Starting phenix.real_space_refine on Tue Jul 29 07:48:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6psx_20467/07_2025/6psx_20467_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6psx_20467/07_2025/6psx_20467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6psx_20467/07_2025/6psx_20467.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6psx_20467/07_2025/6psx_20467.map" model { file = "/net/cci-nas-00/data/ceres_data/6psx_20467/07_2025/6psx_20467_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6psx_20467/07_2025/6psx_20467_neut.cif" } resolution = 3.3 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 7170 2.51 5 N 1799 2.21 5 O 2058 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11074 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8259 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 29, 'TRANS': 1003} Chain breaks: 1 Chain: "E" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2759 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 21, 'TRANS': 317} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.44, per 1000 atoms: 0.58 Number of scatterers: 11074 At special positions: 0 Unit cell: (151.263, 101.871, 131.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 2058 8.00 N 1799 7.00 C 7170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 80 " - pdb=" SG CYS E 123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 176 " - pdb=" SG CYS E 190 " distance=2.05 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN E 199 " " NAG E 403 " - " ASN E 216 " " NAG E 404 " - " ASN E 288 " Time building additional restraints: 2.46 Conformation dependent library (CDL) restraints added in 1.4 seconds 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2594 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 11 sheets defined 44.1% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 212 through 222 removed outlier: 4.001A pdb=" N LYS A 216 " --> pdb=" O THR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 249 through 281 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.565A pdb=" N THR A 354 " --> pdb=" O ARG A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 365 removed outlier: 3.946A pdb=" N LYS A 364 " --> pdb=" O LYS A 361 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN A 365 " --> pdb=" O THR A 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 365' Processing helix chain 'A' and resid 441 through 473 Processing helix chain 'A' and resid 486 through 502 Processing helix chain 'A' and resid 510 through 527 removed outlier: 3.521A pdb=" N GLU A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 532 Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.618A pdb=" N LEU A 547 " --> pdb=" O THR A 544 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 548 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU A 549 " --> pdb=" O SER A 546 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 551 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 613 removed outlier: 4.131A pdb=" N PHE A 605 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 633 Processing helix chain 'A' and resid 652 through 664 Processing helix chain 'A' and resid 723 through 728 Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 765 through 779 Processing helix chain 'A' and resid 788 through 794 Processing helix chain 'A' and resid 816 through 827 Processing helix chain 'A' and resid 838 through 849 Processing helix chain 'A' and resid 867 through 881 removed outlier: 4.112A pdb=" N ARG A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 904 removed outlier: 3.913A pdb=" N PHE A 904 " --> pdb=" O LYS A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 919 removed outlier: 4.713A pdb=" N VAL A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 944 removed outlier: 4.141A pdb=" N ALA A 935 " --> pdb=" O PRO A 931 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 944 " --> pdb=" O MET A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 963 Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 991 through 1029 removed outlier: 4.265A pdb=" N LYS A 995 " --> pdb=" O LYS A 991 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR A1025 " --> pdb=" O ALA A1021 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN A1026 " --> pdb=" O LEU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1053 removed outlier: 3.602A pdb=" N MET A1046 " --> pdb=" O GLU A1042 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A1047 " --> pdb=" O SER A1043 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASN A1050 " --> pdb=" O MET A1046 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A1053 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1063 removed outlier: 3.738A pdb=" N PHE A1059 " --> pdb=" O VAL A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1073 Processing helix chain 'A' and resid 1077 through 1086 removed outlier: 3.835A pdb=" N LYS A1081 " --> pdb=" O PRO A1077 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A1082 " --> pdb=" O GLN A1078 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY A1086 " --> pdb=" O LEU A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1116 Processing helix chain 'A' and resid 1130 through 1153 removed outlier: 3.527A pdb=" N TRP A1134 " --> pdb=" O ASP A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1183 removed outlier: 4.055A pdb=" N LEU A1169 " --> pdb=" O ILE A1165 " (cutoff:3.500A) Proline residue: A1177 - end of helix Processing helix chain 'A' and resid 1194 through 1200 Processing helix chain 'A' and resid 1205 through 1215 Proline residue: A1213 - end of helix Processing helix chain 'A' and resid 1216 through 1227 Processing helix chain 'A' and resid 1233 through 1239 Processing helix chain 'E' and resid 41 through 69 Proline residue: E 47 - end of helix Proline residue: E 58 - end of helix Processing helix chain 'E' and resid 78 through 81 removed outlier: 4.253A pdb=" N ASP E 81 " --> pdb=" O SER E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 81' Processing helix chain 'E' and resid 150 through 155 removed outlier: 4.241A pdb=" N GLN E 155 " --> pdb=" O ARG E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 163 Processing helix chain 'E' and resid 173 through 179 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 190 through 195 removed outlier: 4.494A pdb=" N ALA E 194 " --> pdb=" O CYS E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 231 Processing helix chain 'E' and resid 245 through 249 removed outlier: 3.619A pdb=" N MET E 248 " --> pdb=" O PRO E 245 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS E 249 " --> pdb=" O ASN E 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 245 through 249' Processing helix chain 'E' and resid 262 through 267 removed outlier: 3.911A pdb=" N GLU E 267 " --> pdb=" O ILE E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 273 removed outlier: 3.615A pdb=" N TRP E 272 " --> pdb=" O GLU E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 343 removed outlier: 3.941A pdb=" N VAL E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 356 removed outlier: 4.520A pdb=" N LEU E 351 " --> pdb=" O GLY E 347 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU E 354 " --> pdb=" O PHE E 350 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 295 through 297 removed outlier: 4.007A pdb=" N GLU A 285 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 401 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 314 through 315 removed outlier: 3.869A pdb=" N GLU A 314 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR A 406 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A 335 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 334 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 384 through 387 removed outlier: 3.824A pdb=" N GLY A 384 " --> pdb=" O LEU A 395 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 554 through 557 removed outlier: 7.537A pdb=" N LEU A 950 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE A 557 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE A 952 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL A 969 " --> pdb=" O LEU A 949 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ALA A 951 " --> pdb=" O VAL A 969 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE A 971 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY A 953 " --> pdb=" O ILE A 971 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLY A 968 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL A 987 " --> pdb=" O GLY A 968 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLY A 970 " --> pdb=" O VAL A 987 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 570 through 576 removed outlier: 7.173A pdb=" N ALA A 808 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N CYS A 575 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA A 806 " --> pdb=" O CYS A 575 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LEU A 803 " --> pdb=" O MET A 761 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N MET A 761 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 637 through 640 Processing sheet with id=AA7, first strand: chain 'A' and resid 833 through 834 removed outlier: 6.622A pdb=" N VAL A 833 " --> pdb=" O CYS A 926 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU A 895 " --> pdb=" O ILE A 925 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N CYS A 927 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 897 " --> pdb=" O CYS A 927 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU A 859 " --> pdb=" O VAL A 896 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ASP A 898 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE A 861 " --> pdb=" O ASP A 898 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 74 through 76 removed outlier: 6.491A pdb=" N TYR E 141 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU E 284 " --> pdb=" O TYR E 141 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE E 143 " --> pdb=" O TYR E 282 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N TYR E 282 " --> pdb=" O ILE E 143 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 91 removed outlier: 3.588A pdb=" N THR E 201 " --> pdb=" O GLU E 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 91 removed outlier: 4.388A pdb=" N LYS E 297 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ASN E 301 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N VAL E 205 " --> pdb=" O ASN E 301 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 181 through 182 removed outlier: 6.484A pdb=" N ILE E 186 " --> pdb=" O VAL E 242 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1287 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: 3.74 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3425 1.34 - 1.47: 2800 1.47 - 1.59: 5031 1.59 - 1.71: 0 1.71 - 1.84: 75 Bond restraints: 11331 Sorted by residual: bond pdb=" C1 NAG E 403 " pdb=" O5 NAG E 403 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.90e+00 bond pdb=" CG1 ILE A1113 " pdb=" CD1 ILE A1113 " ideal model delta sigma weight residual 1.513 1.424 0.089 3.90e-02 6.57e+02 5.19e+00 bond pdb=" CB ILE A1040 " pdb=" CG2 ILE A1040 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.27e+00 bond pdb=" C1 NAG E 404 " pdb=" O5 NAG E 404 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C GLN E 357 " pdb=" N PRO E 358 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.09e+00 ... (remaining 11326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 14824 2.63 - 5.27: 454 5.27 - 7.90: 68 7.90 - 10.53: 16 10.53 - 13.16: 4 Bond angle restraints: 15366 Sorted by residual: angle pdb=" C SER E 85 " pdb=" N THR E 86 " pdb=" CA THR E 86 " ideal model delta sigma weight residual 121.54 131.00 -9.46 1.91e+00 2.74e-01 2.45e+01 angle pdb=" C ALA A 735 " pdb=" N ASN A 736 " pdb=" CA ASN A 736 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" N PHE A1183 " pdb=" CA PHE A1183 " pdb=" C PHE A1183 " ideal model delta sigma weight residual 109.81 120.47 -10.66 2.21e+00 2.05e-01 2.33e+01 angle pdb=" C GLY A 816 " pdb=" N VAL A 817 " pdb=" CA VAL A 817 " ideal model delta sigma weight residual 120.33 124.16 -3.83 8.00e-01 1.56e+00 2.29e+01 angle pdb=" C LYS A 799 " pdb=" N ASN A 800 " pdb=" CA ASN A 800 " ideal model delta sigma weight residual 122.82 129.51 -6.69 1.42e+00 4.96e-01 2.22e+01 ... (remaining 15361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.49: 6214 14.49 - 28.97: 457 28.97 - 43.46: 107 43.46 - 57.95: 10 57.95 - 72.43: 7 Dihedral angle restraints: 6795 sinusoidal: 2772 harmonic: 4023 Sorted by residual: dihedral pdb=" CA THR A1158 " pdb=" C THR A1158 " pdb=" N LYS A1159 " pdb=" CA LYS A1159 " ideal model delta harmonic sigma weight residual 180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CB CYS E 176 " pdb=" SG CYS E 176 " pdb=" SG CYS E 190 " pdb=" CB CYS E 190 " ideal model delta sinusoidal sigma weight residual 93.00 49.20 43.80 1 1.00e+01 1.00e-02 2.67e+01 dihedral pdb=" CA GLN E 270 " pdb=" C GLN E 270 " pdb=" N VAL E 271 " pdb=" CA VAL E 271 " ideal model delta harmonic sigma weight residual 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 6792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1426 0.075 - 0.150: 283 0.150 - 0.225: 35 0.225 - 0.300: 6 0.300 - 0.375: 1 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CB ILE A 861 " pdb=" CA ILE A 861 " pdb=" CG1 ILE A 861 " pdb=" CG2 ILE A 861 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE A 443 " pdb=" CA ILE A 443 " pdb=" CG1 ILE A 443 " pdb=" CG2 ILE A 443 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA PHE A1183 " pdb=" N PHE A1183 " pdb=" C PHE A1183 " pdb=" CB PHE A1183 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1748 not shown) Planarity restraints: 1928 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 336 " -0.020 2.00e-02 2.50e+03 2.13e-02 9.08e+00 pdb=" CG TYR E 336 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR E 336 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR E 336 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 336 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR E 336 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR E 336 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 336 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 506 " 0.047 5.00e-02 4.00e+02 7.18e-02 8.24e+00 pdb=" N PRO A 507 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 507 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 507 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1212 " 0.045 5.00e-02 4.00e+02 6.67e-02 7.12e+00 pdb=" N PRO A1213 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A1213 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1213 " 0.038 5.00e-02 4.00e+02 ... (remaining 1925 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2183 2.77 - 3.31: 10264 3.31 - 3.84: 18738 3.84 - 4.37: 22137 4.37 - 4.90: 37377 Nonbonded interactions: 90699 Sorted by model distance: nonbonded pdb=" O VAL A1136 " pdb=" OG1 THR A1140 " model vdw 2.243 3.040 nonbonded pdb=" OG SER A 930 " pdb=" OE1 GLN A 933 " model vdw 2.252 3.040 nonbonded pdb=" OG SER A 509 " pdb=" O ASN A1050 " model vdw 2.281 3.040 nonbonded pdb=" OG SER E 122 " pdb=" OD1 ASN E 301 " model vdw 2.296 3.040 nonbonded pdb=" O ASN A 624 " pdb=" OG1 THR A 628 " model vdw 2.300 3.040 ... (remaining 90694 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.830 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.006 0.089 11337 Z= 0.256 Angle : 1.070 13.164 15382 Z= 0.555 Chirality : 0.060 0.375 1751 Planarity : 0.007 0.072 1925 Dihedral : 11.061 72.433 4195 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.41 % Allowed : 4.20 % Favored : 95.39 % 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: -5.01 (0.17), residues: 1366 helix: -3.74 (0.13), residues: 532 sheet: -3.08 (0.33), residues: 181 loop : -2.94 (0.21), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP E 247 HIS 0.014 0.002 HIS A1125 PHE 0.029 0.003 PHE A1120 TYR 0.045 0.003 TYR E 336 ARG 0.005 0.001 ARG A 272 Details of bonding type rmsd link_NAG-ASN : bond 0.00652 ( 3) link_NAG-ASN : angle 2.95059 ( 9) link_BETA1-4 : bond 0.00096 ( 1) link_BETA1-4 : angle 2.21092 ( 3) hydrogen bonds : bond 0.14300 ( 441) hydrogen bonds : angle 11.15405 ( 1287) SS BOND : bond 0.01242 ( 2) SS BOND : angle 3.23627 ( 4) covalent geometry : bond 0.00585 (11331) covalent geometry : angle 1.06670 (15366) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 269 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASN cc_start: 0.5815 (t0) cc_final: 0.5112 (t0) REVERT: A 263 MET cc_start: 0.7232 (ttt) cc_final: 0.6941 (ttp) REVERT: A 280 ASN cc_start: 0.6729 (t0) cc_final: 0.6357 (m-40) REVERT: A 573 LYS cc_start: 0.8166 (tptt) cc_final: 0.7782 (tptp) REVERT: A 745 HIS cc_start: 0.7075 (m90) cc_final: 0.6645 (m170) REVERT: A 867 ASP cc_start: 0.8102 (t70) cc_final: 0.7847 (t0) REVERT: A 977 MET cc_start: 0.6711 (tpt) cc_final: 0.6432 (tpp) REVERT: E 69 LYS cc_start: 0.8242 (tppt) cc_final: 0.7710 (tttt) REVERT: E 94 LYS cc_start: 0.8411 (tttt) cc_final: 0.8176 (ttmm) REVERT: E 98 LYS cc_start: 0.8052 (mttm) cc_final: 0.7613 (mttp) REVERT: E 104 LYS cc_start: 0.8387 (pttt) cc_final: 0.7998 (tttm) REVERT: E 107 ASN cc_start: 0.8154 (m-40) cc_final: 0.7917 (m-40) REVERT: E 273 MET cc_start: 0.8942 (mmm) cc_final: 0.8546 (mmm) outliers start: 5 outliers final: 1 residues processed: 273 average time/residue: 0.2783 time to fit residues: 102.2355 Evaluate side-chains 127 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.8980 chunk 103 optimal weight: 0.0270 chunk 57 optimal weight: 50.0000 chunk 35 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 ASN A 445 ASN A 839 GLN A 881 ASN A 963 GLN A 966 HIS A1038 GLN E 126 GLN E 131 ASN E 155 GLN ** E 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.192632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140651 restraints weight = 14569.112| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 3.91 r_work: 0.3385 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11337 Z= 0.163 Angle : 0.706 9.296 15382 Z= 0.367 Chirality : 0.046 0.151 1751 Planarity : 0.006 0.059 1925 Dihedral : 6.228 41.119 1565 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.29 % Allowed : 9.30 % Favored : 87.41 % 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: -3.48 (0.20), residues: 1366 helix: -1.87 (0.20), residues: 532 sheet: -2.48 (0.35), residues: 177 loop : -2.61 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 247 HIS 0.006 0.001 HIS A 745 PHE 0.023 0.002 PHE A1067 TYR 0.029 0.002 TYR E 336 ARG 0.005 0.001 ARG A 755 Details of bonding type rmsd link_NAG-ASN : bond 0.00572 ( 3) link_NAG-ASN : angle 2.21301 ( 9) link_BETA1-4 : bond 0.00019 ( 1) link_BETA1-4 : angle 1.95185 ( 3) hydrogen bonds : bond 0.04664 ( 441) hydrogen bonds : angle 6.62422 ( 1287) SS BOND : bond 0.00642 ( 2) SS BOND : angle 1.65642 ( 4) covalent geometry : bond 0.00361 (11331) covalent geometry : angle 0.70375 (15366) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 135 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8083 (ttt) cc_final: 0.7624 (ttp) REVERT: A 573 LYS cc_start: 0.7962 (tptt) cc_final: 0.7744 (tptp) REVERT: A 745 HIS cc_start: 0.7258 (m90) cc_final: 0.6958 (m170) REVERT: A 961 MET cc_start: 0.8112 (ttp) cc_final: 0.7877 (ttp) REVERT: A 977 MET cc_start: 0.6987 (tpt) cc_final: 0.6369 (tpp) REVERT: A 1041 MET cc_start: 0.8242 (mpt) cc_final: 0.7928 (mpt) REVERT: E 69 LYS cc_start: 0.8407 (tppt) cc_final: 0.8093 (ttpt) REVERT: E 94 LYS cc_start: 0.8730 (tttt) cc_final: 0.8426 (tppt) REVERT: E 98 LYS cc_start: 0.8524 (mttm) cc_final: 0.8107 (mttp) REVERT: E 273 MET cc_start: 0.8942 (mmm) cc_final: 0.8688 (mmm) REVERT: E 317 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.7473 (p90) outliers start: 40 outliers final: 21 residues processed: 166 average time/residue: 0.2526 time to fit residues: 61.9444 Evaluate side-chains 128 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 604 LYS Chi-restraints excluded: chain A residue 919 LYS Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1067 PHE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 335 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 85 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 ASN A1100 ASN A1131 HIS A1239 GLN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.190936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.129548 restraints weight = 14610.688| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.89 r_work: 0.3378 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11337 Z= 0.162 Angle : 0.665 8.527 15382 Z= 0.345 Chirality : 0.046 0.158 1751 Planarity : 0.005 0.047 1925 Dihedral : 5.695 32.411 1563 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.29 % Allowed : 11.03 % Favored : 85.68 % 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: -2.90 (0.21), residues: 1366 helix: -1.20 (0.21), residues: 548 sheet: -2.37 (0.37), residues: 178 loop : -2.40 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 247 HIS 0.004 0.001 HIS A 745 PHE 0.033 0.002 PHE E 89 TYR 0.023 0.002 TYR E 336 ARG 0.003 0.000 ARG E 230 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 3) link_NAG-ASN : angle 2.18903 ( 9) link_BETA1-4 : bond 0.00109 ( 1) link_BETA1-4 : angle 1.99663 ( 3) hydrogen bonds : bond 0.04380 ( 441) hydrogen bonds : angle 5.98753 ( 1287) SS BOND : bond 0.00721 ( 2) SS BOND : angle 1.64626 ( 4) covalent geometry : bond 0.00365 (11331) covalent geometry : angle 0.66188 (15366) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 128 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8062 (ttt) cc_final: 0.7598 (ttp) REVERT: A 573 LYS cc_start: 0.8131 (tptt) cc_final: 0.7739 (tptp) REVERT: A 580 HIS cc_start: 0.7352 (t-90) cc_final: 0.7135 (t70) REVERT: A 629 LEU cc_start: 0.8515 (mt) cc_final: 0.8253 (mt) REVERT: A 745 HIS cc_start: 0.7327 (m90) cc_final: 0.6963 (m170) REVERT: A 761 MET cc_start: 0.1074 (ptt) cc_final: 0.0147 (ppp) REVERT: A 961 MET cc_start: 0.8209 (ttp) cc_final: 0.7940 (ttp) REVERT: A 977 MET cc_start: 0.7025 (tpt) cc_final: 0.6429 (tpp) REVERT: A 1041 MET cc_start: 0.8482 (mpt) cc_final: 0.7937 (mpt) REVERT: E 48 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7578 (tt) REVERT: E 94 LYS cc_start: 0.8733 (tttt) cc_final: 0.8312 (tppt) REVERT: E 98 LYS cc_start: 0.8504 (mttm) cc_final: 0.8076 (mttp) REVERT: E 247 TRP cc_start: 0.7838 (OUTLIER) cc_final: 0.7552 (p-90) outliers start: 40 outliers final: 21 residues processed: 160 average time/residue: 0.2881 time to fit residues: 70.5889 Evaluate side-chains 125 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 549 GLU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 919 LYS Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 335 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 42 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1239 GLN ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.191361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127704 restraints weight = 14356.347| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.78 r_work: 0.3388 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11337 Z= 0.137 Angle : 0.630 7.959 15382 Z= 0.324 Chirality : 0.045 0.221 1751 Planarity : 0.004 0.045 1925 Dihedral : 5.331 28.546 1563 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.21 % Allowed : 12.51 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.22), residues: 1366 helix: -0.81 (0.22), residues: 555 sheet: -2.17 (0.37), residues: 184 loop : -2.20 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 247 HIS 0.005 0.001 HIS A 745 PHE 0.045 0.002 PHE E 89 TYR 0.017 0.001 TYR E 336 ARG 0.002 0.000 ARG E 29 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 3) link_NAG-ASN : angle 2.01184 ( 9) link_BETA1-4 : bond 0.00504 ( 1) link_BETA1-4 : angle 1.82479 ( 3) hydrogen bonds : bond 0.04109 ( 441) hydrogen bonds : angle 5.56438 ( 1287) SS BOND : bond 0.00619 ( 2) SS BOND : angle 1.56974 ( 4) covalent geometry : bond 0.00307 (11331) covalent geometry : angle 0.62698 (15366) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8275 (ttt) cc_final: 0.7752 (ttp) REVERT: A 447 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8063 (mt0) REVERT: A 580 HIS cc_start: 0.7370 (t-90) cc_final: 0.7007 (t70) REVERT: A 745 HIS cc_start: 0.7468 (m90) cc_final: 0.7012 (m170) REVERT: A 761 MET cc_start: 0.1194 (ptt) cc_final: 0.0225 (ppp) REVERT: A 961 MET cc_start: 0.8206 (ttp) cc_final: 0.7990 (ttp) REVERT: A 977 MET cc_start: 0.6919 (tpt) cc_final: 0.6210 (tpp) REVERT: E 48 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7512 (tt) REVERT: E 94 LYS cc_start: 0.8836 (tttt) cc_final: 0.8359 (tppt) REVERT: E 98 LYS cc_start: 0.8687 (mttm) cc_final: 0.8275 (mttp) REVERT: E 230 ARG cc_start: 0.7801 (ttt180) cc_final: 0.7598 (ttt90) REVERT: E 247 TRP cc_start: 0.7933 (OUTLIER) cc_final: 0.7630 (p-90) outliers start: 39 outliers final: 24 residues processed: 155 average time/residue: 0.3506 time to fit residues: 84.6505 Evaluate side-chains 132 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 335 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 67 optimal weight: 0.0030 chunk 85 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 17 optimal weight: 40.0000 chunk 134 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 839 GLN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.189144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126775 restraints weight = 14600.225| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.99 r_work: 0.3342 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11337 Z= 0.171 Angle : 0.645 8.212 15382 Z= 0.331 Chirality : 0.046 0.163 1751 Planarity : 0.004 0.046 1925 Dihedral : 5.286 23.557 1563 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.37 % Allowed : 13.33 % Favored : 83.29 % 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: -2.29 (0.22), residues: 1366 helix: -0.60 (0.22), residues: 557 sheet: -2.09 (0.37), residues: 184 loop : -2.15 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 247 HIS 0.006 0.001 HIS A 745 PHE 0.038 0.002 PHE E 89 TYR 0.017 0.001 TYR A1023 ARG 0.003 0.000 ARG A1007 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 3) link_NAG-ASN : angle 2.15397 ( 9) link_BETA1-4 : bond 0.00087 ( 1) link_BETA1-4 : angle 2.10307 ( 3) hydrogen bonds : bond 0.04164 ( 441) hydrogen bonds : angle 5.47413 ( 1287) SS BOND : bond 0.00675 ( 2) SS BOND : angle 1.74796 ( 4) covalent geometry : bond 0.00396 (11331) covalent geometry : angle 0.64181 (15366) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8276 (ttt) cc_final: 0.7746 (ttp) REVERT: A 447 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8147 (mt0) REVERT: A 580 HIS cc_start: 0.7406 (t-90) cc_final: 0.7033 (t70) REVERT: A 629 LEU cc_start: 0.8445 (mt) cc_final: 0.8209 (mt) REVERT: A 745 HIS cc_start: 0.7535 (m90) cc_final: 0.6973 (m170) REVERT: A 761 MET cc_start: 0.1509 (ptt) cc_final: 0.0402 (ppp) REVERT: A 977 MET cc_start: 0.7056 (tpt) cc_final: 0.6296 (tpp) REVERT: E 48 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7569 (tt) REVERT: E 94 LYS cc_start: 0.8859 (tttt) cc_final: 0.8363 (tppt) REVERT: E 98 LYS cc_start: 0.8692 (mttm) cc_final: 0.8252 (mttp) REVERT: E 171 ASP cc_start: 0.7779 (t0) cc_final: 0.7465 (t0) REVERT: E 230 ARG cc_start: 0.7815 (ttt180) cc_final: 0.7592 (ttt90) REVERT: E 247 TRP cc_start: 0.8121 (OUTLIER) cc_final: 0.7770 (p-90) outliers start: 41 outliers final: 24 residues processed: 147 average time/residue: 0.2088 time to fit residues: 46.6065 Evaluate side-chains 131 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1052 PHE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1220 ASP Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 335 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 83 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 0.0050 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 822 HIS ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.191593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.139886 restraints weight = 14593.887| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.83 r_work: 0.3340 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11337 Z= 0.121 Angle : 0.608 7.925 15382 Z= 0.309 Chirality : 0.044 0.182 1751 Planarity : 0.004 0.045 1925 Dihedral : 5.072 24.426 1563 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.05 % Allowed : 14.24 % Favored : 82.72 % 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: -2.06 (0.23), residues: 1366 helix: -0.36 (0.23), residues: 557 sheet: -2.01 (0.38), residues: 182 loop : -2.07 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 247 HIS 0.005 0.001 HIS A 745 PHE 0.023 0.001 PHE E 89 TYR 0.016 0.001 TYR A 913 ARG 0.003 0.000 ARG A1007 Details of bonding type rmsd link_NAG-ASN : bond 0.00446 ( 3) link_NAG-ASN : angle 1.89899 ( 9) link_BETA1-4 : bond 0.00256 ( 1) link_BETA1-4 : angle 1.67367 ( 3) hydrogen bonds : bond 0.03896 ( 441) hydrogen bonds : angle 5.26157 ( 1287) SS BOND : bond 0.00564 ( 2) SS BOND : angle 1.42959 ( 4) covalent geometry : bond 0.00270 (11331) covalent geometry : angle 0.60590 (15366) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8219 (ttt) cc_final: 0.7645 (ttp) REVERT: A 400 MET cc_start: 0.7189 (mpp) cc_final: 0.6846 (mpp) REVERT: A 447 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: A 580 HIS cc_start: 0.7401 (t-90) cc_final: 0.7124 (t70) REVERT: A 629 LEU cc_start: 0.8462 (mt) cc_final: 0.8201 (mt) REVERT: A 745 HIS cc_start: 0.7389 (m90) cc_final: 0.6993 (m170) REVERT: A 761 MET cc_start: 0.1608 (ptt) cc_final: 0.0511 (ppp) REVERT: A 977 MET cc_start: 0.7159 (tpt) cc_final: 0.6658 (tpp) REVERT: E 48 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7537 (tt) REVERT: E 94 LYS cc_start: 0.8788 (tttt) cc_final: 0.8349 (tppt) REVERT: E 98 LYS cc_start: 0.8617 (mttm) cc_final: 0.8227 (mttp) REVERT: E 121 GLN cc_start: 0.8300 (tt0) cc_final: 0.7672 (pt0) REVERT: E 171 ASP cc_start: 0.7645 (t0) cc_final: 0.7369 (t0) REVERT: E 247 TRP cc_start: 0.7854 (OUTLIER) cc_final: 0.7492 (p-90) outliers start: 37 outliers final: 24 residues processed: 147 average time/residue: 0.2115 time to fit residues: 47.1594 Evaluate side-chains 127 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 564 THR Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 919 LYS Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1220 ASP Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 335 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 26 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 0.0370 chunk 76 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.190857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.126223 restraints weight = 14699.534| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.26 r_work: 0.3379 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11337 Z= 0.130 Angle : 0.608 8.284 15382 Z= 0.310 Chirality : 0.044 0.173 1751 Planarity : 0.004 0.045 1925 Dihedral : 4.963 22.969 1563 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.96 % Allowed : 15.06 % Favored : 81.98 % 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: -1.94 (0.23), residues: 1366 helix: -0.24 (0.23), residues: 556 sheet: -1.97 (0.38), residues: 183 loop : -2.01 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 247 HIS 0.004 0.001 HIS A 745 PHE 0.020 0.002 PHE A 626 TYR 0.016 0.001 TYR A 913 ARG 0.002 0.000 ARG A1007 Details of bonding type rmsd link_NAG-ASN : bond 0.00492 ( 3) link_NAG-ASN : angle 1.94611 ( 9) link_BETA1-4 : bond 0.00210 ( 1) link_BETA1-4 : angle 1.76603 ( 3) hydrogen bonds : bond 0.03876 ( 441) hydrogen bonds : angle 5.17184 ( 1287) SS BOND : bond 0.00599 ( 2) SS BOND : angle 1.40964 ( 4) covalent geometry : bond 0.00295 (11331) covalent geometry : angle 0.60518 (15366) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 1.987 Fit side-chains revert: symmetry clash REVERT: A 263 MET cc_start: 0.8275 (ttt) cc_final: 0.7608 (ttp) REVERT: A 447 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8061 (mt0) REVERT: A 629 LEU cc_start: 0.8457 (mt) cc_final: 0.8212 (mt) REVERT: A 761 MET cc_start: 0.1631 (ptt) cc_final: 0.0515 (ppp) REVERT: A 977 MET cc_start: 0.7140 (tpt) cc_final: 0.6564 (tpp) REVERT: E 48 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7498 (tt) REVERT: E 94 LYS cc_start: 0.8868 (tttt) cc_final: 0.8365 (tppt) REVERT: E 98 LYS cc_start: 0.8728 (mttm) cc_final: 0.8293 (mttp) REVERT: E 121 GLN cc_start: 0.8382 (tt0) cc_final: 0.7672 (pt0) REVERT: E 171 ASP cc_start: 0.7837 (t0) cc_final: 0.7534 (t0) REVERT: E 247 TRP cc_start: 0.8057 (OUTLIER) cc_final: 0.7630 (p-90) REVERT: E 299 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8325 (tt0) outliers start: 36 outliers final: 26 residues processed: 132 average time/residue: 0.2296 time to fit residues: 47.7704 Evaluate side-chains 124 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1220 ASP Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 317 PHE Chi-restraints excluded: chain E residue 335 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 110 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 123 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 70 optimal weight: 9.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 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 = 0.4310 r_free = 0.4310 target = 0.186733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.125384 restraints weight = 14508.878| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.80 r_work: 0.3336 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11337 Z= 0.203 Angle : 0.660 11.277 15382 Z= 0.337 Chirality : 0.046 0.249 1751 Planarity : 0.004 0.048 1925 Dihedral : 5.122 21.831 1563 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.05 % Allowed : 15.56 % Favored : 81.40 % 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: -1.95 (0.23), residues: 1366 helix: -0.33 (0.22), residues: 556 sheet: -1.89 (0.39), residues: 175 loop : -1.97 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 247 HIS 0.008 0.001 HIS A 745 PHE 0.021 0.002 PHE A 626 TYR 0.019 0.001 TYR A1023 ARG 0.005 0.000 ARG E 112 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 3) link_NAG-ASN : angle 2.27711 ( 9) link_BETA1-4 : bond 0.00182 ( 1) link_BETA1-4 : angle 2.21760 ( 3) hydrogen bonds : bond 0.04223 ( 441) hydrogen bonds : angle 5.22750 ( 1287) SS BOND : bond 0.00790 ( 2) SS BOND : angle 1.93553 ( 4) covalent geometry : bond 0.00476 (11331) covalent geometry : angle 0.65678 (15366) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8360 (ttt) cc_final: 0.7817 (ttp) REVERT: A 400 MET cc_start: 0.7133 (mpp) cc_final: 0.6864 (mpp) REVERT: A 447 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.8155 (mt0) REVERT: A 629 LEU cc_start: 0.8425 (mt) cc_final: 0.8143 (mt) REVERT: A 761 MET cc_start: 0.1646 (ptt) cc_final: 0.0550 (ppp) REVERT: A 977 MET cc_start: 0.7220 (tpt) cc_final: 0.6629 (tpp) REVERT: A 1024 MET cc_start: 0.8483 (tpp) cc_final: 0.8189 (mmm) REVERT: E 37 GLN cc_start: 0.8625 (tt0) cc_final: 0.8422 (tt0) REVERT: E 48 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7550 (tt) REVERT: E 94 LYS cc_start: 0.8903 (tttt) cc_final: 0.8397 (tppt) REVERT: E 121 GLN cc_start: 0.8233 (tt0) cc_final: 0.7535 (pt0) REVERT: E 171 ASP cc_start: 0.7847 (t0) cc_final: 0.7533 (t0) REVERT: E 247 TRP cc_start: 0.8255 (OUTLIER) cc_final: 0.7922 (p-90) outliers start: 37 outliers final: 25 residues processed: 126 average time/residue: 0.2801 time to fit residues: 57.7038 Evaluate side-chains 120 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1220 ASP Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 335 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 109 optimal weight: 0.7980 chunk 23 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 134 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 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 = 0.4339 r_free = 0.4339 target = 0.189268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124388 restraints weight = 14636.943| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.88 r_work: 0.3376 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11337 Z= 0.132 Angle : 0.612 8.474 15382 Z= 0.311 Chirality : 0.044 0.165 1751 Planarity : 0.004 0.046 1925 Dihedral : 4.946 23.310 1563 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 2.80 % Allowed : 15.80 % Favored : 81.40 % 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: -1.74 (0.23), residues: 1366 helix: -0.13 (0.23), residues: 556 sheet: -1.81 (0.39), residues: 176 loop : -1.87 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 247 HIS 0.005 0.001 HIS A 745 PHE 0.018 0.001 PHE A 626 TYR 0.016 0.001 TYR A 519 ARG 0.003 0.000 ARG A1007 Details of bonding type rmsd link_NAG-ASN : bond 0.00448 ( 3) link_NAG-ASN : angle 1.88345 ( 9) link_BETA1-4 : bond 0.00267 ( 1) link_BETA1-4 : angle 1.72689 ( 3) hydrogen bonds : bond 0.03907 ( 441) hydrogen bonds : angle 5.07152 ( 1287) SS BOND : bond 0.00624 ( 2) SS BOND : angle 1.42089 ( 4) covalent geometry : bond 0.00302 (11331) covalent geometry : angle 0.60957 (15366) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8387 (ttt) cc_final: 0.7787 (ttp) REVERT: A 400 MET cc_start: 0.7066 (mpp) cc_final: 0.6787 (mpp) REVERT: A 447 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8000 (mt0) REVERT: A 629 LEU cc_start: 0.8424 (mt) cc_final: 0.8158 (mt) REVERT: A 761 MET cc_start: 0.1634 (ptt) cc_final: 0.0532 (ppp) REVERT: A 977 MET cc_start: 0.7171 (tpt) cc_final: 0.6527 (tpp) REVERT: E 48 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7530 (tt) REVERT: E 94 LYS cc_start: 0.8841 (tttt) cc_final: 0.8378 (tppt) REVERT: E 98 LYS cc_start: 0.8697 (mttm) cc_final: 0.8269 (mttp) REVERT: E 121 GLN cc_start: 0.8252 (tt0) cc_final: 0.7585 (pt0) REVERT: E 171 ASP cc_start: 0.7793 (t0) cc_final: 0.7486 (t0) REVERT: E 247 TRP cc_start: 0.8076 (OUTLIER) cc_final: 0.7712 (p-90) REVERT: E 335 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8305 (mt) outliers start: 34 outliers final: 22 residues processed: 126 average time/residue: 0.2646 time to fit residues: 53.3498 Evaluate side-chains 121 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 447 GLN Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1220 ASP Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 116 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 30 optimal weight: 0.2980 chunk 61 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 83 optimal weight: 0.0770 chunk 38 optimal weight: 0.0070 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.191903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.139402 restraints weight = 14525.235| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 3.58 r_work: 0.3369 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11337 Z= 0.114 Angle : 0.605 8.472 15382 Z= 0.306 Chirality : 0.044 0.198 1751 Planarity : 0.004 0.045 1925 Dihedral : 4.811 22.448 1563 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.30 % Allowed : 16.54 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.60 (0.23), residues: 1366 helix: 0.07 (0.23), residues: 551 sheet: -1.71 (0.39), residues: 174 loop : -1.87 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 247 HIS 0.006 0.001 HIS A 745 PHE 0.016 0.001 PHE A 626 TYR 0.017 0.001 TYR A 519 ARG 0.002 0.000 ARG A1007 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 3) link_NAG-ASN : angle 1.68084 ( 9) link_BETA1-4 : bond 0.00245 ( 1) link_BETA1-4 : angle 1.50031 ( 3) hydrogen bonds : bond 0.03745 ( 441) hydrogen bonds : angle 4.96224 ( 1287) SS BOND : bond 0.00539 ( 2) SS BOND : angle 1.38084 ( 4) covalent geometry : bond 0.00252 (11331) covalent geometry : angle 0.60310 (15366) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2732 Ramachandran restraints generated. 1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 MET cc_start: 0.8214 (ttt) cc_final: 0.7552 (ttp) REVERT: A 400 MET cc_start: 0.6983 (mpp) cc_final: 0.6695 (mpp) REVERT: A 629 LEU cc_start: 0.8390 (mt) cc_final: 0.8118 (mt) REVERT: A 761 MET cc_start: 0.1723 (ptt) cc_final: 0.0617 (ppp) REVERT: A 977 MET cc_start: 0.7158 (tpt) cc_final: 0.6707 (tpp) REVERT: E 48 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7499 (tt) REVERT: E 94 LYS cc_start: 0.8755 (tttt) cc_final: 0.8332 (tppt) REVERT: E 98 LYS cc_start: 0.8555 (mttm) cc_final: 0.8165 (mttp) REVERT: E 121 GLN cc_start: 0.8216 (tt0) cc_final: 0.7568 (pt0) REVERT: E 247 TRP cc_start: 0.7817 (OUTLIER) cc_final: 0.7489 (p-90) outliers start: 28 outliers final: 21 residues processed: 123 average time/residue: 0.2233 time to fit residues: 43.2069 Evaluate side-chains 122 residues out of total 1215 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 809 ILE Chi-restraints excluded: chain A residue 845 ILE Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 952 ILE Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1045 THR Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1220 ASP Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 222 ILE Chi-restraints excluded: chain E residue 247 TRP Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 317 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 22 optimal weight: 0.0270 chunk 2 optimal weight: 0.8980 chunk 130 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 85 optimal weight: 0.0870 chunk 131 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN ** E 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.190485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.139349 restraints weight = 14641.742| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.88 r_work: 0.3335 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11337 Z= 0.133 Angle : 0.612 9.198 15382 Z= 0.310 Chirality : 0.044 0.189 1751 Planarity : 0.004 0.046 1925 Dihedral : 4.803 23.540 1563 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.06 % Allowed : 16.87 % Favored : 81.07 % 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: -1.54 (0.23), residues: 1366 helix: 0.14 (0.23), residues: 551 sheet: -1.72 (0.39), residues: 180 loop : -1.85 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 247 HIS 0.005 0.001 HIS A 745 PHE 0.016 0.001 PHE A 626 TYR 0.016 0.001 TYR A 519 ARG 0.002 0.000 ARG A 755 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 3) link_NAG-ASN : angle 1.78347 ( 9) link_BETA1-4 : bond 0.00152 ( 1) link_BETA1-4 : angle 1.71916 ( 3) hydrogen bonds : bond 0.03812 ( 441) hydrogen bonds : angle 4.92680 ( 1287) SS BOND : bond 0.00558 ( 2) SS BOND : angle 1.55819 ( 4) covalent geometry : bond 0.00305 (11331) covalent geometry : angle 0.60988 (15366) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8688.05 seconds wall clock time: 158 minutes 10.53 seconds (9490.53 seconds total)