Starting phenix.real_space_refine on Thu Sep 26 03:59:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bdc_44448/09_2024/9bdc_44448.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bdc_44448/09_2024/9bdc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bdc_44448/09_2024/9bdc_44448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bdc_44448/09_2024/9bdc_44448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bdc_44448/09_2024/9bdc_44448.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bdc_44448/09_2024/9bdc_44448.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP: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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 6} 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, 'ARG:plan': 11, 'HIS:plan': 3, 'GLU:plan': 14, 'ASP:plan': 10} 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: 7.56, per 1000 atoms: 0.63 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: 2.97 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 4.06 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: 5.16 Time building geometry restraints manager: 3.51 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: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.930 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.800 ------------------------------------------------------------------------------- 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= 0.221 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 : 4.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (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 TRP 0.011 0.001 TRP E 271 HIS 0.005 0.001 HIS B 249 PHE 0.017 0.001 PHE E1044 TYR 0.021 0.001 TYR B 258 ARG 0.005 0.001 ARG E1083 *********************** 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 fitting. rotamer outliers: 2 poor density : 287 time to evaluate : 1.150 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: 1.2499 time to fit residues: 391.8640 Evaluate side-chains 238 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 120 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 73 optimal weight: 0.3980 chunk 57 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4997 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12432 Z= 0.212 Angle : 0.541 7.542 17164 Z= 0.287 Chirality : 0.038 0.177 1967 Planarity : 0.005 0.045 1981 Dihedral : 18.497 178.735 2205 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.51 % Allowed : 10.40 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1380 helix: 1.55 (0.19), residues: 742 sheet: 0.14 (0.48), residues: 124 loop : -0.74 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E1070 HIS 0.005 0.001 HIS B 249 PHE 0.015 0.001 PHE E 497 TYR 0.013 0.001 TYR E 610 ARG 0.005 0.000 ARG A 268 *********************** 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 fitting. rotamer outliers: 28 poor density : 233 time to evaluate : 1.224 Fit side-chains REVERT: A 318 PHE cc_start: 0.6892 (m-80) cc_final: 0.6646 (m-80) REVERT: B 189 LEU cc_start: 0.6887 (mm) cc_final: 0.6580 (mm) REVERT: E 375 ARG cc_start: 0.6889 (ttm170) cc_final: 0.6605 (ttm170) REVERT: E 385 SER cc_start: 0.7282 (m) cc_final: 0.6874 (t) REVERT: E 411 ARG cc_start: 0.7429 (ttm170) cc_final: 0.7120 (mtp180) REVERT: E 485 GLN cc_start: 0.6132 (mt0) cc_final: 0.5851 (mt0) REVERT: E 495 GLU cc_start: 0.6652 (pt0) cc_final: 0.6218 (pt0) REVERT: E 531 ARG cc_start: 0.7172 (mtp85) cc_final: 0.6937 (mtp-110) REVERT: E 539 SER cc_start: 0.7613 (t) cc_final: 0.7288 (p) REVERT: E 633 LYS cc_start: 0.6606 (ttpt) cc_final: 0.6367 (tttp) REVERT: E 668 THR cc_start: 0.7404 (m) cc_final: 0.7108 (p) REVERT: E 682 GLU cc_start: 0.6225 (tt0) cc_final: 0.5961 (tt0) REVERT: E 685 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6445 (mt-10) REVERT: E 781 TYR cc_start: 0.6228 (m-80) cc_final: 0.5671 (m-80) REVERT: E 814 ASN cc_start: 0.7458 (p0) cc_final: 0.7233 (p0) REVERT: E 816 LEU cc_start: 0.7179 (mt) cc_final: 0.6663 (mp) REVERT: E 831 ARG cc_start: 0.6439 (mtt-85) cc_final: 0.6086 (mtt90) REVERT: E 855 GLU cc_start: 0.6577 (mm-30) cc_final: 0.6248 (mm-30) REVERT: E 873 ASP cc_start: 0.6830 (t70) cc_final: 0.6552 (t0) REVERT: E 882 ARG cc_start: 0.6517 (mtm180) cc_final: 0.6145 (mtm110) REVERT: E 946 LEU cc_start: 0.5933 (mt) cc_final: 0.5732 (mt) REVERT: E 975 MET cc_start: 0.6684 (mtm) cc_final: 0.6348 (mtp) REVERT: E 1020 PHE cc_start: 0.5910 (m-80) cc_final: 0.5709 (m-80) REVERT: E 1056 GLU cc_start: 0.5540 (tt0) cc_final: 0.5065 (tm-30) REVERT: E 1057 SER cc_start: 0.4718 (t) cc_final: 0.4505 (m) REVERT: E 1182 ASP cc_start: 0.5397 (m-30) cc_final: 0.5131 (m-30) REVERT: E 1189 LYS cc_start: 0.6446 (tttm) cc_final: 0.6240 (ttpp) REVERT: E 1213 LYS cc_start: 0.7516 (mttt) cc_final: 0.7011 (mtpp) REVERT: E 1221 GLN cc_start: 0.6458 (mm-40) cc_final: 0.6116 (mm110) REVERT: E 1224 ARG cc_start: 0.6816 (mtp-110) cc_final: 0.6501 (mtp-110) outliers start: 28 outliers final: 8 residues processed: 248 average time/residue: 1.2398 time to fit residues: 333.1217 Evaluate side-chains 234 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 226 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 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 72 optimal weight: 0.3980 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN E 454 ASN E 512 HIS E 710 ASN E 829 GLN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5026 moved from start: 0.1818 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= 0.238 Angle : 0.538 7.334 17164 Z= 0.288 Chirality : 0.039 0.172 1967 Planarity : 0.005 0.047 1981 Dihedral : 18.356 179.284 2203 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.51 % Allowed : 12.91 % Favored : 84.57 % 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: 0.87 (0.23), residues: 1380 helix: 1.54 (0.19), residues: 751 sheet: 0.12 (0.48), residues: 125 loop : -0.73 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E1070 HIS 0.004 0.001 HIS B 251 PHE 0.018 0.001 PHE A 334 TYR 0.015 0.002 TYR E 610 ARG 0.004 0.000 ARG E1034 *********************** 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 fitting. rotamer outliers: 28 poor density : 237 time to evaluate : 1.284 Fit side-chains REVERT: B 316 PHE cc_start: 0.6861 (t80) cc_final: 0.6303 (t80) REVERT: E 375 ARG cc_start: 0.6854 (ttm170) cc_final: 0.6464 (ttm110) REVERT: E 485 GLN cc_start: 0.6096 (mt0) cc_final: 0.5828 (mt0) REVERT: E 495 GLU cc_start: 0.6656 (pt0) cc_final: 0.6273 (pt0) REVERT: E 539 SER cc_start: 0.7596 (t) cc_final: 0.7275 (p) REVERT: E 633 LYS cc_start: 0.6614 (ttpt) cc_final: 0.6381 (tttp) REVERT: E 668 THR cc_start: 0.7438 (m) cc_final: 0.7142 (p) REVERT: E 682 GLU cc_start: 0.6257 (tt0) cc_final: 0.5982 (tt0) REVERT: E 781 TYR cc_start: 0.6087 (m-80) cc_final: 0.5487 (m-80) REVERT: E 831 ARG cc_start: 0.6446 (mtt-85) cc_final: 0.6095 (mtt90) REVERT: E 855 GLU cc_start: 0.6536 (mm-30) cc_final: 0.6282 (mm-30) REVERT: E 873 ASP cc_start: 0.6834 (t70) cc_final: 0.6576 (t0) REVERT: E 882 ARG cc_start: 0.6602 (mtm180) cc_final: 0.6223 (mtm110) REVERT: E 900 GLU cc_start: 0.6078 (mm-30) cc_final: 0.5808 (mm-30) REVERT: E 975 MET cc_start: 0.6468 (mtm) cc_final: 0.6180 (mtp) REVERT: E 1020 PHE cc_start: 0.5849 (m-80) cc_final: 0.5619 (m-80) REVERT: E 1056 GLU cc_start: 0.5441 (tt0) cc_final: 0.4978 (tm-30) REVERT: E 1057 SER cc_start: 0.4676 (t) cc_final: 0.4402 (m) REVERT: E 1182 ASP cc_start: 0.5357 (m-30) cc_final: 0.5084 (m-30) REVERT: E 1213 LYS cc_start: 0.7520 (mttt) cc_final: 0.7020 (mtpp) REVERT: E 1221 GLN cc_start: 0.6462 (mm-40) cc_final: 0.6199 (mm110) REVERT: E 1224 ARG cc_start: 0.6866 (mtp-110) cc_final: 0.6572 (mtp-110) outliers start: 28 outliers final: 11 residues processed: 247 average time/residue: 1.2055 time to fit residues: 322.3650 Evaluate side-chains 240 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 208 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 922 ASP Chi-restraints excluded: chain E residue 998 VAL Chi-restraints excluded: chain E residue 1001 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 67 optimal weight: 0.0000 chunk 14 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- 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 529 HIS E 920 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5025 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12432 Z= 0.204 Angle : 0.518 7.587 17164 Z= 0.277 Chirality : 0.038 0.164 1967 Planarity : 0.005 0.046 1981 Dihedral : 18.269 179.149 2203 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.33 % Allowed : 14.44 % Favored : 83.23 % 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: 1.05 (0.23), residues: 1380 helix: 1.69 (0.19), residues: 751 sheet: 0.22 (0.48), residues: 120 loop : -0.66 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E1070 HIS 0.004 0.001 HIS B 249 PHE 0.021 0.001 PHE E 966 TYR 0.013 0.001 TYR E1227 ARG 0.004 0.000 ARG E 502 *********************** 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 255 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 229 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: B 276 MET cc_start: 0.6721 (ptp) cc_final: 0.6142 (mtm) REVERT: B 316 PHE cc_start: 0.6850 (t80) cc_final: 0.6285 (t80) REVERT: E 375 ARG cc_start: 0.6876 (ttm170) cc_final: 0.6553 (ttp-170) REVERT: E 485 GLN cc_start: 0.6082 (mt0) cc_final: 0.5813 (mt0) REVERT: E 495 GLU cc_start: 0.6663 (pt0) cc_final: 0.6128 (pt0) REVERT: E 500 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.5276 (mp) REVERT: E 539 SER cc_start: 0.7603 (t) cc_final: 0.7281 (p) REVERT: E 545 GLU cc_start: 0.6471 (pm20) cc_final: 0.6051 (pm20) REVERT: E 633 LYS cc_start: 0.6614 (ttpt) cc_final: 0.6376 (tttp) REVERT: E 668 THR cc_start: 0.7369 (m) cc_final: 0.7068 (p) REVERT: E 682 GLU cc_start: 0.6255 (tt0) cc_final: 0.5983 (tt0) REVERT: E 781 TYR cc_start: 0.6080 (m-80) cc_final: 0.5521 (m-80) REVERT: E 831 ARG cc_start: 0.6456 (mtt-85) cc_final: 0.6102 (mtt90) REVERT: E 855 GLU cc_start: 0.6517 (mm-30) cc_final: 0.6257 (mm-30) REVERT: E 873 ASP cc_start: 0.6808 (t70) cc_final: 0.6558 (t0) REVERT: E 900 GLU cc_start: 0.6121 (mm-30) cc_final: 0.5705 (mm-30) REVERT: E 975 MET cc_start: 0.6441 (mtm) cc_final: 0.6128 (mtp) REVERT: E 1001 VAL cc_start: 0.5004 (OUTLIER) cc_final: 0.4734 (p) REVERT: E 1020 PHE cc_start: 0.5834 (m-80) cc_final: 0.5589 (m-80) REVERT: E 1056 GLU cc_start: 0.5456 (tt0) cc_final: 0.5036 (tm-30) REVERT: E 1182 ASP cc_start: 0.5320 (m-30) cc_final: 0.5034 (m-30) REVERT: E 1213 LYS cc_start: 0.7505 (mttt) cc_final: 0.7016 (mtpp) REVERT: E 1221 GLN cc_start: 0.6455 (mm-40) cc_final: 0.6158 (mm110) outliers start: 26 outliers final: 15 residues processed: 239 average time/residue: 1.2622 time to fit residues: 326.8189 Evaluate side-chains 243 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 226 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 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 500 LEU 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 1035 GLN Chi-restraints excluded: chain E residue 1165 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 722 GLN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5062 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12432 Z= 0.350 Angle : 0.584 8.453 17164 Z= 0.311 Chirality : 0.042 0.161 1967 Planarity : 0.005 0.050 1981 Dihedral : 18.305 177.261 2203 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.42 % Allowed : 15.70 % Favored : 81.88 % 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: 0.70 (0.23), residues: 1380 helix: 1.37 (0.19), residues: 764 sheet: 0.30 (0.50), residues: 114 loop : -0.86 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E1070 HIS 0.007 0.001 HIS E 250 PHE 0.023 0.002 PHE A 334 TYR 0.019 0.002 TYR E 610 ARG 0.007 0.000 ARG E1034 *********************** 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 256 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 229 time to evaluate : 1.319 Fit side-chains REVERT: B 316 PHE cc_start: 0.6834 (t80) cc_final: 0.6185 (t80) REVERT: E 375 ARG cc_start: 0.6819 (ttm170) cc_final: 0.6568 (ttp-170) REVERT: E 411 ARG cc_start: 0.7427 (mtp180) cc_final: 0.7170 (mtt180) REVERT: E 485 GLN cc_start: 0.6121 (mt0) cc_final: 0.5847 (mt0) REVERT: E 495 GLU cc_start: 0.6690 (pt0) cc_final: 0.6323 (pt0) REVERT: E 500 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5448 (mt) REVERT: E 518 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6308 (mtm-85) REVERT: E 539 SER cc_start: 0.7617 (t) cc_final: 0.7276 (p) REVERT: E 545 GLU cc_start: 0.6475 (pm20) cc_final: 0.6074 (pm20) REVERT: E 668 THR cc_start: 0.7426 (m) cc_final: 0.7135 (p) REVERT: E 682 GLU cc_start: 0.6227 (tt0) cc_final: 0.5963 (tt0) REVERT: E 781 TYR cc_start: 0.6145 (m-80) cc_final: 0.5463 (m-80) REVERT: E 826 GLU cc_start: 0.6934 (tt0) cc_final: 0.6613 (tt0) REVERT: E 831 ARG cc_start: 0.6464 (mtt-85) cc_final: 0.6120 (mtt90) REVERT: E 849 THR cc_start: 0.6416 (m) cc_final: 0.5942 (p) REVERT: E 855 GLU cc_start: 0.6583 (mm-30) cc_final: 0.6372 (mm-30) REVERT: E 882 ARG cc_start: 0.6719 (mtm180) cc_final: 0.6415 (mtm110) REVERT: E 975 MET cc_start: 0.6345 (mtm) cc_final: 0.6067 (mtp) REVERT: E 1056 GLU cc_start: 0.5472 (tt0) cc_final: 0.5055 (tm-30) REVERT: E 1128 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5702 (p0) REVERT: E 1182 ASP cc_start: 0.5324 (m-30) cc_final: 0.5013 (m-30) REVERT: E 1213 LYS cc_start: 0.7556 (mttt) cc_final: 0.7044 (mtpp) REVERT: E 1221 GLN cc_start: 0.6527 (mm-40) cc_final: 0.6223 (mm110) outliers start: 27 outliers final: 18 residues processed: 239 average time/residue: 1.2602 time to fit residues: 325.6532 Evaluate side-chains 245 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 224 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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 406 MET Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 458 ARG Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 518 ARG 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 1128 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5047 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12432 Z= 0.236 Angle : 0.533 8.064 17164 Z= 0.285 Chirality : 0.039 0.160 1967 Planarity : 0.005 0.048 1981 Dihedral : 18.225 178.332 2203 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.42 % Allowed : 16.32 % Favored : 81.26 % 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: 0.97 (0.23), residues: 1380 helix: 1.62 (0.19), residues: 759 sheet: 0.32 (0.49), residues: 114 loop : -0.75 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E1070 HIS 0.004 0.001 HIS E 250 PHE 0.020 0.001 PHE A 318 TYR 0.013 0.001 TYR E1227 ARG 0.009 0.000 ARG E1034 *********************** 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 253 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 226 time to evaluate : 1.295 Fit side-chains REVERT: B 276 MET cc_start: 0.6748 (ptp) cc_final: 0.6270 (mtm) REVERT: B 316 PHE cc_start: 0.6902 (t80) cc_final: 0.6262 (t80) REVERT: E 375 ARG cc_start: 0.6842 (ttm170) cc_final: 0.6602 (ttp-170) REVERT: E 411 ARG cc_start: 0.7407 (mtp180) cc_final: 0.7103 (mtt180) REVERT: E 485 GLN cc_start: 0.6097 (mt0) cc_final: 0.5778 (mt0) REVERT: E 495 GLU cc_start: 0.6725 (pt0) cc_final: 0.6338 (pt0) REVERT: E 500 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5437 (mt) REVERT: E 518 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6269 (mtm-85) REVERT: E 539 SER cc_start: 0.7619 (t) cc_final: 0.7293 (p) REVERT: E 668 THR cc_start: 0.7369 (m) cc_final: 0.7075 (p) REVERT: E 682 GLU cc_start: 0.6154 (tt0) cc_final: 0.5904 (tt0) REVERT: E 781 TYR cc_start: 0.6040 (m-80) cc_final: 0.5384 (m-80) REVERT: E 814 ASN cc_start: 0.7449 (p0) cc_final: 0.7177 (p0) REVERT: E 826 GLU cc_start: 0.6937 (tt0) cc_final: 0.6635 (tt0) REVERT: E 831 ARG cc_start: 0.6456 (mtt-85) cc_final: 0.6106 (mtt90) REVERT: E 855 GLU cc_start: 0.6560 (mm-30) cc_final: 0.6347 (mm-30) REVERT: E 873 ASP cc_start: 0.6713 (t70) cc_final: 0.6482 (t0) REVERT: E 975 MET cc_start: 0.6363 (mtm) cc_final: 0.6074 (mtp) REVERT: E 1030 HIS cc_start: 0.5697 (m-70) cc_final: 0.5457 (m-70) REVERT: E 1056 GLU cc_start: 0.5477 (tt0) cc_final: 0.5046 (tm-30) REVERT: E 1128 ASP cc_start: 0.5920 (OUTLIER) cc_final: 0.5643 (p0) REVERT: E 1177 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6841 (tt0) REVERT: E 1182 ASP cc_start: 0.5311 (m-30) cc_final: 0.5043 (m-30) REVERT: E 1213 LYS cc_start: 0.7500 (mttt) cc_final: 0.7002 (mtpp) REVERT: E 1221 GLN cc_start: 0.6548 (mm-40) cc_final: 0.6245 (mm110) outliers start: 27 outliers final: 17 residues processed: 235 average time/residue: 1.2696 time to fit residues: 323.2422 Evaluate side-chains 242 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 222 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 208 SER 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 417 VAL Chi-restraints excluded: chain E residue 458 ARG Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 518 ARG 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 1128 ASP Chi-restraints excluded: chain E residue 1165 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 chunk 101 optimal weight: 0.5980 chunk 116 optimal weight: 0.0570 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5036 moved from start: 0.2498 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= 0.189 Angle : 0.508 7.826 17164 Z= 0.272 Chirality : 0.038 0.159 1967 Planarity : 0.005 0.046 1981 Dihedral : 18.113 178.402 2203 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.24 % Allowed : 17.58 % 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 (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: 1.14 (0.23), residues: 1380 helix: 1.78 (0.19), residues: 759 sheet: 0.35 (0.49), residues: 113 loop : -0.70 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E1070 HIS 0.004 0.001 HIS B 249 PHE 0.014 0.001 PHE A 334 TYR 0.011 0.001 TYR E1227 ARG 0.009 0.000 ARG E1034 *********************** 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 247 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 222 time to evaluate : 1.229 Fit side-chains REVERT: A 420 LEU cc_start: 0.6983 (mt) cc_final: 0.6752 (mm) REVERT: B 276 MET cc_start: 0.6775 (ptp) cc_final: 0.6470 (mtm) REVERT: B 316 PHE cc_start: 0.6958 (t80) cc_final: 0.6297 (t80) REVERT: E 375 ARG cc_start: 0.6830 (ttm170) cc_final: 0.6497 (ttp-170) REVERT: E 411 ARG cc_start: 0.7415 (mtp180) cc_final: 0.7205 (mtp180) REVERT: E 485 GLN cc_start: 0.6036 (mt0) cc_final: 0.5726 (mt0) REVERT: E 495 GLU cc_start: 0.6724 (pt0) cc_final: 0.6339 (pt0) REVERT: E 500 LEU cc_start: 0.5722 (OUTLIER) cc_final: 0.5424 (mt) REVERT: E 539 SER cc_start: 0.7601 (t) cc_final: 0.7283 (p) REVERT: E 668 THR cc_start: 0.7364 (m) cc_final: 0.7055 (p) REVERT: E 682 GLU cc_start: 0.6059 (tt0) cc_final: 0.5821 (tt0) REVERT: E 781 TYR cc_start: 0.6010 (m-80) cc_final: 0.5403 (m-80) REVERT: E 814 ASN cc_start: 0.7449 (p0) cc_final: 0.7182 (p0) REVERT: E 826 GLU cc_start: 0.6931 (tt0) cc_final: 0.6643 (tt0) REVERT: E 831 ARG cc_start: 0.6463 (mtt-85) cc_final: 0.6111 (mtt90) REVERT: E 855 GLU cc_start: 0.6529 (mm-30) cc_final: 0.6274 (mm-30) REVERT: E 873 ASP cc_start: 0.6740 (t70) cc_final: 0.6509 (t0) REVERT: E 900 GLU cc_start: 0.6123 (mm-30) cc_final: 0.5699 (mm-30) REVERT: E 975 MET cc_start: 0.6331 (mtm) cc_final: 0.6026 (mtp) REVERT: E 1035 GLN cc_start: 0.3816 (OUTLIER) cc_final: 0.3525 (tp40) REVERT: E 1056 GLU cc_start: 0.5467 (tt0) cc_final: 0.5016 (tm-30) REVERT: E 1128 ASP cc_start: 0.5858 (OUTLIER) cc_final: 0.5586 (p0) REVERT: E 1177 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6918 (tt0) REVERT: E 1182 ASP cc_start: 0.5311 (m-30) cc_final: 0.5040 (m-30) REVERT: E 1213 LYS cc_start: 0.7497 (mttt) cc_final: 0.7002 (mtpp) REVERT: E 1221 GLN cc_start: 0.6502 (mm-40) cc_final: 0.6225 (mm110) outliers start: 25 outliers final: 10 residues processed: 229 average time/residue: 1.2562 time to fit residues: 312.3314 Evaluate side-chains 234 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 221 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER 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 268 MET Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 853 LYS Chi-restraints excluded: chain E residue 905 VAL Chi-restraints excluded: chain E residue 997 VAL Chi-restraints excluded: chain E residue 1001 VAL Chi-restraints excluded: chain E residue 1035 GLN Chi-restraints excluded: chain E residue 1128 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.0050 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 565 GLN ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 992 GLN ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5040 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12432 Z= 0.198 Angle : 0.517 9.311 17164 Z= 0.275 Chirality : 0.038 0.155 1967 Planarity : 0.005 0.046 1981 Dihedral : 18.093 178.142 2203 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.97 % Allowed : 18.12 % Favored : 79.91 % 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: 1.14 (0.23), residues: 1380 helix: 1.80 (0.19), residues: 764 sheet: 0.33 (0.49), residues: 113 loop : -0.76 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E1070 HIS 0.004 0.001 HIS E 250 PHE 0.016 0.001 PHE E1044 TYR 0.012 0.001 TYR E1227 ARG 0.008 0.000 ARG E1034 *********************** 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 247 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 225 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 420 LEU cc_start: 0.6990 (mt) cc_final: 0.6758 (mm) REVERT: B 316 PHE cc_start: 0.6990 (t80) cc_final: 0.6314 (t80) REVERT: E 375 ARG cc_start: 0.6800 (ttm170) cc_final: 0.6468 (ttp-170) REVERT: E 411 ARG cc_start: 0.7432 (mtp180) cc_final: 0.7168 (mtp180) REVERT: E 485 GLN cc_start: 0.6043 (mt0) cc_final: 0.5720 (mt0) REVERT: E 495 GLU cc_start: 0.6716 (pt0) cc_final: 0.6340 (pt0) REVERT: E 500 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5489 (mt) REVERT: E 539 SER cc_start: 0.7605 (t) cc_final: 0.7284 (p) REVERT: E 668 THR cc_start: 0.7360 (m) cc_final: 0.7051 (p) REVERT: E 682 GLU cc_start: 0.6042 (tt0) cc_final: 0.5813 (tt0) REVERT: E 781 TYR cc_start: 0.6013 (m-80) cc_final: 0.5395 (m-80) REVERT: E 814 ASN cc_start: 0.7452 (p0) cc_final: 0.7177 (p0) REVERT: E 826 GLU cc_start: 0.6936 (tt0) cc_final: 0.6652 (tt0) REVERT: E 831 ARG cc_start: 0.6462 (mtt-85) cc_final: 0.6107 (mtt90) REVERT: E 855 GLU cc_start: 0.6536 (mm-30) cc_final: 0.6312 (mm-30) REVERT: E 873 ASP cc_start: 0.6743 (t70) cc_final: 0.6508 (t0) REVERT: E 900 GLU cc_start: 0.6142 (mm-30) cc_final: 0.5712 (mm-30) REVERT: E 975 MET cc_start: 0.6150 (mtm) cc_final: 0.5884 (mtp) REVERT: E 1056 GLU cc_start: 0.5464 (tt0) cc_final: 0.5015 (tm-30) REVERT: E 1128 ASP cc_start: 0.5874 (OUTLIER) cc_final: 0.5600 (p0) REVERT: E 1177 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6907 (tt0) REVERT: E 1182 ASP cc_start: 0.5307 (m-30) cc_final: 0.5037 (m-30) REVERT: E 1213 LYS cc_start: 0.7498 (mttt) cc_final: 0.7003 (mtpp) REVERT: E 1221 GLN cc_start: 0.6505 (mm-40) cc_final: 0.6151 (mm110) REVERT: E 1224 ARG cc_start: 0.6828 (mtp-110) cc_final: 0.6133 (mtp-110) outliers start: 22 outliers final: 14 residues processed: 235 average time/residue: 1.2314 time to fit residues: 313.4966 Evaluate side-chains 239 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 223 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 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 500 LEU Chi-restraints excluded: chain E residue 853 LYS Chi-restraints excluded: chain E residue 905 VAL 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 1035 GLN Chi-restraints excluded: chain E residue 1128 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS 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 ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1131 HIS ** E1175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5081 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12432 Z= 0.396 Angle : 0.620 8.362 17164 Z= 0.330 Chirality : 0.044 0.288 1967 Planarity : 0.005 0.049 1981 Dihedral : 18.218 176.475 2203 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.42 % Allowed : 17.13 % Favored : 80.45 % 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: 0.65 (0.23), residues: 1380 helix: 1.39 (0.19), residues: 769 sheet: 0.27 (0.51), residues: 107 loop : -1.01 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E1070 HIS 0.007 0.001 HIS E 250 PHE 0.027 0.002 PHE A 318 TYR 0.028 0.002 TYR B 229 ARG 0.005 0.001 ARG E1034 *********************** 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 255 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 228 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 420 LEU cc_start: 0.7086 (mt) cc_final: 0.6808 (mm) REVERT: B 316 PHE cc_start: 0.6921 (t80) cc_final: 0.6239 (t80) REVERT: E 375 ARG cc_start: 0.6802 (ttm170) cc_final: 0.6519 (ttm110) REVERT: E 411 ARG cc_start: 0.7402 (mtp180) cc_final: 0.7065 (mtt180) REVERT: E 485 GLN cc_start: 0.6005 (mt0) cc_final: 0.5715 (mt0) REVERT: E 495 GLU cc_start: 0.6723 (pt0) cc_final: 0.6349 (pt0) REVERT: E 500 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5455 (mt) REVERT: E 539 SER cc_start: 0.7626 (t) cc_final: 0.7277 (p) REVERT: E 668 THR cc_start: 0.7503 (m) cc_final: 0.7211 (p) REVERT: E 685 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6436 (mt-10) REVERT: E 781 TYR cc_start: 0.6274 (m-80) cc_final: 0.5535 (m-80) REVERT: E 814 ASN cc_start: 0.7442 (p0) cc_final: 0.7207 (p0) REVERT: E 831 ARG cc_start: 0.6463 (mtt-85) cc_final: 0.6110 (mtt90) REVERT: E 849 THR cc_start: 0.6417 (m) cc_final: 0.5953 (p) REVERT: E 882 ARG cc_start: 0.6791 (mtm180) cc_final: 0.6493 (mtm110) REVERT: E 975 MET cc_start: 0.6073 (mtm) cc_final: 0.5823 (mtp) REVERT: E 985 ILE cc_start: 0.6574 (tt) cc_final: 0.6306 (mt) REVERT: E 1056 GLU cc_start: 0.5521 (tt0) cc_final: 0.5073 (tm-30) REVERT: E 1128 ASP cc_start: 0.5983 (OUTLIER) cc_final: 0.5704 (p0) REVERT: E 1182 ASP cc_start: 0.5305 (m-30) cc_final: 0.5029 (m-30) REVERT: E 1213 LYS cc_start: 0.7562 (mttt) cc_final: 0.7053 (mtpp) REVERT: E 1221 GLN cc_start: 0.6578 (mm-40) cc_final: 0.6213 (mm110) REVERT: E 1224 ARG cc_start: 0.6818 (mtp-110) cc_final: 0.6201 (mtp180) outliers start: 27 outliers final: 19 residues processed: 239 average time/residue: 1.2131 time to fit residues: 314.7615 Evaluate side-chains 247 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 226 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 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 269 LEU Chi-restraints excluded: chain E residue 368 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 458 ARG Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 853 LYS Chi-restraints excluded: chain E residue 905 VAL 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 1035 GLN Chi-restraints excluded: chain E residue 1128 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 272 GLN ** E 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 992 GLN ** E1035 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5057 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12432 Z= 0.239 Angle : 0.548 10.508 17164 Z= 0.292 Chirality : 0.039 0.197 1967 Planarity : 0.005 0.048 1981 Dihedral : 18.147 177.036 2203 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.79 % Allowed : 17.67 % Favored : 80.54 % 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: 0.96 (0.23), residues: 1380 helix: 1.66 (0.19), residues: 763 sheet: 0.29 (0.49), residues: 113 loop : -0.87 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E1070 HIS 0.004 0.001 HIS E 250 PHE 0.026 0.001 PHE E 465 TYR 0.016 0.001 TYR B 229 ARG 0.007 0.000 ARG E1034 ********************** 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 243 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 223 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 420 LEU cc_start: 0.7140 (mt) cc_final: 0.6869 (mm) REVERT: B 316 PHE cc_start: 0.6943 (t80) cc_final: 0.6275 (t80) REVERT: E 375 ARG cc_start: 0.6790 (ttm170) cc_final: 0.6525 (ttm110) REVERT: E 485 GLN cc_start: 0.5990 (mt0) cc_final: 0.5660 (mt0) REVERT: E 495 GLU cc_start: 0.6752 (pt0) cc_final: 0.6359 (pt0) REVERT: E 500 LEU cc_start: 0.5751 (OUTLIER) cc_final: 0.5455 (mt) REVERT: E 539 SER cc_start: 0.7609 (t) cc_final: 0.7281 (p) REVERT: E 668 THR cc_start: 0.7358 (m) cc_final: 0.7049 (p) REVERT: E 781 TYR cc_start: 0.6072 (m-80) cc_final: 0.5399 (m-80) REVERT: E 814 ASN cc_start: 0.7439 (p0) cc_final: 0.7163 (p0) REVERT: E 831 ARG cc_start: 0.6446 (mtt-85) cc_final: 0.6095 (mtt90) REVERT: E 975 MET cc_start: 0.6129 (mtm) cc_final: 0.5867 (mtp) REVERT: E 985 ILE cc_start: 0.6542 (tt) cc_final: 0.6338 (mt) REVERT: E 1056 GLU cc_start: 0.5547 (tt0) cc_final: 0.5099 (tm-30) REVERT: E 1128 ASP cc_start: 0.5910 (OUTLIER) cc_final: 0.5625 (p0) REVERT: E 1177 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6844 (tt0) REVERT: E 1182 ASP cc_start: 0.5319 (m-30) cc_final: 0.5060 (m-30) REVERT: E 1213 LYS cc_start: 0.7519 (mttt) cc_final: 0.7011 (mtpp) REVERT: E 1221 GLN cc_start: 0.6509 (mm-40) cc_final: 0.6183 (mm110) REVERT: E 1224 ARG cc_start: 0.6786 (mtp-110) cc_final: 0.6121 (mtp180) outliers start: 20 outliers final: 15 residues processed: 231 average time/residue: 1.2865 time to fit residues: 323.7691 Evaluate side-chains 240 residues out of total 1226 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 223 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 SER 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 458 ARG Chi-restraints excluded: chain E residue 500 LEU Chi-restraints excluded: chain E residue 853 LYS Chi-restraints excluded: chain E residue 905 VAL 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 1035 GLN Chi-restraints excluded: chain E residue 1128 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 104 optimal weight: 0.0980 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 0.0770 chunk 47 optimal weight: 0.5980 chunk 116 optimal weight: 0.0770 chunk 14 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.0170 overall best weight: 0.1534 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.168119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.137630 restraints weight = 15232.117| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.63 r_work: 0.3661 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12432 Z= 0.143 Angle : 0.500 8.025 17164 Z= 0.266 Chirality : 0.037 0.158 1967 Planarity : 0.005 0.045 1981 Dihedral : 17.964 178.633 2203 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.81 % Allowed : 18.92 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.23), residues: 1380 helix: 2.06 (0.19), residues: 752 sheet: 0.25 (0.50), residues: 113 loop : -0.59 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E1070 HIS 0.004 0.001 HIS B 249 PHE 0.027 0.001 PHE E 465 TYR 0.011 0.001 TYR E 282 ARG 0.010 0.000 ARG E1034 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5497.91 seconds wall clock time: 97 minutes 57.21 seconds (5877.21 seconds total)