Starting phenix.real_space_refine on Sun Dec 29 19:03:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bsq_30164/12_2024/7bsq_30164_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bsq_30164/12_2024/7bsq_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_30164/12_2024/7bsq_30164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bsq_30164/12_2024/7bsq_30164.map" model { file = "/net/cci-nas-00/data/ceres_data/7bsq_30164/12_2024/7bsq_30164_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bsq_30164/12_2024/7bsq_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.98, per 1000 atoms: 0.63 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: 3.07 Conformation dependent library (CDL) restraints added in 1.4 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: 1.43 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: 4.01 Time building geometry restraints manager: 3.49 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.630 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.360 ------------------------------------------------------------------------------- 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 : 0.014 0.112 11279 Z= 0.890 Angle : 1.301 69.486 15292 Z= 0.596 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 *********************** 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 : 1.275 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: 0.2914 time to fit residues: 95.0465 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 : 1.266 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 11279 Z= 0.222 Angle : 0.905 29.259 15292 Z= 0.411 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 *********************** 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 : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.6733 (OUTLIER) cc_final: 0.6527 (p-80) REVERT: A 135 ARG cc_start: 0.7332 (ptm-80) cc_final: 0.7056 (ttp80) REVERT: A 212 GLU cc_start: 0.6926 (tp30) cc_final: 0.6604 (tp30) REVERT: A 330 LYS cc_start: 0.8030 (tttt) cc_final: 0.7811 (tttm) REVERT: A 367 LYS cc_start: 0.7989 (mttt) cc_final: 0.7594 (mtmt) REVERT: A 628 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7203 (tptt) REVERT: A 780 MET cc_start: 0.7343 (mmp) cc_final: 0.6202 (mtp) REVERT: A 1055 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7738 (t80) REVERT: A 1075 PHE cc_start: 0.7936 (t80) cc_final: 0.7167 (m-80) REVERT: C 69 PHE cc_start: 0.8449 (t80) cc_final: 0.8233 (t80) REVERT: C 162 ARG cc_start: 0.7748 (mtp85) cc_final: 0.7268 (ttm110) REVERT: C 275 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8135 (pp) outliers start: 48 outliers final: 30 residues processed: 217 average time/residue: 0.2824 time to fit residues: 83.8490 Evaluate side-chains 194 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 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 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 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 777 GLN A 828 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11279 Z= 0.193 Angle : 0.833 31.390 15292 Z= 0.371 Chirality : 0.045 0.479 1727 Planarity : 0.004 0.041 1919 Dihedral : 9.169 122.669 1620 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.07 % Allowed : 20.60 % Favored : 76.33 % 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: -2.38 (0.22), residues: 1342 helix: -0.65 (0.21), residues: 580 sheet: -1.21 (0.38), residues: 195 loop : -2.70 (0.24), residues: 567 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 0.022 0.001 PHE A 633 TYR 0.015 0.001 TYR A 876 ARG 0.011 0.000 ARG A 613 *********************** 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: 37 poor density : 177 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7225 (ptm-80) cc_final: 0.7016 (ttp80) REVERT: A 181 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6932 (mt-10) REVERT: A 212 GLU cc_start: 0.6843 (tp30) cc_final: 0.6545 (tp30) REVERT: A 252 LYS cc_start: 0.7133 (mmmt) cc_final: 0.6890 (mmtt) REVERT: A 256 LYS cc_start: 0.8211 (pttm) cc_final: 0.7965 (pttp) REVERT: A 330 LYS cc_start: 0.8024 (tttt) cc_final: 0.7803 (tttm) REVERT: A 367 LYS cc_start: 0.7938 (mttt) cc_final: 0.7569 (mtmt) REVERT: A 507 ARG cc_start: 0.7778 (mtp180) cc_final: 0.7508 (ttm170) REVERT: A 628 LYS cc_start: 0.8106 (ttmt) cc_final: 0.7213 (tptt) REVERT: A 941 LEU cc_start: 0.5388 (OUTLIER) cc_final: 0.5160 (tt) REVERT: A 1075 PHE cc_start: 0.7938 (t80) cc_final: 0.7163 (m-80) REVERT: C 162 ARG cc_start: 0.7733 (mtp85) cc_final: 0.7511 (ttm110) REVERT: C 275 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8121 (pp) outliers start: 37 outliers final: 26 residues processed: 203 average time/residue: 0.2872 time to fit residues: 79.5548 Evaluate side-chains 192 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 151 LEU 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 120 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 777 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11279 Z= 0.327 Angle : 0.864 30.871 15292 Z= 0.386 Chirality : 0.048 0.532 1727 Planarity : 0.004 0.043 1919 Dihedral : 8.992 126.658 1606 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.57 % Allowed : 20.76 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.13 (0.22), residues: 1342 helix: -0.45 (0.21), residues: 576 sheet: -1.01 (0.39), residues: 195 loop : -2.57 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 260 HIS 0.004 0.001 HIS C 131 PHE 0.024 0.002 PHE A 633 TYR 0.019 0.002 TYR A 324 ARG 0.010 0.000 ARG A 613 *********************** 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 229 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 174 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7417 (tptp) REVERT: A 181 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6880 (mt-10) REVERT: A 212 GLU cc_start: 0.6948 (tp30) cc_final: 0.6647 (tp30) REVERT: A 330 LYS cc_start: 0.8057 (tttt) cc_final: 0.7792 (tttm) REVERT: A 367 LYS cc_start: 0.8036 (mttt) cc_final: 0.7655 (mtmt) REVERT: A 628 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7226 (tptt) REVERT: A 816 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8528 (p0) REVERT: A 843 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7549 (ptm-80) REVERT: A 1075 PHE cc_start: 0.7963 (t80) cc_final: 0.7236 (m-80) REVERT: C 162 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7228 (ttm110) REVERT: C 275 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8145 (pp) outliers start: 55 outliers final: 37 residues processed: 212 average time/residue: 0.2861 time to fit residues: 84.0233 Evaluate side-chains 208 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 222 VAL 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 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 714 ARG 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 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 151 LEU Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 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 73 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 43 optimal weight: 30.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11279 Z= 0.234 Angle : 0.827 30.870 15292 Z= 0.366 Chirality : 0.046 0.494 1727 Planarity : 0.004 0.045 1919 Dihedral : 8.818 127.142 1606 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.49 % Allowed : 20.27 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.23), residues: 1342 helix: -0.13 (0.22), residues: 578 sheet: -0.82 (0.39), residues: 196 loop : -2.45 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 323 HIS 0.003 0.001 HIS C 131 PHE 0.022 0.001 PHE A 633 TYR 0.018 0.001 TYR A 311 ARG 0.015 0.000 ARG A 613 *********************** 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 227 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 173 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.7890 (ttmt) cc_final: 0.7359 (tptp) REVERT: A 181 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6947 (mt-10) REVERT: A 212 GLU cc_start: 0.6846 (tp30) cc_final: 0.6530 (tp30) REVERT: A 330 LYS cc_start: 0.7983 (tttt) cc_final: 0.7716 (tttm) REVERT: A 367 LYS cc_start: 0.7958 (mttt) cc_final: 0.7598 (mtmt) REVERT: A 577 GLU cc_start: 0.6294 (mm-30) cc_final: 0.5681 (pm20) REVERT: A 628 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7184 (tptt) REVERT: A 816 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8505 (p0) REVERT: A 1075 PHE cc_start: 0.7874 (t80) cc_final: 0.7171 (m-80) REVERT: C 161 ARG cc_start: 0.8026 (ttt180) cc_final: 0.7790 (ttp-170) REVERT: C 275 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8118 (pp) outliers start: 54 outliers final: 38 residues processed: 215 average time/residue: 0.2708 time to fit residues: 80.6656 Evaluate side-chains 206 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 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 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 885 ILE Chi-restraints excluded: chain A residue 926 LEU Chi-restraints excluded: chain A residue 934 THR 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11279 Z= 0.366 Angle : 0.875 30.728 15292 Z= 0.390 Chirality : 0.048 0.539 1727 Planarity : 0.004 0.046 1919 Dihedral : 8.784 131.243 1602 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 5.07 % Allowed : 20.35 % Favored : 74.58 % 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: -1.85 (0.23), residues: 1342 helix: -0.22 (0.22), residues: 581 sheet: -0.98 (0.37), residues: 210 loop : -2.41 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 260 HIS 0.004 0.001 HIS C 131 PHE 0.024 0.002 PHE A 971 TYR 0.020 0.002 TYR A 311 ARG 0.010 0.000 ARG A 613 *********************** 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 232 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7403 (tptp) REVERT: A 181 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6916 (mt-10) REVERT: A 212 GLU cc_start: 0.6880 (tp30) cc_final: 0.6565 (tp30) REVERT: A 330 LYS cc_start: 0.8007 (tttt) cc_final: 0.7744 (tttm) REVERT: A 367 LYS cc_start: 0.8059 (mttt) cc_final: 0.7688 (mtmt) REVERT: A 577 GLU cc_start: 0.6347 (mm-30) cc_final: 0.5723 (pm20) REVERT: A 628 LYS cc_start: 0.8052 (ttmt) cc_final: 0.7197 (tptt) REVERT: A 843 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7596 (ptm-80) REVERT: A 1075 PHE cc_start: 0.7926 (t80) cc_final: 0.7185 (m-80) REVERT: C 275 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8226 (pp) REVERT: C 294 ASN cc_start: 0.7534 (OUTLIER) cc_final: 0.7085 (t0) outliers start: 61 outliers final: 43 residues processed: 220 average time/residue: 0.2701 time to fit residues: 82.1047 Evaluate side-chains 214 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 1.254 ------------------------------------------------------------------------------- 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 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 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 788 CYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 909 THR 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 176 ASN 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 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 262 ARG Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 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 14 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 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 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11279 Z= 0.192 Angle : 0.821 31.103 15292 Z= 0.360 Chirality : 0.045 0.479 1727 Planarity : 0.004 0.043 1919 Dihedral : 8.457 129.084 1600 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.82 % Allowed : 21.10 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.52 (0.23), residues: 1342 helix: 0.09 (0.22), residues: 580 sheet: -0.69 (0.39), residues: 199 loop : -2.33 (0.25), residues: 563 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 0.021 0.001 PHE A 633 TYR 0.013 0.001 TYR A 311 ARG 0.007 0.000 ARG A 613 *********************** 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 220 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 174 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.7885 (ttmt) cc_final: 0.7359 (tptm) REVERT: A 212 GLU cc_start: 0.6799 (tp30) cc_final: 0.6492 (tp30) REVERT: A 330 LYS cc_start: 0.7910 (tttt) cc_final: 0.7643 (tttm) REVERT: A 367 LYS cc_start: 0.7925 (mttt) cc_final: 0.7574 (mtmt) REVERT: A 577 GLU cc_start: 0.6284 (mm-30) cc_final: 0.5685 (pm20) REVERT: A 628 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7084 (tptt) REVERT: A 639 ASN cc_start: 0.8181 (p0) cc_final: 0.7968 (p0) REVERT: A 843 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7446 (ptm-80) REVERT: A 1075 PHE cc_start: 0.7842 (t80) cc_final: 0.7158 (m-80) REVERT: C 190 GLN cc_start: 0.6260 (OUTLIER) cc_final: 0.6019 (tt0) REVERT: C 275 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8102 (pp) REVERT: C 294 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.7099 (t0) outliers start: 46 outliers final: 30 residues processed: 211 average time/residue: 0.2786 time to fit residues: 80.6052 Evaluate side-chains 197 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 431 TYR 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 709 GLU Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 899 GLN Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 190 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 82 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11279 Z= 0.233 Angle : 0.831 31.218 15292 Z= 0.364 Chirality : 0.046 0.484 1727 Planarity : 0.004 0.044 1919 Dihedral : 8.351 126.880 1600 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.99 % Allowed : 21.51 % 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: -1.42 (0.23), residues: 1342 helix: 0.14 (0.22), residues: 584 sheet: -0.32 (0.40), residues: 186 loop : -2.33 (0.24), residues: 572 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 0.007 0.000 ARG A 613 *********************** 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 211 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 163 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6787 (tp30) cc_final: 0.6499 (tp30) REVERT: A 330 LYS cc_start: 0.7927 (tttt) cc_final: 0.7654 (tttm) REVERT: A 367 LYS cc_start: 0.7953 (mttt) cc_final: 0.7604 (mtmt) REVERT: A 577 GLU cc_start: 0.6235 (mm-30) cc_final: 0.5657 (pm20) REVERT: A 628 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7075 (tptm) REVERT: A 721 GLU cc_start: 0.4398 (OUTLIER) cc_final: 0.3778 (mp0) REVERT: A 843 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7432 (ptm-80) REVERT: A 1075 PHE cc_start: 0.7883 (t80) cc_final: 0.7183 (m-80) REVERT: C 275 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8175 (pp) REVERT: C 294 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.7100 (t0) outliers start: 48 outliers final: 36 residues processed: 201 average time/residue: 0.2766 time to fit residues: 76.5111 Evaluate side-chains 199 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ARG Chi-restraints excluded: chain A residue 54 ASN Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 431 TYR 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 631 LYS 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 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 1055 PHE Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 176 ASN Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 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 120 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 108 optimal weight: 0.8980 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 0.0270 overall best weight: 0.7640 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11279 Z= 0.187 Angle : 0.816 31.473 15292 Z= 0.355 Chirality : 0.045 0.456 1727 Planarity : 0.004 0.043 1919 Dihedral : 8.071 124.399 1598 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.32 % Allowed : 22.18 % 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: -1.24 (0.23), residues: 1342 helix: 0.28 (0.22), residues: 583 sheet: -0.28 (0.40), residues: 190 loop : -2.21 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 323 HIS 0.003 0.001 HIS A 576 PHE 0.024 0.001 PHE A 633 TYR 0.013 0.001 TYR A 311 ARG 0.009 0.000 ARG A 613 *********************** 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 210 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6764 (tp30) cc_final: 0.6488 (tp30) REVERT: A 225 ILE cc_start: 0.8013 (mm) cc_final: 0.7791 (mm) REVERT: A 252 LYS cc_start: 0.7228 (mmmt) cc_final: 0.6902 (mmtt) REVERT: A 330 LYS cc_start: 0.7913 (tttt) cc_final: 0.7642 (tttm) REVERT: A 367 LYS cc_start: 0.7897 (mttt) cc_final: 0.7556 (mtmt) REVERT: A 577 GLU cc_start: 0.6202 (mm-30) cc_final: 0.5643 (pm20) REVERT: A 628 LYS cc_start: 0.7727 (ttmt) cc_final: 0.6938 (tptt) REVERT: A 639 ASN cc_start: 0.8123 (p0) cc_final: 0.7923 (p0) REVERT: A 721 GLU cc_start: 0.4406 (OUTLIER) cc_final: 0.3835 (mp0) REVERT: A 843 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7364 (ptm-80) REVERT: A 1055 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7660 (t80) REVERT: A 1075 PHE cc_start: 0.7844 (t80) cc_final: 0.7168 (m-80) REVERT: C 275 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8092 (pp) REVERT: C 294 ASN cc_start: 0.7328 (OUTLIER) cc_final: 0.7125 (t0) outliers start: 40 outliers final: 30 residues processed: 204 average time/residue: 0.2911 time to fit residues: 81.9134 Evaluate side-chains 194 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 413 THR Chi-restraints excluded: chain A residue 431 TYR 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 821 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 899 GLN Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1055 PHE 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 237 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 11 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11279 Z= 0.224 Angle : 0.828 31.347 15292 Z= 0.362 Chirality : 0.046 0.467 1727 Planarity : 0.004 0.043 1919 Dihedral : 8.042 124.196 1598 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.49 % Allowed : 21.93 % Favored : 74.58 % 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: -1.21 (0.23), residues: 1342 helix: 0.29 (0.22), residues: 583 sheet: -0.31 (0.40), residues: 191 loop : -2.16 (0.25), residues: 568 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 0.025 0.001 PHE A 633 TYR 0.018 0.001 TYR A 311 ARG 0.009 0.000 ARG A 613 ********************** 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 204 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6805 (tp30) cc_final: 0.6514 (tp30) REVERT: A 252 LYS cc_start: 0.7231 (mmmt) cc_final: 0.6982 (mmtt) REVERT: A 256 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.6849 (pttm) REVERT: A 330 LYS cc_start: 0.7966 (tttt) cc_final: 0.7701 (tttm) REVERT: A 367 LYS cc_start: 0.7925 (mttt) cc_final: 0.7559 (mtpt) REVERT: A 577 GLU cc_start: 0.6204 (mm-30) cc_final: 0.5640 (pm20) REVERT: A 613 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7366 (mtm-85) REVERT: A 628 LYS cc_start: 0.7715 (ttmt) cc_final: 0.6920 (tptm) REVERT: A 721 GLU cc_start: 0.4425 (OUTLIER) cc_final: 0.3853 (mp0) REVERT: A 843 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7330 (ptm-80) REVERT: A 1075 PHE cc_start: 0.7869 (t80) cc_final: 0.7163 (m-80) REVERT: C 275 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8177 (pp) REVERT: C 294 ASN cc_start: 0.7353 (OUTLIER) cc_final: 0.7085 (t0) outliers start: 42 outliers final: 32 residues processed: 196 average time/residue: 0.2864 time to fit residues: 77.4696 Evaluate side-chains 198 residues out of total 1205 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 256 LYS Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 431 TYR 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 780 MET Chi-restraints excluded: chain A residue 788 CYS Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 843 ARG Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 934 THR Chi-restraints excluded: chain A residue 1055 PHE Chi-restraints excluded: chain A residue 1081 GLU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 191 ASP Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 44 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.171652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.135216 restraints weight = 11172.677| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.41 r_work: 0.3008 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11279 Z= 0.186 Angle : 0.813 31.419 15292 Z= 0.354 Chirality : 0.045 0.442 1727 Planarity : 0.004 0.043 1919 Dihedral : 7.918 122.070 1598 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.74 % Allowed : 23.01 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.23), residues: 1342 helix: 0.38 (0.22), residues: 589 sheet: -0.17 (0.40), residues: 190 loop : -2.13 (0.25), residues: 563 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 0.024 0.001 PHE A 633 TYR 0.015 0.001 TYR A 311 ARG 0.009 0.000 ARG A 613 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2532.04 seconds wall clock time: 47 minutes 56.19 seconds (2876.19 seconds total)