Starting phenix.real_space_refine on Thu Mar 13 00:29:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9baz_44415/03_2025/9baz_44415.cif Found real_map, /net/cci-nas-00/data/ceres_data/9baz_44415/03_2025/9baz_44415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9baz_44415/03_2025/9baz_44415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9baz_44415/03_2025/9baz_44415.map" model { file = "/net/cci-nas-00/data/ceres_data/9baz_44415/03_2025/9baz_44415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9baz_44415/03_2025/9baz_44415.cif" } resolution = 2.76 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= -0.001 sd= 0.015 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 40 5.16 5 C 5305 2.51 5 N 1477 2.21 5 O 1460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8283 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 965, 7271 Classifications: {'peptide': 965} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PCIS': 2, 'PTRANS': 63, 'TRANS': 899} Chain breaks: 6 Unresolved non-hydrogen bonds: 472 Unresolved non-hydrogen angles: 571 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 10, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 21, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 274 Chain: "B" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 506 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 59} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 59} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2806 SG CYS A 635 39.533 50.422 27.871 1.00170.88 S ATOM 2819 SG CYS A 637 39.129 49.591 23.881 1.00169.76 S ATOM 3230 SG CYS A 692 41.609 51.872 25.032 1.00176.61 S Time building chain proxies: 5.84, per 1000 atoms: 0.71 Number of scatterers: 8283 At special positions: 0 Unit cell: (82.017, 100.944, 140.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 40 16.00 O 1460 8.00 N 1477 7.00 C 5305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1302 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 637 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 635 " pdb="ZN ZN A1302 " - pdb=" ND1 HIS A 694 " pdb="ZN ZN A1302 " - pdb=" SG CYS A 692 " Number of angles added : 3 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 13 sheets defined 31.8% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 163 through 178 Processing helix chain 'A' and resid 208 through 214 removed outlier: 4.044A pdb=" N THR A 214 " --> pdb=" O GLN A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 268 removed outlier: 3.526A pdb=" N ALA A 268 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 310 Proline residue: A 289 - end of helix removed outlier: 3.843A pdb=" N TRP A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 334 through 343 removed outlier: 3.785A pdb=" N GLN A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 356 through 367 Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.635A pdb=" N GLY A 375 " --> pdb=" O ARG A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 382 removed outlier: 3.696A pdb=" N ARG A 380 " --> pdb=" O ASP A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 423 removed outlier: 4.514A pdb=" N HIS A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 687 through 691 removed outlier: 3.847A pdb=" N LEU A 690 " --> pdb=" O LYS A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 752 No H-bonds generated for 'chain 'A' and resid 750 through 752' Processing helix chain 'A' and resid 850 through 860 removed outlier: 3.580A pdb=" N GLY A 860 " --> pdb=" O LEU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 894 through 904 Processing helix chain 'A' and resid 938 through 959 removed outlier: 4.359A pdb=" N VAL A 948 " --> pdb=" O ASN A 944 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 977 through 980 Processing helix chain 'A' and resid 981 through 993 Processing helix chain 'A' and resid 1005 through 1008 Processing helix chain 'A' and resid 1068 through 1073 Processing helix chain 'A' and resid 1100 through 1110 removed outlier: 3.571A pdb=" N ILE A1110 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing helix chain 'A' and resid 1118 through 1124 Processing helix chain 'A' and resid 1125 through 1127 No H-bonds generated for 'chain 'A' and resid 1125 through 1127' Processing helix chain 'A' and resid 1131 through 1138 removed outlier: 3.603A pdb=" N PHE A1138 " --> pdb=" O ASP A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1197 Processing helix chain 'A' and resid 1208 through 1218 Processing helix chain 'A' and resid 1221 through 1237 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 236 through 246 removed outlier: 3.897A pdb=" N MET B 240 " --> pdb=" O CYS B 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 228 through 236 removed outlier: 3.880A pdb=" N ILE C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 247 removed outlier: 3.656A pdb=" N MET C 240 " --> pdb=" O CYS C 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 248 through 249 removed outlier: 5.985A pdb=" N VAL A 132 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148 removed outlier: 3.922A pdb=" N GLN B 226 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 206 removed outlier: 3.653A pdb=" N GLU A 205 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU A 190 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS A 228 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ASP A 192 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 226 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE A 223 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 238 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 206 removed outlier: 3.653A pdb=" N GLU A 205 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP A 192 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASN A 194 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 402 Processing sheet with id=AA6, first strand: chain 'A' and resid 411 through 412 removed outlier: 5.650A pdb=" N THR A 411 " --> pdb=" O ARG A 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 559 removed outlier: 4.594A pdb=" N PHE A 582 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP A 606 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL A 588 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N SER A 604 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 607 " --> pdb=" O HIS A 634 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS A 634 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TRP A 609 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 629 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR A 675 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU A 631 " --> pdb=" O TYR A 675 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 671 " --> pdb=" O ASP A 657 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 556 through 559 removed outlier: 4.594A pdb=" N PHE A 582 " --> pdb=" O PHE A 610 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP A 606 " --> pdb=" O GLN A 586 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL A 588 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N SER A 604 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A 607 " --> pdb=" O HIS A 634 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N HIS A 634 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N TRP A 609 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 629 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N TYR A 675 " --> pdb=" O LEU A 629 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU A 631 " --> pdb=" O TYR A 675 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 779 removed outlier: 3.616A pdb=" N GLY A 778 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 11.821A pdb=" N ASP A 723 " --> pdb=" O ARG A 748 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N ARG A 748 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR A 725 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 746 " --> pdb=" O TYR A 725 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL A 727 " --> pdb=" O ARG A 744 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG A 744 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 729 " --> pdb=" O ARG A 742 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP A 767 " --> pdb=" O LYS A 745 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 747 " --> pdb=" O THR A 765 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR A 765 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 762 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HIS A 808 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLU A 766 " --> pdb=" O GLN A 810 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 781 " --> pdb=" O PHE A 804 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE A 806 " --> pdb=" O ILE A 781 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 776 through 779 removed outlier: 3.616A pdb=" N GLY A 778 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 11.821A pdb=" N ASP A 723 " --> pdb=" O ARG A 748 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N ARG A 748 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N TYR A 725 " --> pdb=" O LEU A 746 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 746 " --> pdb=" O TYR A 725 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL A 727 " --> pdb=" O ARG A 744 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ARG A 744 " --> pdb=" O VAL A 727 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU A 729 " --> pdb=" O ARG A 742 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP A 767 " --> pdb=" O LYS A 745 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 747 " --> pdb=" O THR A 765 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR A 765 " --> pdb=" O LEU A 747 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 762 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N HIS A 808 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLU A 766 " --> pdb=" O GLN A 810 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 862 through 866 removed outlier: 5.512A pdb=" N LEU A 840 " --> pdb=" O GLU A 863 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG A 865 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLY A 842 " --> pdb=" O ARG A 865 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG A 841 " --> pdb=" O PHE A 919 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA A 921 " --> pdb=" O ARG A 841 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N MET A 843 " --> pdb=" O ALA A 921 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 920 " --> pdb=" O VAL A 964 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N GLU A 966 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA A 922 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N VAL A 968 " --> pdb=" O ALA A 922 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 868 through 869 removed outlier: 3.534A pdb=" N ASP A 869 " --> pdb=" O PHE A 891 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 199 through 206 309 hydrogen bonds defined for protein. 843 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: 3.13 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2729 1.34 - 1.46: 2075 1.46 - 1.58: 3656 1.58 - 1.70: 0 1.70 - 1.82: 59 Bond restraints: 8519 Sorted by residual: bond pdb=" CA SER A1221 " pdb=" CB SER A1221 " ideal model delta sigma weight residual 1.531 1.477 0.054 1.69e-02 3.50e+03 1.01e+01 bond pdb=" N VAL A1216 " pdb=" CA VAL A1216 " ideal model delta sigma weight residual 1.460 1.494 -0.035 1.21e-02 6.83e+03 8.16e+00 bond pdb=" N VAL A1220 " pdb=" CA VAL A1220 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.19e-02 7.06e+03 6.28e+00 bond pdb=" N SER A1219 " pdb=" CA SER A1219 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.14e-02 7.69e+03 6.09e+00 bond pdb=" N ASN A1218 " pdb=" CA ASN A1218 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.32e-02 5.74e+03 5.66e+00 ... (remaining 8514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 11400 1.89 - 3.79: 177 3.79 - 5.68: 29 5.68 - 7.58: 10 7.58 - 9.47: 8 Bond angle restraints: 11624 Sorted by residual: angle pdb=" N ARG A1222 " pdb=" CA ARG A1222 " pdb=" C ARG A1222 " ideal model delta sigma weight residual 113.01 106.42 6.59 1.20e+00 6.94e-01 3.02e+01 angle pdb=" C SER A1221 " pdb=" CA SER A1221 " pdb=" CB SER A1221 " ideal model delta sigma weight residual 109.80 115.93 -6.13 1.23e+00 6.61e-01 2.49e+01 angle pdb=" N SER A1221 " pdb=" CA SER A1221 " pdb=" C SER A1221 " ideal model delta sigma weight residual 110.64 103.48 7.16 1.48e+00 4.57e-01 2.34e+01 angle pdb=" CA THR B 225 " pdb=" CB THR B 225 " pdb=" OG1 THR B 225 " ideal model delta sigma weight residual 109.60 103.41 6.19 1.50e+00 4.44e-01 1.70e+01 angle pdb=" CB LYS A 215 " pdb=" CG LYS A 215 " pdb=" CD LYS A 215 " ideal model delta sigma weight residual 111.30 119.68 -8.38 2.30e+00 1.89e-01 1.33e+01 ... (remaining 11619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4280 16.94 - 33.87: 493 33.87 - 50.81: 158 50.81 - 67.75: 28 67.75 - 84.69: 9 Dihedral angle restraints: 4968 sinusoidal: 1822 harmonic: 3146 Sorted by residual: dihedral pdb=" CA VAL A 862 " pdb=" C VAL A 862 " pdb=" N GLU A 863 " pdb=" CA GLU A 863 " ideal model delta harmonic sigma weight residual 180.00 162.79 17.21 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" N MET B 214 " pdb=" CA MET B 214 " pdb=" CB MET B 214 " pdb=" CG MET B 214 " ideal model delta sinusoidal sigma weight residual -180.00 -120.01 -59.99 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 206 " pdb=" CG MET A 206 " pdb=" SD MET A 206 " pdb=" CE MET A 206 " ideal model delta sinusoidal sigma weight residual -60.00 -118.79 58.79 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 4965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1128 0.068 - 0.135: 127 0.135 - 0.202: 5 0.202 - 0.270: 2 0.270 - 0.337: 1 Chirality restraints: 1263 Sorted by residual: chirality pdb=" CA VAL A1220 " pdb=" N VAL A1220 " pdb=" C VAL A1220 " pdb=" CB VAL A1220 " both_signs ideal model delta sigma weight residual False 2.44 2.78 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA ARG A1222 " pdb=" N ARG A1222 " pdb=" C ARG A1222 " pdb=" CB ARG A1222 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB VAL A1220 " pdb=" CA VAL A1220 " pdb=" CG1 VAL A1220 " pdb=" CG2 VAL A1220 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 1260 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1215 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C LEU A1215 " -0.038 2.00e-02 2.50e+03 pdb=" O LEU A1215 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL A1216 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 616 " -0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO A 617 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 617 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 617 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1222 " 0.182 9.50e-02 1.11e+02 8.14e-02 4.08e+00 pdb=" NE ARG A1222 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A1222 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A1222 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A1222 " 0.006 2.00e-02 2.50e+03 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 177 2.67 - 3.23: 7829 3.23 - 3.79: 13595 3.79 - 4.34: 17776 4.34 - 4.90: 29447 Nonbonded interactions: 68824 Sorted by model distance: nonbonded pdb=" OH TYR A 249 " pdb=" OE1 GLU A 363 " model vdw 2.117 3.040 nonbonded pdb=" OG SER A 722 " pdb=" O PRO A1061 " model vdw 2.153 3.040 nonbonded pdb=" OD2 ASP A 869 " pdb=" O3' SAH A1301 " model vdw 2.162 3.040 nonbonded pdb=" O ARG A 207 " pdb=" OH TYR A 283 " model vdw 2.228 3.040 nonbonded pdb=" O ASP A 872 " pdb=" ND1 HIS A 876 " model vdw 2.229 3.120 ... (remaining 68819 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 191 through 195 or (resid 196 through 197 and (name N or n \ ame CA or name C or name O or name CB )) or resid 198 through 200 or (resid 201 \ and (name N or name CA or name C or name O or name CB )) or resid 202 or (resid \ 203 through 204 and (name N or name CA or name C or name O or name CB )) or resi \ d 205 or (resid 206 and (name N or name CA or name C or name O or name CB )) or \ resid 207 through 211 or (resid 212 through 214 and (name N or name CA or name C \ or name O or name CB )) or resid 215 through 251)) selection = (chain 'C' and (resid 191 through 207 or (resid 208 through 209 and (name N or n \ ame CA or name C or name O or name CB )) or resid 210 through 233 or (resid 234 \ and (name N or name CA or name C or name O or name CB )) or resid 235 through 24 \ 8 or (resid 249 and (name N or name CA or name C or name O or name CB )) or resi \ d 250 through 251)) } 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: 2.330 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.290 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 42.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 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 : 0.004 0.054 8519 Z= 0.240 Angle : 0.633 9.473 11624 Z= 0.321 Chirality : 0.044 0.337 1263 Planarity : 0.005 0.081 1514 Dihedral : 16.560 84.686 2946 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.50 % Allowed : 33.33 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.19 (0.26), residues: 1071 helix: 0.71 (0.31), residues: 302 sheet: -0.46 (0.39), residues: 182 loop : 0.14 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 361 HIS 0.003 0.001 HIS A1223 PHE 0.012 0.001 PHE A 805 TYR 0.009 0.001 TYR A 725 ARG 0.007 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 133 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 215 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8082 (tmtp) REVERT: A 954 PHE cc_start: 0.7672 (m-80) cc_final: 0.7206 (m-80) REVERT: B 244 TYR cc_start: 0.7698 (m-10) cc_final: 0.7377 (m-10) REVERT: C 198 HIS cc_start: 0.8170 (m170) cc_final: 0.7827 (m-70) REVERT: C 242 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8139 (mm-40) REVERT: C 249 ARG cc_start: 0.7581 (ttp-170) cc_final: 0.7362 (mmt-90) outliers start: 4 outliers final: 5 residues processed: 134 average time/residue: 0.7439 time to fit residues: 110.3384 Evaluate side-chains 123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain C residue 230 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 43 optimal weight: 0.0060 chunk 84 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 802 ASN C 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.137138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.116308 restraints weight = 16040.290| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 3.50 r_work: 0.3621 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8519 Z= 0.209 Angle : 0.561 9.411 11624 Z= 0.274 Chirality : 0.042 0.162 1263 Planarity : 0.004 0.052 1514 Dihedral : 4.468 42.568 1194 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 5.79 % Allowed : 26.79 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.24 (0.26), residues: 1071 helix: 0.90 (0.31), residues: 304 sheet: -0.51 (0.39), residues: 178 loop : 0.11 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 361 HIS 0.002 0.001 HIS A1007 PHE 0.011 0.001 PHE A 323 TYR 0.010 0.001 TYR A 730 ARG 0.005 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 129 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7457 (mp10) REVERT: A 844 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: A 947 LEU cc_start: 0.8311 (mt) cc_final: 0.8094 (mp) REVERT: A 954 PHE cc_start: 0.7795 (m-80) cc_final: 0.7186 (m-80) REVERT: A 1085 ASP cc_start: 0.8474 (t70) cc_final: 0.8246 (t70) REVERT: B 244 TYR cc_start: 0.7731 (m-10) cc_final: 0.7264 (m-10) REVERT: C 198 HIS cc_start: 0.8163 (m170) cc_final: 0.7948 (m-70) REVERT: C 242 GLN cc_start: 0.8573 (mm-40) cc_final: 0.7965 (mm-40) REVERT: C 249 ARG cc_start: 0.7880 (ttp-170) cc_final: 0.7576 (mmt180) outliers start: 46 outliers final: 17 residues processed: 155 average time/residue: 0.6926 time to fit residues: 119.7441 Evaluate side-chains 132 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 70 optimal weight: 0.0000 chunk 94 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.137288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.116474 restraints weight = 16286.089| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.52 r_work: 0.3622 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8519 Z= 0.198 Angle : 0.557 9.395 11624 Z= 0.268 Chirality : 0.042 0.159 1263 Planarity : 0.004 0.051 1514 Dihedral : 4.060 24.665 1187 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.16 % Allowed : 27.55 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.27 (0.26), residues: 1071 helix: 0.93 (0.31), residues: 305 sheet: -0.59 (0.39), residues: 178 loop : 0.16 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 361 HIS 0.002 0.001 HIS A1007 PHE 0.012 0.001 PHE A 605 TYR 0.009 0.001 TYR A 725 ARG 0.003 0.000 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 284 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: A 320 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7737 (mmtp) REVERT: A 761 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7833 (mm-30) REVERT: A 947 LEU cc_start: 0.8312 (mt) cc_final: 0.8082 (mp) REVERT: A 954 PHE cc_start: 0.7819 (m-80) cc_final: 0.7132 (m-80) REVERT: A 1085 ASP cc_start: 0.8439 (t70) cc_final: 0.8087 (t70) REVERT: B 240 MET cc_start: 0.8649 (tpt) cc_final: 0.8140 (tpt) REVERT: B 244 TYR cc_start: 0.7815 (m-10) cc_final: 0.7363 (m-10) REVERT: C 242 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8004 (mm-40) REVERT: C 249 ARG cc_start: 0.7814 (ttp-170) cc_final: 0.7584 (mmt180) outliers start: 41 outliers final: 18 residues processed: 151 average time/residue: 0.8092 time to fit residues: 135.2859 Evaluate side-chains 137 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 0.0000 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.136016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.115195 restraints weight = 16257.580| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.49 r_work: 0.3601 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8519 Z= 0.235 Angle : 0.575 9.440 11624 Z= 0.278 Chirality : 0.042 0.148 1263 Planarity : 0.004 0.052 1514 Dihedral : 4.080 26.106 1185 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 5.41 % Allowed : 27.67 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.24 (0.26), residues: 1071 helix: 0.87 (0.31), residues: 311 sheet: -0.56 (0.40), residues: 166 loop : 0.12 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 361 HIS 0.005 0.001 HIS C 198 PHE 0.021 0.002 PHE A 146 TYR 0.009 0.001 TYR A 725 ARG 0.003 0.000 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 123 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 284 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7425 (mp10) REVERT: A 320 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7678 (mmtp) REVERT: A 761 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7851 (mm-30) REVERT: A 844 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: A 947 LEU cc_start: 0.8323 (mt) cc_final: 0.8053 (mp) REVERT: A 954 PHE cc_start: 0.7882 (m-80) cc_final: 0.7156 (m-80) REVERT: A 1085 ASP cc_start: 0.8434 (t70) cc_final: 0.8017 (t70) REVERT: B 240 MET cc_start: 0.8599 (tpt) cc_final: 0.8086 (tpt) REVERT: B 244 TYR cc_start: 0.7903 (m-10) cc_final: 0.7389 (m-10) REVERT: C 198 HIS cc_start: 0.7499 (m-70) cc_final: 0.7199 (m90) REVERT: C 242 GLN cc_start: 0.8656 (mm-40) cc_final: 0.7973 (mm-40) outliers start: 43 outliers final: 21 residues processed: 148 average time/residue: 0.7554 time to fit residues: 124.0034 Evaluate side-chains 142 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 844 ASP Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 0.0170 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 HIS C 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.135989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.115310 restraints weight = 16078.109| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 3.48 r_work: 0.3604 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8519 Z= 0.220 Angle : 0.568 9.443 11624 Z= 0.274 Chirality : 0.042 0.147 1263 Planarity : 0.004 0.053 1514 Dihedral : 4.081 25.193 1185 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.16 % Allowed : 27.80 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.25 (0.26), residues: 1071 helix: 0.86 (0.31), residues: 312 sheet: -0.54 (0.40), residues: 161 loop : 0.12 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 361 HIS 0.003 0.001 HIS C 198 PHE 0.013 0.001 PHE A 146 TYR 0.009 0.001 TYR A 725 ARG 0.003 0.000 ARG A 748 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.902 Fit side-chains REVERT: A 284 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.7407 (mp10) REVERT: A 320 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7736 (mmtp) REVERT: A 761 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.7844 (mm-30) REVERT: A 947 LEU cc_start: 0.8316 (mt) cc_final: 0.8036 (mp) REVERT: A 954 PHE cc_start: 0.7914 (m-80) cc_final: 0.7108 (m-80) REVERT: A 980 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6386 (mp10) REVERT: A 1085 ASP cc_start: 0.8443 (t70) cc_final: 0.7977 (t70) REVERT: A 1089 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7695 (tpm170) REVERT: B 240 MET cc_start: 0.8592 (tpt) cc_final: 0.8093 (tpt) REVERT: B 244 TYR cc_start: 0.7770 (m-10) cc_final: 0.7239 (m-10) REVERT: C 198 HIS cc_start: 0.7563 (m-70) cc_final: 0.7283 (m90) REVERT: C 242 GLN cc_start: 0.8686 (mm-40) cc_final: 0.7962 (mm-40) REVERT: C 249 ARG cc_start: 0.7946 (ttp-170) cc_final: 0.7629 (mmt180) outliers start: 41 outliers final: 22 residues processed: 151 average time/residue: 0.8996 time to fit residues: 148.5975 Evaluate side-chains 146 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 72 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 27 optimal weight: 0.0030 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.137299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.116851 restraints weight = 16189.946| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 3.47 r_work: 0.3607 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8519 Z= 0.219 Angle : 0.577 9.456 11624 Z= 0.277 Chirality : 0.042 0.144 1263 Planarity : 0.004 0.053 1514 Dihedral : 4.082 24.021 1185 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.16 % Allowed : 28.68 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.22 (0.26), residues: 1071 helix: 0.85 (0.30), residues: 311 sheet: -0.60 (0.40), residues: 161 loop : 0.11 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 361 HIS 0.002 0.000 HIS C 198 PHE 0.014 0.001 PHE A 323 TYR 0.009 0.001 TYR A 725 ARG 0.006 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 284 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: A 320 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7752 (mmtp) REVERT: A 761 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7825 (mm-30) REVERT: A 947 LEU cc_start: 0.8329 (mt) cc_final: 0.8037 (mp) REVERT: A 954 PHE cc_start: 0.7944 (m-80) cc_final: 0.7078 (m-80) REVERT: A 980 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6401 (mp10) REVERT: A 1085 ASP cc_start: 0.8465 (t70) cc_final: 0.8011 (t70) REVERT: A 1089 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7706 (tpm170) REVERT: B 240 MET cc_start: 0.8598 (tpt) cc_final: 0.8076 (tpt) REVERT: B 244 TYR cc_start: 0.7787 (m-10) cc_final: 0.7316 (m-10) REVERT: C 198 HIS cc_start: 0.7642 (m-70) cc_final: 0.7272 (m90) REVERT: C 199 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8296 (mt) REVERT: C 249 ARG cc_start: 0.7981 (ttp-170) cc_final: 0.7675 (mmt180) outliers start: 41 outliers final: 25 residues processed: 153 average time/residue: 0.7386 time to fit residues: 124.8757 Evaluate side-chains 151 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 LYS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 950 SER Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1089 ARG Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1205 LEU Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.133025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.112334 restraints weight = 16367.779| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.47 r_work: 0.3557 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8519 Z= 0.321 Angle : 0.630 9.753 11624 Z= 0.306 Chirality : 0.044 0.177 1263 Planarity : 0.005 0.055 1514 Dihedral : 4.387 32.070 1185 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.53 % Allowed : 28.18 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: -0.02 (0.26), residues: 1071 helix: 0.68 (0.30), residues: 312 sheet: -0.74 (0.39), residues: 166 loop : -0.06 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 361 HIS 0.003 0.001 HIS A 876 PHE 0.014 0.002 PHE A 290 TYR 0.009 0.001 TYR A 286 ARG 0.007 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 121 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 284 GLN cc_start: 0.7714 (OUTLIER) cc_final: 0.7422 (mp10) REVERT: A 761 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.7938 (mm-30) REVERT: A 947 LEU cc_start: 0.8335 (mt) cc_final: 0.8035 (mp) REVERT: A 980 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6421 (mp10) REVERT: A 1085 ASP cc_start: 0.8525 (t70) cc_final: 0.8080 (t70) REVERT: B 203 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: B 220 LYS cc_start: 0.6937 (pttt) cc_final: 0.6721 (pttt) REVERT: B 240 MET cc_start: 0.8569 (tpt) cc_final: 0.8022 (tpt) REVERT: B 244 TYR cc_start: 0.7898 (m-10) cc_final: 0.7387 (m-10) REVERT: C 198 HIS cc_start: 0.7706 (m-70) cc_final: 0.7333 (m90) REVERT: C 199 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8291 (mt) REVERT: C 249 ARG cc_start: 0.7994 (ttp-170) cc_final: 0.7682 (mmt180) outliers start: 44 outliers final: 28 residues processed: 147 average time/residue: 0.7418 time to fit residues: 120.9801 Evaluate side-chains 149 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 781 ILE Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1130 MET Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 214 MET Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 96 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 43 optimal weight: 0.0570 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 0.0570 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN C 211 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.136269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.115726 restraints weight = 16205.990| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.48 r_work: 0.3609 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8519 Z= 0.192 Angle : 0.597 9.430 11624 Z= 0.284 Chirality : 0.042 0.162 1263 Planarity : 0.004 0.053 1514 Dihedral : 4.218 27.694 1185 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.40 % Allowed : 29.31 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.11 (0.26), residues: 1071 helix: 0.79 (0.30), residues: 311 sheet: -0.65 (0.40), residues: 161 loop : 0.02 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 361 HIS 0.002 0.001 HIS A1113 PHE 0.012 0.001 PHE A 146 TYR 0.009 0.001 TYR A 725 ARG 0.004 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 215 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8188 (tttt) REVERT: A 284 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: A 742 ARG cc_start: 0.7099 (tpp80) cc_final: 0.6270 (mmt180) REVERT: A 744 ARG cc_start: 0.8065 (ttm-80) cc_final: 0.7841 (ttm110) REVERT: A 761 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7896 (mm-30) REVERT: A 768 LEU cc_start: 0.8796 (mp) cc_final: 0.8073 (tm) REVERT: A 858 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6953 (mt-10) REVERT: A 947 LEU cc_start: 0.8321 (mt) cc_final: 0.8051 (mp) REVERT: A 980 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6446 (mp10) REVERT: A 1085 ASP cc_start: 0.8418 (t70) cc_final: 0.7939 (t70) REVERT: A 1202 GLU cc_start: 0.8252 (mp0) cc_final: 0.7860 (mp0) REVERT: A 1221 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8260 (p) REVERT: B 240 MET cc_start: 0.8557 (tpt) cc_final: 0.7898 (tpt) REVERT: B 244 TYR cc_start: 0.7702 (m-10) cc_final: 0.7210 (m-10) REVERT: C 198 HIS cc_start: 0.7718 (m-70) cc_final: 0.7361 (m90) REVERT: C 199 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8340 (mt) REVERT: C 249 ARG cc_start: 0.7979 (ttp-170) cc_final: 0.7650 (mmt180) outliers start: 35 outliers final: 21 residues processed: 147 average time/residue: 0.8679 time to fit residues: 140.5307 Evaluate side-chains 148 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 969 SER Chi-restraints excluded: chain A residue 980 GLN Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1092 ASP Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain C residue 199 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 0.0070 chunk 19 optimal weight: 0.0980 chunk 24 optimal weight: 0.3980 chunk 3 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 95 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 96 optimal weight: 0.0010 chunk 101 optimal weight: 0.7980 overall best weight: 0.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.139830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.119612 restraints weight = 16203.242| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 3.48 r_work: 0.3642 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8519 Z= 0.162 Angle : 0.600 10.154 11624 Z= 0.283 Chirality : 0.042 0.182 1263 Planarity : 0.004 0.054 1514 Dihedral : 4.075 21.089 1185 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.14 % Allowed : 30.94 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.20 (0.26), residues: 1071 helix: 0.82 (0.30), residues: 311 sheet: -0.64 (0.39), residues: 171 loop : 0.13 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 361 HIS 0.005 0.001 HIS A1093 PHE 0.012 0.001 PHE A1020 TYR 0.010 0.001 TYR A 725 ARG 0.005 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 215 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8202 (tttt) REVERT: A 243 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7624 (tm-30) REVERT: A 284 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7414 (mp10) REVERT: A 742 ARG cc_start: 0.7107 (tpp80) cc_final: 0.6423 (mmt-90) REVERT: A 744 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7818 (ttm110) REVERT: A 761 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.7878 (mm-30) REVERT: A 768 LEU cc_start: 0.8770 (mp) cc_final: 0.8031 (tm) REVERT: A 947 LEU cc_start: 0.8337 (mt) cc_final: 0.8070 (mp) REVERT: A 1085 ASP cc_start: 0.8399 (t70) cc_final: 0.7924 (t70) REVERT: B 201 GLN cc_start: 0.8476 (tm-30) cc_final: 0.7583 (tm-30) REVERT: B 203 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: B 240 MET cc_start: 0.8516 (tpt) cc_final: 0.7743 (tpt) REVERT: B 244 TYR cc_start: 0.7614 (m-10) cc_final: 0.7164 (m-10) REVERT: C 198 HIS cc_start: 0.7767 (m-70) cc_final: 0.7500 (m90) REVERT: C 249 ARG cc_start: 0.8007 (ttp-170) cc_final: 0.7711 (mmt180) outliers start: 25 outliers final: 15 residues processed: 147 average time/residue: 0.9020 time to fit residues: 145.0843 Evaluate side-chains 145 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.134413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.113876 restraints weight = 16356.760| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 3.47 r_work: 0.3580 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8519 Z= 0.281 Angle : 0.641 9.509 11624 Z= 0.307 Chirality : 0.043 0.171 1263 Planarity : 0.004 0.053 1514 Dihedral : 4.290 29.985 1185 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.77 % Allowed : 32.45 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.16 (0.26), residues: 1071 helix: 0.78 (0.30), residues: 312 sheet: -0.52 (0.42), residues: 154 loop : 0.03 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 361 HIS 0.003 0.001 HIS C 247 PHE 0.013 0.002 PHE A 290 TYR 0.010 0.001 TYR A 725 ARG 0.004 0.000 ARG A 744 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 215 LYS cc_start: 0.8760 (mmmt) cc_final: 0.8554 (mmmt) REVERT: A 284 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: A 742 ARG cc_start: 0.7106 (tpp80) cc_final: 0.6329 (mmt-90) REVERT: A 744 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7945 (ttm110) REVERT: A 761 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.7902 (mm-30) REVERT: A 768 LEU cc_start: 0.8803 (mp) cc_final: 0.8052 (tm) REVERT: A 947 LEU cc_start: 0.8334 (mt) cc_final: 0.8047 (mp) REVERT: A 1085 ASP cc_start: 0.8444 (t70) cc_final: 0.7990 (t70) REVERT: B 240 MET cc_start: 0.8635 (tpt) cc_final: 0.7752 (tpt) REVERT: B 244 TYR cc_start: 0.7579 (m-10) cc_final: 0.7170 (m-10) REVERT: C 198 HIS cc_start: 0.7737 (m-70) cc_final: 0.7496 (m90) REVERT: C 249 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7703 (mmt180) outliers start: 22 outliers final: 16 residues processed: 138 average time/residue: 0.7640 time to fit residues: 116.1524 Evaluate side-chains 139 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 HIS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 147 GLN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 618 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1055 VAL Chi-restraints excluded: chain A residue 1209 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 248 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 106 optimal weight: 0.0870 chunk 79 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.135902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.115328 restraints weight = 16263.099| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 3.49 r_work: 0.3606 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8519 Z= 0.223 Angle : 0.630 10.326 11624 Z= 0.299 Chirality : 0.042 0.157 1263 Planarity : 0.004 0.053 1514 Dihedral : 4.267 28.060 1185 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.27 % Allowed : 31.82 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % 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: 0.19 (0.26), residues: 1071 helix: 0.76 (0.30), residues: 311 sheet: -0.55 (0.42), residues: 154 loop : 0.10 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 361 HIS 0.002 0.000 HIS A 876 PHE 0.014 0.001 PHE A 954 TYR 0.010 0.001 TYR A 725 ARG 0.004 0.000 ARG A 744 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6669.87 seconds wall clock time: 117 minutes 2.69 seconds (7022.69 seconds total)