Starting phenix.real_space_refine on Sat Aug 23 12:28:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bdc_44448/08_2025/9bdc_44448.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bdc_44448/08_2025/9bdc_44448.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bdc_44448/08_2025/9bdc_44448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bdc_44448/08_2025/9bdc_44448.map" model { file = "/net/cci-nas-00/data/ceres_data/9bdc_44448/08_2025/9bdc_44448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bdc_44448/08_2025/9bdc_44448.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 61 5.49 5 S 59 5.16 5 C 7503 2.51 5 N 2128 2.21 5 O 2275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12026 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1625 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1534 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 1, 'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "E" Number of atoms: 7607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 7607 Classifications: {'peptide': 990} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 68, 'TRANS': 921} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 294 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 10, 'HIS:plan': 3, 'ARG:plan': 11, 'GLU:plan': 14} Unresolved non-hydrogen planarities: 200 Chain: "N" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 473 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain breaks: 1 Chain: "R" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 592 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Time building chain proxies: 2.51, per 1000 atoms: 0.21 Number of scatterers: 12026 At special positions: 0 Unit cell: (106.854, 129.394, 106.854, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 P 61 15.00 O 2275 8.00 N 2128 7.00 C 7503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 351.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2664 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 12 sheets defined 58.8% alpha, 7.8% beta 25 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 239 through 245 removed outlier: 3.673A pdb=" N LYS A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.533A pdb=" N TYR A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N MET A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 352 removed outlier: 3.517A pdb=" N ASN A 352 " --> pdb=" O TYR A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.888A pdb=" N ASP A 358 " --> pdb=" O THR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 375 Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 411 through 421 removed outlier: 3.779A pdb=" N TYR A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 444 removed outlier: 3.930A pdb=" N TYR A 431 " --> pdb=" O VAL A 427 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 160 through 166 Processing helix chain 'B' and resid 208 through 222 removed outlier: 3.713A pdb=" N LYS B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 262 Processing helix chain 'B' and resid 277 through 285 removed outlier: 3.539A pdb=" N VAL B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 321 through 331 Processing helix chain 'B' and resid 337 through 355 removed outlier: 5.557A pdb=" N SER B 343 " --> pdb=" O GLU B 339 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 237 Processing helix chain 'E' and resid 238 through 252 removed outlier: 3.554A pdb=" N GLN E 252 " --> pdb=" O VAL E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 257 removed outlier: 4.297A pdb=" N LYS E 257 " --> pdb=" O ARG E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 274 removed outlier: 3.697A pdb=" N TYR E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLN E 274 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 291 removed outlier: 3.621A pdb=" N GLY E 291 " --> pdb=" O VAL E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 309 Processing helix chain 'E' and resid 312 through 325 removed outlier: 4.366A pdb=" N GLN E 322 " --> pdb=" O ARG E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 328 No H-bonds generated for 'chain 'E' and resid 326 through 328' Processing helix chain 'E' and resid 331 through 336 removed outlier: 3.621A pdb=" N THR E 335 " --> pdb=" O GLN E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 353 removed outlier: 3.593A pdb=" N LYS E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 409 removed outlier: 3.882A pdb=" N ALA E 409 " --> pdb=" O HIS E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 462 Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 475 through 489 Processing helix chain 'E' and resid 497 through 521 removed outlier: 4.187A pdb=" N GLN E 517 " --> pdb=" O VAL E 513 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG E 518 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL E 519 " --> pdb=" O GLN E 515 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY E 521 " --> pdb=" O GLN E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 534 removed outlier: 3.738A pdb=" N ALA E 525 " --> pdb=" O GLY E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 555 Processing helix chain 'E' and resid 568 through 587 removed outlier: 3.658A pdb=" N THR E 587 " --> pdb=" O LEU E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 600 removed outlier: 3.541A pdb=" N SER E 600 " --> pdb=" O HIS E 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 597 through 600' Processing helix chain 'E' and resid 624 through 634 Processing helix chain 'E' and resid 644 through 646 No H-bonds generated for 'chain 'E' and resid 644 through 646' Processing helix chain 'E' and resid 679 through 684 Processing helix chain 'E' and resid 688 through 691 Processing helix chain 'E' and resid 692 through 704 Processing helix chain 'E' and resid 710 through 722 removed outlier: 3.610A pdb=" N LEU E 716 " --> pdb=" O ARG E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 730 Processing helix chain 'E' and resid 734 through 738 Processing helix chain 'E' and resid 756 through 789 removed outlier: 4.004A pdb=" N ARG E 760 " --> pdb=" O ALA E 756 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N HIS E 764 " --> pdb=" O ARG E 760 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N CYS E 765 " --> pdb=" O GLU E 761 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 789 " --> pdb=" O LEU E 785 " (cutoff:3.500A) Processing helix chain 'E' and resid 818 through 824 Processing helix chain 'E' and resid 836 through 850 Processing helix chain 'E' and resid 856 through 867 Processing helix chain 'E' and resid 867 through 877 Processing helix chain 'E' and resid 890 through 906 Processing helix chain 'E' and resid 925 through 935 removed outlier: 3.519A pdb=" N HIS E 930 " --> pdb=" O ASN E 926 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA E 933 " --> pdb=" O GLN E 929 " (cutoff:3.500A) Processing helix chain 'E' and resid 937 through 944 removed outlier: 3.627A pdb=" N ALA E 942 " --> pdb=" O SER E 938 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N SER E 943 " --> pdb=" O VAL E 939 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL E 944 " --> pdb=" O GLY E 940 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 973 removed outlier: 3.502A pdb=" N GLY E 958 " --> pdb=" O ASP E 954 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG E 973 " --> pdb=" O GLN E 969 " (cutoff:3.500A) Processing helix chain 'E' and resid 975 through 981 removed outlier: 3.864A pdb=" N GLN E 979 " --> pdb=" O MET E 975 " (cutoff:3.500A) Processing helix chain 'E' and resid 986 through 998 removed outlier: 3.870A pdb=" N VAL E 990 " --> pdb=" O THR E 986 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN E 992 " --> pdb=" O LYS E 988 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR E 993 " --> pdb=" O VAL E 989 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL E 998 " --> pdb=" O VAL E 994 " (cutoff:3.500A) Processing helix chain 'E' and resid 1002 through 1015 Processing helix chain 'E' and resid 1025 through 1043 removed outlier: 4.437A pdb=" N SER E1029 " --> pdb=" O VAL E1025 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS E1030 " --> pdb=" O TRP E1026 " (cutoff:3.500A) Processing helix chain 'E' and resid 1044 through 1064 removed outlier: 3.554A pdb=" N MET E1064 " --> pdb=" O LEU E1060 " (cutoff:3.500A) Processing helix chain 'E' and resid 1111 through 1117 Processing helix chain 'E' and resid 1118 through 1141 removed outlier: 3.847A pdb=" N ARG E1141 " --> pdb=" O LEU E1137 " (cutoff:3.500A) Processing helix chain 'E' and resid 1156 through 1158 No H-bonds generated for 'chain 'E' and resid 1156 through 1158' Processing helix chain 'E' and resid 1159 through 1175 Processing helix chain 'E' and resid 1178 through 1190 Processing helix chain 'E' and resid 1197 through 1209 removed outlier: 3.685A pdb=" N GLN E1203 " --> pdb=" O LEU E1199 " (cutoff:3.500A) Processing helix chain 'E' and resid 1218 through 1225 removed outlier: 3.660A pdb=" N GLN E1221 " --> pdb=" O ASP E1218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 281 through 287 removed outlier: 4.116A pdb=" N ASP A 283 " --> pdb=" O HIS A 274 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N PHE A 265 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR A 319 " --> pdb=" O LEU A 364 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N MET A 366 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 321 " --> pdb=" O MET A 366 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AA3, first strand: chain 'B' and resid 191 through 197 removed outlier: 6.711A pdb=" N VAL B 191 " --> pdb=" O ASP B 186 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ASP B 186 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER B 169 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL B 230 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE B 171 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N GLU B 232 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ILE B 173 " --> pdb=" O GLU B 232 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N TYR B 229 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N MET B 276 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU B 231 " --> pdb=" O MET B 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 411 through 415 Processing sheet with id=AA5, first strand: chain 'E' and resid 495 through 496 removed outlier: 3.516A pdb=" N GLU E 495 " --> pdb=" O LEU E 621 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 588 through 590 Processing sheet with id=AA7, first strand: chain 'E' and resid 653 through 657 removed outlier: 5.024A pdb=" N ALA E 662 " --> pdb=" O PRO E 654 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER E 660 " --> pdb=" O THR E 656 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 794 through 795 Processing sheet with id=AA9, first strand: chain 'E' and resid 798 through 800 Processing sheet with id=AB1, first strand: chain 'E' and resid 831 through 832 Processing sheet with id=AB2, first strand: chain 'E' and resid 919 through 922 Processing sheet with id=AB3, first strand: chain 'E' and resid 1069 through 1071 579 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 1.88 Time building geometry restraints manager: 0.86 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: 3094 1.34 - 1.45: 2554 1.45 - 1.57: 6571 1.57 - 1.69: 118 1.69 - 1.81: 95 Bond restraints: 12432 Sorted by residual: bond pdb=" N LEU B 261 " pdb=" CA LEU B 261 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.29e-02 6.01e+03 1.33e+01 bond pdb=" N LEU B 257 " pdb=" CA LEU B 257 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.21e-02 6.83e+03 1.20e+01 bond pdb=" CA ALA B 255 " pdb=" CB ALA B 255 " ideal model delta sigma weight residual 1.530 1.482 0.048 1.57e-02 4.06e+03 9.54e+00 bond pdb=" N CYS E 305 " pdb=" CA CYS E 305 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.44e+00 bond pdb=" N GLU E 317 " pdb=" CA GLU E 317 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.23e-02 6.61e+03 7.35e+00 ... (remaining 12427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 16563 1.58 - 3.16: 478 3.16 - 4.74: 80 4.74 - 6.33: 34 6.33 - 7.91: 9 Bond angle restraints: 17164 Sorted by residual: angle pdb=" N ILE E 316 " pdb=" CA ILE E 316 " pdb=" C ILE E 316 " ideal model delta sigma weight residual 110.42 106.31 4.11 9.60e-01 1.09e+00 1.83e+01 angle pdb=" CA MET B 256 " pdb=" C MET B 256 " pdb=" O MET B 256 " ideal model delta sigma weight residual 120.55 116.31 4.24 1.06e+00 8.90e-01 1.60e+01 angle pdb=" CA LEU B 260 " pdb=" C LEU B 260 " pdb=" O LEU B 260 " ideal model delta sigma weight residual 120.42 116.45 3.97 1.06e+00 8.90e-01 1.40e+01 angle pdb=" C THR E 315 " pdb=" N ILE E 316 " pdb=" CA ILE E 316 " ideal model delta sigma weight residual 120.56 115.85 4.71 1.26e+00 6.30e-01 1.40e+01 angle pdb=" CA TYR B 258 " pdb=" C TYR B 258 " pdb=" O TYR B 258 " ideal model delta sigma weight residual 120.82 117.21 3.61 1.05e+00 9.07e-01 1.18e+01 ... (remaining 17159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 6991 35.49 - 70.97: 333 70.97 - 106.46: 8 106.46 - 141.95: 0 141.95 - 177.43: 1 Dihedral angle restraints: 7333 sinusoidal: 3245 harmonic: 4088 Sorted by residual: dihedral pdb=" CA SER E1148 " pdb=" C SER E1148 " pdb=" N VAL E1149 " pdb=" CA VAL E1149 " ideal model delta harmonic sigma weight residual 180.00 154.80 25.20 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" C4' DT T 9 " pdb=" C3' DT T 9 " pdb=" O3' DT T 9 " pdb=" P DT T 10 " ideal model delta sinusoidal sigma weight residual 220.00 42.57 177.43 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA GLN E1035 " pdb=" C GLN E1035 " pdb=" N VAL E1036 " pdb=" CA VAL E1036 " ideal model delta harmonic sigma weight residual 180.00 161.74 18.26 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 7330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1942 0.128 - 0.256: 17 0.256 - 0.383: 0 0.383 - 0.511: 3 0.511 - 0.639: 5 Chirality restraints: 1967 Sorted by residual: chirality pdb=" P DA N -24 " pdb=" OP1 DA N -24 " pdb=" OP2 DA N -24 " pdb=" O5' DA N -24 " both_signs ideal model delta sigma weight residual True 2.35 -2.98 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" P DC T 14 " pdb=" OP1 DC T 14 " pdb=" OP2 DC T 14 " pdb=" O5' DC T 14 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" P DT N -23 " pdb=" OP1 DT N -23 " pdb=" OP2 DT N -23 " pdb=" O5' DT N -23 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.15e+00 ... (remaining 1964 not shown) Planarity restraints: 1981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 316 " -0.014 2.00e-02 2.50e+03 2.97e-02 8.83e+00 pdb=" C ILE E 316 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE E 316 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU E 317 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E1149 " -0.012 2.00e-02 2.50e+03 2.33e-02 5.43e+00 pdb=" C VAL E1149 " 0.040 2.00e-02 2.50e+03 pdb=" O VAL E1149 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS E1150 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 254 " 0.012 2.00e-02 2.50e+03 2.29e-02 5.24e+00 pdb=" C GLU B 254 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU B 254 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA B 255 " 0.013 2.00e-02 2.50e+03 ... (remaining 1978 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2909 2.80 - 3.33: 10802 3.33 - 3.85: 19806 3.85 - 4.38: 22665 4.38 - 4.90: 38060 Nonbonded interactions: 94242 Sorted by model distance: nonbonded pdb=" O LEU B 287 " pdb=" OG1 THR B 294 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR E 530 " pdb=" O PRO E 651 " model vdw 2.295 3.040 nonbonded pdb=" NH1 ARG E 563 " pdb=" OE2 GLU E 685 " model vdw 2.297 3.120 nonbonded pdb=" OG1 THR E 260 " pdb=" OD1 ASP E 262 " model vdw 2.349 3.040 nonbonded pdb=" OD1 ASP E 715 " pdb=" NH2 ARG E 790 " model vdw 2.351 3.120 ... (remaining 94237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 239 through 240 and (name N or name CA or name C or name \ O or name CB )) or resid 241 through 242 or (resid 243 and (name N or name CA or \ name C or name O or name CB )) or resid 244 through 245 or (resid 246 and (name \ N or name CA or name C or name O or name CB )) or resid 247 through 254 or (res \ id 255 through 256 and (name N or name CA or name C or name O or name CB )) or r \ esid 257 through 268 or (resid 269 and (name N or name CA or name C or name O or \ name CB )) or resid 270 through 275 or (resid 276 through 278 and (name N or na \ me CA or name C or name O or name CB )) or resid 279 through 287 or (resid 288 t \ hrough 289 and (name N or name CA or name C or name O or name CB )) or resid 290 \ through 352 or (resid 353 and (name N or name CA or name C or name O or name CB \ )) or resid 354 through 372 or (resid 373 and (name N or name CA or name C or n \ ame O or name CB )) or resid 374 through 375 or (resid 376 and (name N or name C \ A or name C or name O or name CB )) or resid 377 or (resid 378 and (name N or na \ me CA or name C or name O or name CB )) or resid 379 through 391 or (resid 392 a \ nd (name N or name CA or name C or name O or name CB )) or resid 393 through 410 \ or (resid 411 and (name N or name CA or name C or name O or name CB )) or resid \ 412 through 415 or (resid 416 through 417 and (name N or name CA or name C or n \ ame O or name CB )) or resid 418 through 419 or (resid 420 and (name N or name C \ A or name C or name O or name CB )) or resid 421 or (resid 422 through 424 and ( \ name N or name CA or name C or name O or name CB )) or resid 425 through 430 or \ (resid 431 and (name N or name CA or name C or name O or name CB )) or resid 432 \ through 441 or (resid 442 and (name N or name CA or name C or name O or name CB \ )) or resid 443 through 445)) selection = (chain 'B' and (resid 149 through 160 or (resid 161 and (name N or name CA or na \ me C or name O or name CB )) or resid 162 through 224 or (resid 225 through 226 \ and (name N or name CA or name C or name O or name CB )) or resid 227 through 30 \ 3 or (resid 304 and (name N or name CA or name C or name O or name CB )) or resi \ d 305 or (resid 313 and (name N or name CA or name C or name O or name CB )) or \ resid 314 through 332 or (resid 333 through 334 and (name N or name CA or name C \ or name O or name CB )) or resid 335 through 355)) } 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: 0.010 Normalize map: mean=0, sd=1: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.730 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4950 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 : 0.003 0.048 12432 Z= 0.190 Angle : 0.673 7.908 17164 Z= 0.371 Chirality : 0.053 0.639 1967 Planarity : 0.006 0.067 1981 Dihedral : 17.855 177.432 4669 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.18 % Allowed : 1.79 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.22), residues: 1380 helix: 1.02 (0.19), residues: 721 sheet: -0.06 (0.48), residues: 114 loop : -0.83 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E1083 TYR 0.021 0.001 TYR B 258 PHE 0.017 0.001 PHE E1044 TRP 0.011 0.001 TRP E 271 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00348 (12432) covalent geometry : angle 0.67254 (17164) hydrogen bonds : bond 0.13667 ( 647) hydrogen bonds : angle 4.84769 ( 1810) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 287 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: B 258 TYR cc_start: 0.6238 (OUTLIER) cc_final: 0.5006 (t80) REVERT: E 375 ARG cc_start: 0.6902 (ttm170) cc_final: 0.6544 (ttp-170) REVERT: E 385 SER cc_start: 0.7244 (m) cc_final: 0.6840 (t) REVERT: E 411 ARG cc_start: 0.7257 (ttm170) cc_final: 0.6996 (mtp180) REVERT: E 485 GLN cc_start: 0.6342 (mt0) cc_final: 0.6035 (mt0) REVERT: E 495 GLU cc_start: 0.6756 (pt0) cc_final: 0.6239 (pt0) REVERT: E 539 SER cc_start: 0.7594 (t) cc_final: 0.7243 (p) REVERT: E 574 GLU cc_start: 0.5975 (tt0) cc_final: 0.5760 (tt0) REVERT: E 622 LYS cc_start: 0.6720 (tttm) cc_final: 0.6420 (tttp) REVERT: E 633 LYS cc_start: 0.6736 (ttpt) cc_final: 0.6444 (tttp) REVERT: E 668 THR cc_start: 0.7425 (m) cc_final: 0.7107 (p) REVERT: E 669 LYS cc_start: 0.7159 (pttm) cc_final: 0.6828 (pttm) REVERT: E 682 GLU cc_start: 0.6184 (tt0) cc_final: 0.5917 (tt0) REVERT: E 685 GLU cc_start: 0.6227 (mt-10) cc_final: 0.5999 (mt-10) REVERT: E 781 TYR cc_start: 0.6129 (m-80) cc_final: 0.5588 (m-80) REVERT: E 800 MET cc_start: 0.7249 (ptp) cc_final: 0.6989 (ptp) REVERT: E 814 ASN cc_start: 0.7435 (p0) cc_final: 0.7218 (p0) REVERT: E 816 LEU cc_start: 0.7131 (mt) cc_final: 0.6586 (mp) REVERT: E 831 ARG cc_start: 0.6541 (mtt-85) cc_final: 0.6299 (mtt90) REVERT: E 853 LYS cc_start: 0.7246 (mttt) cc_final: 0.6997 (mtpp) REVERT: E 854 ARG cc_start: 0.7076 (mtp85) cc_final: 0.6842 (mtp180) REVERT: E 855 GLU cc_start: 0.6580 (mm-30) cc_final: 0.6221 (mm-30) REVERT: E 873 ASP cc_start: 0.6816 (t70) cc_final: 0.6446 (t0) REVERT: E 900 GLU cc_start: 0.6193 (tp30) cc_final: 0.5777 (mm-30) REVERT: E 949 SER cc_start: 0.7213 (t) cc_final: 0.6966 (p) REVERT: E 975 MET cc_start: 0.6692 (mtm) cc_final: 0.6344 (mtp) REVERT: E 992 GLN cc_start: 0.5676 (tt0) cc_final: 0.5411 (tt0) REVERT: E 1056 GLU cc_start: 0.5546 (tt0) cc_final: 0.5077 (tm-30) REVERT: E 1057 SER cc_start: 0.4722 (t) cc_final: 0.4487 (m) REVERT: E 1124 ILE cc_start: 0.5947 (mm) cc_final: 0.5587 (mm) REVERT: E 1182 ASP cc_start: 0.5456 (m-30) cc_final: 0.5242 (m-30) REVERT: E 1189 LYS cc_start: 0.6340 (tttm) cc_final: 0.6062 (mtpp) REVERT: E 1221 GLN cc_start: 0.6450 (mm-40) cc_final: 0.6138 (mm110) outliers start: 2 outliers final: 0 residues processed: 289 average time/residue: 0.5059 time to fit residues: 158.1993 Evaluate side-chains 238 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 258 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 0.0970 chunk 55 optimal weight: 2.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 369 ASN A 436 GLN B 262 ASN B 272 GLN B 346 GLN E 309 GLN E 485 GLN ** E 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 616 GLN E 617 GLN E 624 HIS E 710 ASN E 829 GLN E 847 ASN E 903 ASN E 920 HIS E 921 GLN ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 945 ASN E1009 GLN E1022 GLN E1063 HIS E1115 GLN E1196 GLN E1209 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.169665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138375 restraints weight = 15118.562| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.85 r_work: 0.3650 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12432 Z= 0.134 Angle : 0.536 7.586 17164 Z= 0.284 Chirality : 0.038 0.180 1967 Planarity : 0.005 0.045 1981 Dihedral : 18.443 178.722 2205 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.60 % Allowed : 10.40 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.23), residues: 1380 helix: 1.56 (0.19), residues: 743 sheet: 0.16 (0.48), residues: 124 loop : -0.73 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 268 TYR 0.013 0.001 TYR E 610 PHE 0.015 0.001 PHE E 497 TRP 0.012 0.001 TRP E1070 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00294 (12432) covalent geometry : angle 0.53608 (17164) hydrogen bonds : bond 0.04369 ( 647) hydrogen bonds : angle 3.71024 ( 1810) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: B 189 LEU cc_start: 0.7608 (mm) cc_final: 0.7365 (mm) REVERT: E 385 SER cc_start: 0.8277 (m) cc_final: 0.8025 (t) REVERT: E 781 TYR cc_start: 0.7799 (m-80) cc_final: 0.7449 (m-80) REVERT: E 900 GLU cc_start: 0.7730 (tp30) cc_final: 0.7094 (mm-30) REVERT: E 1001 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7708 (p) outliers start: 29 outliers final: 9 residues processed: 247 average time/residue: 0.5418 time to fit residues: 144.2879 Evaluate side-chains 229 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 219 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 256 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 905 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain E residue 1001 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 141 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN E 250 HIS E 512 HIS E 529 HIS E 710 ASN E 920 HIS ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 992 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.165875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.134553 restraints weight = 15355.762| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.88 r_work: 0.3600 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12432 Z= 0.178 Angle : 0.557 7.612 17164 Z= 0.297 Chirality : 0.040 0.165 1967 Planarity : 0.005 0.048 1981 Dihedral : 18.375 178.746 2203 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.78 % Allowed : 13.90 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.23), residues: 1380 helix: 1.45 (0.19), residues: 757 sheet: 0.17 (0.46), residues: 131 loop : -0.85 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 502 TYR 0.017 0.002 TYR E 610 PHE 0.020 0.002 PHE A 334 TRP 0.015 0.002 TRP E1070 HIS 0.005 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00418 (12432) covalent geometry : angle 0.55662 (17164) hydrogen bonds : bond 0.04916 ( 647) hydrogen bonds : angle 3.72232 ( 1810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 0.417 Fit side-chains REVERT: B 276 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6681 (mtm) REVERT: B 316 PHE cc_start: 0.7030 (t80) cc_final: 0.6612 (t80) REVERT: E 737 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: E 781 TYR cc_start: 0.7814 (m-80) cc_final: 0.7394 (m-80) REVERT: E 900 GLU cc_start: 0.7731 (tp30) cc_final: 0.7515 (mm-30) outliers start: 31 outliers final: 11 residues processed: 245 average time/residue: 0.5271 time to fit residues: 139.4547 Evaluate side-chains 241 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 228 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 737 GLU Chi-restraints excluded: chain E residue 853 LYS Chi-restraints excluded: chain E residue 905 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain E residue 1001 VAL Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 123 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 91 optimal weight: 0.0270 chunk 128 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 81 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN E 485 GLN E 529 HIS ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 992 GLN E1035 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.166623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135704 restraints weight = 15275.537| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 1.78 r_work: 0.3621 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12432 Z= 0.131 Angle : 0.516 7.341 17164 Z= 0.276 Chirality : 0.038 0.164 1967 Planarity : 0.005 0.045 1981 Dihedral : 18.272 179.242 2203 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.24 % Allowed : 15.61 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.23), residues: 1380 helix: 1.63 (0.19), residues: 757 sheet: 0.27 (0.47), residues: 124 loop : -0.78 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E1083 TYR 0.013 0.001 TYR E1227 PHE 0.017 0.001 PHE A 318 TRP 0.014 0.001 TRP E1070 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00294 (12432) covalent geometry : angle 0.51610 (17164) hydrogen bonds : bond 0.04097 ( 647) hydrogen bonds : angle 3.59623 ( 1810) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 225 time to evaluate : 0.416 Fit side-chains REVERT: E 545 GLU cc_start: 0.7361 (pm20) cc_final: 0.7100 (pm20) REVERT: E 737 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: E 781 TYR cc_start: 0.7744 (m-80) cc_final: 0.7362 (m-80) REVERT: E 900 GLU cc_start: 0.7707 (tp30) cc_final: 0.7342 (mm-30) REVERT: E 1001 VAL cc_start: 0.8027 (OUTLIER) cc_final: 0.7670 (p) REVERT: E 1034 ARG cc_start: 0.7900 (ttp80) cc_final: 0.7427 (ttp80) REVERT: E 1177 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7795 (mt-10) outliers start: 25 outliers final: 14 residues processed: 234 average time/residue: 0.5384 time to fit residues: 136.1541 Evaluate side-chains 240 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 486 VAL Chi-restraints excluded: chain E residue 737 GLU Chi-restraints excluded: chain E residue 852 LYS Chi-restraints excluded: chain E residue 905 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1001 VAL Chi-restraints excluded: chain E residue 1165 GLN Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 95 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN E 485 GLN E 529 HIS E 565 GLN E 722 GLN ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 992 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.165268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134011 restraints weight = 15284.802| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.81 r_work: 0.3596 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12432 Z= 0.158 Angle : 0.538 7.974 17164 Z= 0.287 Chirality : 0.039 0.158 1967 Planarity : 0.005 0.047 1981 Dihedral : 18.223 178.084 2203 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.96 % Allowed : 16.23 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.23), residues: 1380 helix: 1.67 (0.19), residues: 751 sheet: 0.27 (0.48), residues: 120 loop : -0.70 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1083 TYR 0.015 0.002 TYR E 610 PHE 0.022 0.002 PHE A 318 TRP 0.014 0.001 TRP E1070 HIS 0.005 0.001 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00368 (12432) covalent geometry : angle 0.53762 (17164) hydrogen bonds : bond 0.04532 ( 647) hydrogen bonds : angle 3.64048 ( 1810) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 231 time to evaluate : 0.415 Fit side-chains REVERT: B 316 PHE cc_start: 0.7058 (t80) cc_final: 0.6594 (t80) REVERT: E 285 PHE cc_start: 0.7131 (t80) cc_final: 0.6921 (t80) REVERT: E 518 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7953 (mtm-85) REVERT: E 545 GLU cc_start: 0.7385 (pm20) cc_final: 0.7119 (pm20) REVERT: E 571 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7972 (t) REVERT: E 737 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: E 781 TYR cc_start: 0.7766 (m-80) cc_final: 0.7350 (m-80) REVERT: E 900 GLU cc_start: 0.7744 (tp30) cc_final: 0.7480 (mm-30) REVERT: E 1034 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7498 (ttp80) REVERT: E 1177 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7851 (mt-10) outliers start: 33 outliers final: 17 residues processed: 244 average time/residue: 0.4907 time to fit residues: 129.9243 Evaluate side-chains 246 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 518 ARG Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 737 GLU Chi-restraints excluded: chain E residue 852 LYS Chi-restraints excluded: chain E residue 853 LYS Chi-restraints excluded: chain E residue 905 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain E residue 1001 VAL Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 110 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 108 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 35 optimal weight: 0.0020 chunk 3 optimal weight: 0.7980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN E 529 HIS E 722 GLN ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 992 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.166177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134975 restraints weight = 15312.796| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.80 r_work: 0.3611 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12432 Z= 0.128 Angle : 0.517 7.527 17164 Z= 0.275 Chirality : 0.038 0.157 1967 Planarity : 0.005 0.045 1981 Dihedral : 18.153 178.593 2203 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.51 % Allowed : 16.86 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.23), residues: 1380 helix: 1.81 (0.19), residues: 752 sheet: 0.25 (0.49), residues: 114 loop : -0.67 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 225 TYR 0.011 0.001 TYR E1227 PHE 0.022 0.001 PHE E 465 TRP 0.014 0.001 TRP E1070 HIS 0.004 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00286 (12432) covalent geometry : angle 0.51702 (17164) hydrogen bonds : bond 0.04004 ( 647) hydrogen bonds : angle 3.56309 ( 1810) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.265 Fit side-chains REVERT: B 316 PHE cc_start: 0.7073 (t80) cc_final: 0.6610 (t80) REVERT: E 285 PHE cc_start: 0.7092 (t80) cc_final: 0.6863 (t80) REVERT: E 518 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7923 (mtm-85) REVERT: E 571 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7907 (t) REVERT: E 737 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: E 781 TYR cc_start: 0.7752 (m-80) cc_final: 0.7339 (m-80) REVERT: E 1001 VAL cc_start: 0.8017 (OUTLIER) cc_final: 0.7652 (p) REVERT: E 1032 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7386 (tt) REVERT: E 1034 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7702 (ttt-90) REVERT: E 1177 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7808 (mt-10) outliers start: 28 outliers final: 14 residues processed: 236 average time/residue: 0.5341 time to fit residues: 135.9581 Evaluate side-chains 241 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 222 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 458 ARG Chi-restraints excluded: chain E residue 518 ARG Chi-restraints excluded: chain E residue 571 VAL Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 737 GLU Chi-restraints excluded: chain E residue 852 LYS Chi-restraints excluded: chain E residue 853 LYS Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain E residue 1001 VAL Chi-restraints excluded: chain E residue 1032 LEU Chi-restraints excluded: chain E residue 1165 GLN Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 127 optimal weight: 1.9990 chunk 139 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN E 565 GLN ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 992 GLN E1131 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.161965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130492 restraints weight = 15088.285| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.84 r_work: 0.3533 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 12432 Z= 0.278 Angle : 0.643 8.995 17164 Z= 0.341 Chirality : 0.045 0.162 1967 Planarity : 0.006 0.050 1981 Dihedral : 18.310 176.353 2203 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.96 % Allowed : 16.95 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.22), residues: 1380 helix: 1.26 (0.19), residues: 761 sheet: 0.20 (0.51), residues: 108 loop : -1.03 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 225 TYR 0.034 0.002 TYR B 229 PHE 0.031 0.002 PHE A 318 TRP 0.015 0.002 TRP E1070 HIS 0.008 0.002 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00679 (12432) covalent geometry : angle 0.64269 (17164) hydrogen bonds : bond 0.05896 ( 647) hydrogen bonds : angle 3.92530 ( 1810) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 0.282 Fit side-chains REVERT: A 420 LEU cc_start: 0.8395 (mt) cc_final: 0.8131 (mm) REVERT: B 316 PHE cc_start: 0.7154 (t80) cc_final: 0.6635 (t80) REVERT: E 285 PHE cc_start: 0.7124 (t80) cc_final: 0.6884 (t80) REVERT: E 456 LEU cc_start: 0.7911 (mp) cc_final: 0.7666 (mt) REVERT: E 518 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7916 (mtm-85) REVERT: E 737 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: E 781 TYR cc_start: 0.7877 (m-80) cc_final: 0.7299 (m-80) REVERT: E 900 GLU cc_start: 0.7731 (tp30) cc_final: 0.7410 (mm-30) REVERT: E 1034 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7610 (ttp80) outliers start: 33 outliers final: 19 residues processed: 244 average time/residue: 0.5392 time to fit residues: 142.0679 Evaluate side-chains 249 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 458 ARG Chi-restraints excluded: chain E residue 518 ARG Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 737 GLU Chi-restraints excluded: chain E residue 852 LYS Chi-restraints excluded: chain E residue 905 VAL Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain E residue 1001 VAL Chi-restraints excluded: chain E residue 1165 GLN Chi-restraints excluded: chain E residue 1208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 131 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 91 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 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 992 GLN ** E1175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.164156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133421 restraints weight = 15069.816| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.80 r_work: 0.3575 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12432 Z= 0.153 Angle : 0.551 8.375 17164 Z= 0.294 Chirality : 0.040 0.233 1967 Planarity : 0.005 0.048 1981 Dihedral : 18.217 177.314 2203 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.69 % Allowed : 17.22 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.23), residues: 1380 helix: 1.48 (0.19), residues: 768 sheet: 0.28 (0.49), residues: 113 loop : -0.95 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 225 TYR 0.015 0.001 TYR B 229 PHE 0.026 0.001 PHE E 465 TRP 0.017 0.001 TRP E1070 HIS 0.005 0.001 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00356 (12432) covalent geometry : angle 0.55101 (17164) hydrogen bonds : bond 0.04514 ( 647) hydrogen bonds : angle 3.71021 ( 1810) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.426 Fit side-chains REVERT: A 420 LEU cc_start: 0.8401 (mt) cc_final: 0.8151 (mm) REVERT: B 316 PHE cc_start: 0.7196 (t80) cc_final: 0.6728 (t80) REVERT: E 518 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7936 (mtm-85) REVERT: E 737 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: E 781 TYR cc_start: 0.7773 (m-80) cc_final: 0.7319 (m-80) REVERT: E 900 GLU cc_start: 0.7753 (tp30) cc_final: 0.7463 (mm-30) REVERT: E 985 ILE cc_start: 0.7799 (OUTLIER) cc_final: 0.7336 (mt) REVERT: E 1034 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7579 (ttp80) outliers start: 30 outliers final: 18 residues processed: 235 average time/residue: 0.5377 time to fit residues: 136.5560 Evaluate side-chains 240 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 458 ARG Chi-restraints excluded: chain E residue 518 ARG Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 682 GLU Chi-restraints excluded: chain E residue 737 GLU Chi-restraints excluded: chain E residue 852 LYS Chi-restraints excluded: chain E residue 905 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain E residue 1001 VAL Chi-restraints excluded: chain E residue 1165 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 121 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 112 optimal weight: 0.0670 chunk 23 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN E 572 GLN ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 992 GLN ** E1175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.163711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.132497 restraints weight = 15012.829| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 1.63 r_work: 0.3592 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12432 Z= 0.178 Angle : 0.570 8.782 17164 Z= 0.303 Chirality : 0.041 0.211 1967 Planarity : 0.005 0.048 1981 Dihedral : 18.185 177.206 2203 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.15 % Allowed : 17.67 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.23), residues: 1380 helix: 1.54 (0.19), residues: 763 sheet: 0.28 (0.49), residues: 113 loop : -0.92 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 411 TYR 0.019 0.002 TYR B 229 PHE 0.027 0.002 PHE E 465 TRP 0.016 0.001 TRP E1070 HIS 0.005 0.001 HIS E 250 Details of bonding type rmsd covalent geometry : bond 0.00422 (12432) covalent geometry : angle 0.56985 (17164) hydrogen bonds : bond 0.04747 ( 647) hydrogen bonds : angle 3.71881 ( 1810) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.425 Fit side-chains REVERT: A 420 LEU cc_start: 0.8413 (mt) cc_final: 0.8170 (mm) REVERT: B 316 PHE cc_start: 0.7183 (t80) cc_final: 0.6741 (t80) REVERT: E 518 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7897 (mtm-85) REVERT: E 737 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: E 781 TYR cc_start: 0.7771 (m-80) cc_final: 0.7283 (m-80) REVERT: E 900 GLU cc_start: 0.7728 (tp30) cc_final: 0.7357 (mm-30) REVERT: E 985 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7542 (mt) REVERT: E 1034 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7509 (ttp80) outliers start: 24 outliers final: 19 residues processed: 230 average time/residue: 0.5202 time to fit residues: 129.3323 Evaluate side-chains 242 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 220 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 458 ARG Chi-restraints excluded: chain E residue 518 ARG Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 737 GLU Chi-restraints excluded: chain E residue 852 LYS Chi-restraints excluded: chain E residue 905 VAL Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain E residue 1001 VAL Chi-restraints excluded: chain E residue 1165 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 110 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 133 optimal weight: 0.0870 chunk 92 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 992 GLN ** E1175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.164323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133206 restraints weight = 15248.501| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.64 r_work: 0.3603 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12432 Z= 0.156 Angle : 0.551 7.999 17164 Z= 0.294 Chirality : 0.039 0.155 1967 Planarity : 0.005 0.048 1981 Dihedral : 18.143 177.270 2203 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.06 % Allowed : 18.12 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.23), residues: 1380 helix: 1.65 (0.19), residues: 763 sheet: 0.27 (0.49), residues: 113 loop : -0.87 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 411 TYR 0.015 0.001 TYR B 229 PHE 0.028 0.001 PHE E 465 TRP 0.016 0.001 TRP E1070 HIS 0.005 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00364 (12432) covalent geometry : angle 0.55136 (17164) hydrogen bonds : bond 0.04382 ( 647) hydrogen bonds : angle 3.66325 ( 1810) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.332 Fit side-chains REVERT: A 420 LEU cc_start: 0.8427 (mt) cc_final: 0.8176 (mm) REVERT: B 316 PHE cc_start: 0.7191 (t80) cc_final: 0.6730 (t80) REVERT: E 518 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.7896 (mtm-85) REVERT: E 737 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: E 781 TYR cc_start: 0.7760 (m-80) cc_final: 0.7285 (m-80) REVERT: E 900 GLU cc_start: 0.7709 (tp30) cc_final: 0.7320 (mm-30) REVERT: E 985 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7604 (mt) REVERT: E 1034 ARG cc_start: 0.7801 (ttp80) cc_final: 0.7486 (ttp80) outliers start: 23 outliers final: 17 residues processed: 227 average time/residue: 0.5589 time to fit residues: 137.1474 Evaluate side-chains 237 residues out of total 1226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 518 ARG Chi-restraints excluded: chain E residue 633 LYS Chi-restraints excluded: chain E residue 737 GLU Chi-restraints excluded: chain E residue 852 LYS Chi-restraints excluded: chain E residue 905 VAL Chi-restraints excluded: chain E residue 975 MET Chi-restraints excluded: chain E residue 985 ILE Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain E residue 1001 VAL Chi-restraints excluded: chain E residue 1165 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 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 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN E 529 HIS ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 992 GLN ** E1175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.164546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133455 restraints weight = 15115.682| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.63 r_work: 0.3605 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12432 Z= 0.152 Angle : 0.548 7.792 17164 Z= 0.292 Chirality : 0.039 0.154 1967 Planarity : 0.005 0.048 1981 Dihedral : 18.108 177.319 2203 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.70 % Allowed : 18.30 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.23), residues: 1380 helix: 1.67 (0.19), residues: 763 sheet: 0.28 (0.49), residues: 113 loop : -0.85 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 411 TYR 0.015 0.001 TYR B 229 PHE 0.028 0.001 PHE E 465 TRP 0.016 0.001 TRP E1070 HIS 0.006 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00355 (12432) covalent geometry : angle 0.54774 (17164) hydrogen bonds : bond 0.04351 ( 647) hydrogen bonds : angle 3.64336 ( 1810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4827.06 seconds wall clock time: 82 minutes 30.33 seconds (4950.33 seconds total)