Angle : 0.832 31.029 15310 Z= 0.361 Chirality : 0.045 0.451 1727 Planarity : 0.004 0.046 1919 Dihedral : 8.122 126.153 1600 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.82 % Allowed : 23.09 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.23), residues: 1342 helix: 0.29 (0.22), residues: 583 sheet: -0.24 (0.40), residues: 191 loop : -2.17 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 323 HIS 0.003 0.001 HIS C 131 PHE 0.024 0.001 PHE A 633 TYR 0.016 0.001 TYR A 311 ARG 0.011 0.000 ARG A 613 Details of bonding type rmsd link_NAG-ASN : bond 0.01116 ( 2) link_NAG-ASN : angle 5.37264 ( 6) link_BETA1-4 : bond 0.00449 ( 1) link_BETA1-4 : angle 1.85054 ( 3) link_ALPHA1-3 : bond 0.01149 ( 1) link_ALPHA1-3 : angle 3.09026 ( 3) hydrogen bonds : bond 0.03601 ( 434) hydrogen bonds : angle 4.61924 ( 1236) SS BOND : bond 0.00365 ( 3) SS BOND : angle 1.25036 ( 6) covalent geometry : bond 0.00292 (11279) covalent geometry : angle 0.82388 (15292) Misc. bond : bond 0.00127 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6833.93 seconds wall clock time: 122 minutes 55.08 seconds (7375.08 seconds total)