Starting phenix.real_space_refine on Fri Jul 3 19:41:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9s_62197/07_2026/9k9s_62197.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9s_62197/07_2026/9k9s_62197.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k9s_62197/07_2026/9k9s_62197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9s_62197/07_2026/9k9s_62197.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9s_62197/07_2026/9k9s_62197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9s_62197/07_2026/9k9s_62197.cif" } resolution = 2.39 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2132 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 43 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 8994 2.51 5 N 2369 2.21 5 O 2763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14241 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 8207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 8207 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 37, 'TRANS': 967} Chain: "B" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1773 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204} Chain: "C" Number of atoms: 3418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3418 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 10, 'TRANS': 408} Chain breaks: 1 Chain: "P" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 287 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Classifications: {'DNA': 2} Link IDs: {'rna3p': 1} Chain: "T" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 484 Unusual residues: {'ORP': 1} Classifications: {'DNA': 23, 'undetermined': 1} Link IDs: {'rna3p': 22, None: 1} Not linked: pdbres="ORP T 4 " pdbres=" DA T 5 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {' MG': 1, 'TTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.78, per 1000 atoms: 0.20 Number of scatterers: 14241 At special positions: 0 Unit cell: (98.6, 124.95, 147.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 43 15.00 Mg 1 11.99 O 2763 8.00 N 2369 7.00 C 8994 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 472.3 milliseconds 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3146 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 20 sheets defined 40.3% alpha, 20.5% beta 14 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 209 through 220 Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.504A pdb=" N GLU A 229 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 240 through 253 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 473 removed outlier: 3.775A pdb=" N CYS A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 487 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.768A pdb=" N VAL A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.583A pdb=" N ILE A 502 " --> pdb=" O ALA A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 514 Processing helix chain 'A' and resid 552 through 562 Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.951A pdb=" N GLN A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 643 removed outlier: 3.633A pdb=" N GLN A 643 " --> pdb=" O LYS A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 672 removed outlier: 3.796A pdb=" N TYR A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 782 removed outlier: 3.545A pdb=" N SER A 767 " --> pdb=" O ASP A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 857 removed outlier: 3.511A pdb=" N ASN A 841 " --> pdb=" O LYS A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 883 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.737A pdb=" N LEU A 889 " --> pdb=" O PRO A 886 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 967 through 983 removed outlier: 4.291A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN A 981 " --> pdb=" O SER A 977 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 983 " --> pdb=" O ILE A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 997 Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 19 through 31 removed outlier: 3.639A pdb=" N MET B 23 " --> pdb=" O TRP B 19 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLN B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 50 through 55 removed outlier: 3.875A pdb=" N LYS B 54 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN B 55 " --> pdb=" O GLN B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 101 Processing helix chain 'B' and resid 133 through 150 removed outlier: 5.490A pdb=" N LYS B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ILE B 140 " --> pdb=" O TYR B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 24 through 43 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'C' and resid 107 through 121 removed outlier: 4.066A pdb=" N ASP C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 159 Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.873A pdb=" N ASP C 189 " --> pdb=" O GLU C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 257 removed outlier: 3.717A pdb=" N LEU C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 298 Processing helix chain 'C' and resid 316 through 321 Processing helix chain 'C' and resid 332 through 341 removed outlier: 4.046A pdb=" N ASP C 336 " --> pdb=" O ASP C 332 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU C 337 " --> pdb=" O GLU C 333 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 351 Processing helix chain 'C' and resid 352 through 362 removed outlier: 3.718A pdb=" N LEU C 356 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU C 361 " --> pdb=" O SER C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 373 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 397 through 406 removed outlier: 3.519A pdb=" N GLU C 401 " --> pdb=" O ASN C 397 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 425 removed outlier: 3.758A pdb=" N PHE C 410 " --> pdb=" O ASN C 406 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 423 " --> pdb=" O ASP C 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 5.599A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN A 7 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE A 17 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N TYR A 140 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE A 31 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N CYS A 142 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ARG A 33 " --> pdb=" O CYS A 142 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N CYS A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.849A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N ILE A 516 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ARG A 64 " --> pdb=" O ILE A 516 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL A 518 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE A 66 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.305A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER A 574 " --> pdb=" O SER A 610 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 610 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.252A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL A 237 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N THR A 201 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N CYS A 239 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE A 203 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 163 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 305 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 362 removed outlier: 6.630A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS A 416 " --> pdb=" O LYS A 408 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 408 " --> pdb=" O LYS A 416 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 418 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 732 through 734 removed outlier: 6.831A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA A 793 " --> pdb=" O ILE A 547 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP A 549 " --> pdb=" O PHE A 791 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N PHE A 791 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TYR A 795 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR A 811 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ASN A 797 " --> pdb=" O MET A 809 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N MET A 809 " --> pdb=" O ASN A 797 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AB3, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.526A pdb=" N CYS B 125 " --> pdb=" O SER B 43 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 116 through 120 removed outlier: 6.123A pdb=" N CYS B 63 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU B 158 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N CYS B 65 " --> pdb=" O LEU B 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AB6, first strand: chain 'C' and resid 69 through 71 Processing sheet with id=AB7, first strand: chain 'C' and resid 166 through 168 removed outlier: 6.285A pdb=" N ILE C 77 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR C 199 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU C 79 " --> pdb=" O ILE C 197 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE C 197 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 81 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN C 208 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 95 through 97 removed outlier: 6.214A pdb=" N VAL C 130 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N MET C 138 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 214 through 220 removed outlier: 3.539A pdb=" N LYS C 214 " --> pdb=" O LYS C 268 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR C 262 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N SER C 273 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 246 " --> pdb=" O SER C 273 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU C 275 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ILE C 245 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL C 237 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE C 238 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER C 222 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 302 through 304 Processing sheet with id=AC2, first strand: chain 'C' and resid 375 through 379 592 hydrogen bonds defined for protein. 1677 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4161 1.33 - 1.46: 3025 1.46 - 1.58: 7252 1.58 - 1.70: 83 1.70 - 1.82: 108 Bond restraints: 14629 Sorted by residual: bond pdb=" O3B TTP A1102 " pdb=" PG TTP A1102 " ideal model delta sigma weight residual 1.748 1.598 0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C1' DT T 2 " pdb=" N1 DT T 2 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.24e+01 bond pdb=" O3A TTP A1102 " pdb=" PB TTP A1102 " ideal model delta sigma weight residual 1.675 1.599 0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C3' DA T 8 " pdb=" C2' DA T 8 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.32e+01 bond pdb=" C3' DT P 15 " pdb=" C2' DT P 15 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 14624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 19638 2.43 - 4.85: 264 4.85 - 7.28: 28 7.28 - 9.71: 8 9.71 - 12.14: 3 Bond angle restraints: 19941 Sorted by residual: angle pdb=" N3 DT T 22 " pdb=" C4 DT T 22 " pdb=" O4 DT T 22 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT P 12 " pdb=" C4 DT P 12 " pdb=" O4 DT P 12 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT T 19 " pdb=" C4 DT T 19 " pdb=" O4 DT T 19 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT T 10 " pdb=" C4 DT T 10 " pdb=" O4 DT T 10 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT P 15 " pdb=" C4 DT P 15 " pdb=" O4 DT P 15 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 19936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 7277 17.76 - 35.52: 1019 35.52 - 53.27: 390 53.27 - 71.03: 77 71.03 - 88.79: 13 Dihedral angle restraints: 8776 sinusoidal: 3899 harmonic: 4877 Sorted by residual: dihedral pdb=" CA MET C 95 " pdb=" C MET C 95 " pdb=" N VAL C 96 " pdb=" CA VAL C 96 " ideal model delta harmonic sigma weight residual -180.00 -155.67 -24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ILE C 137 " pdb=" C ILE C 137 " pdb=" N MET C 138 " pdb=" CA MET C 138 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA SER A 836 " pdb=" C SER A 836 " pdb=" N LYS A 837 " pdb=" CA LYS A 837 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 8773 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1525 0.044 - 0.088: 523 0.088 - 0.131: 142 0.131 - 0.175: 12 0.175 - 0.219: 6 Chirality restraints: 2208 Sorted by residual: chirality pdb=" CA VAL C 50 " pdb=" N VAL C 50 " pdb=" C VAL C 50 " pdb=" CB VAL C 50 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE A 732 " pdb=" CA ILE A 732 " pdb=" CG1 ILE A 732 " pdb=" CG2 ILE A 732 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB ILE C 245 " pdb=" CA ILE C 245 " pdb=" CG1 ILE C 245 " pdb=" CG2 ILE C 245 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.81e-01 ... (remaining 2205 not shown) Planarity restraints: 2393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 605 " 0.058 5.00e-02 4.00e+02 8.74e-02 1.22e+01 pdb=" N PRO A 606 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 606 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 606 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 398 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" CG ASP A 398 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP A 398 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP A 398 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 45 " 0.040 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO B 46 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 46 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 46 " 0.034 5.00e-02 4.00e+02 ... (remaining 2390 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 366 2.68 - 3.24: 12855 3.24 - 3.79: 21699 3.79 - 4.35: 29090 4.35 - 4.90: 47836 Nonbonded interactions: 111846 Sorted by model distance: nonbonded pdb=" OD1 ASP A 373 " pdb=" N ASP A 374 " model vdw 2.130 3.120 nonbonded pdb=" OH TYR C 181 " pdb=" O VAL C 210 " model vdw 2.230 3.040 nonbonded pdb=" NH2 ARG A 693 " pdb=" O PRO A 721 " model vdw 2.253 3.120 nonbonded pdb=" O TYR A 473 " pdb=" NZ LYS A 478 " model vdw 2.254 3.120 nonbonded pdb=" NH2 ARG C 135 " pdb=" OD1 ASN C 161 " model vdw 2.262 3.120 ... (remaining 111841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.200 Find NCS groups from input model: 0.040 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:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.150 14631 Z= 0.319 Angle : 0.700 12.137 19941 Z= 0.411 Chirality : 0.047 0.219 2208 Planarity : 0.005 0.087 2393 Dihedral : 18.783 88.789 5630 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.20 % Favored : 94.49 % Rotamer: Outliers : 2.24 % Allowed : 25.77 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 are not related in a simple way. whole: -0.14 (0.21), residues: 1634 helix: 0.89 (0.21), residues: 593 sheet: 0.56 (0.27), residues: 377 loop : -1.38 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 407 TYR 0.019 0.002 TYR A 528 PHE 0.035 0.002 PHE C 188 TRP 0.015 0.001 TRP A 470 HIS 0.007 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.32 (14629) covalent geometry : angle 0.69989 / 0.41 (19941) hydrogen bonds : bond 0.15250 / 10.03 ( 621) hydrogen bonds : angle 5.71906 / 3.88 ( 1743) Misc. bond : bond 0.03915 / 1.96 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 350 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 859 MET cc_start: 0.4505 (tpp) cc_final: 0.4266 (tpt) REVERT: A 978 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7043 (tm-30) REVERT: C 178 ASP cc_start: 0.8051 (t70) cc_final: 0.7594 (p0) outliers start: 34 outliers final: 25 residues processed: 374 average time/residue: 0.5538 time to fit residues: 226.6863 Evaluate side-chains 371 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 346 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 822 GLU Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 878 SER Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 388 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 GLN A 675 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.160043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.124336 restraints weight = 19865.352| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.82 r_work: 0.3464 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.0600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14631 Z= 0.209 Angle : 0.626 10.001 19941 Z= 0.337 Chirality : 0.046 0.197 2208 Planarity : 0.005 0.066 2393 Dihedral : 15.071 88.818 2339 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.47 % Favored : 95.23 % Rotamer: Outliers : 4.09 % Allowed : 21.69 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 are not related in a simple way. whole: -0.02 (0.21), residues: 1634 helix: 1.05 (0.21), residues: 598 sheet: 0.60 (0.28), residues: 368 loop : -1.35 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 407 TYR 0.018 0.002 TYR A 528 PHE 0.036 0.002 PHE C 188 TRP 0.017 0.002 TRP A 470 HIS 0.007 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (14629) covalent geometry : angle 0.62628 / 0.34 (19941) hydrogen bonds : bond 0.06163 / 4.02 ( 621) hydrogen bonds : angle 4.79312 / 3.29 ( 1743) Misc. bond : bond 0.00280 / 0.15 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 353 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 277 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: A 398 ASP cc_start: 0.7785 (t0) cc_final: 0.7386 (t0) REVERT: C 135 ARG cc_start: 0.6313 (tpm-80) cc_final: 0.5931 (tpt90) REVERT: C 181 TYR cc_start: 0.7767 (t80) cc_final: 0.7566 (t80) REVERT: C 224 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6551 (ptpp) REVERT: C 322 LYS cc_start: 0.6826 (mtmt) cc_final: 0.6557 (mtmt) outliers start: 62 outliers final: 38 residues processed: 377 average time/residue: 0.5481 time to fit residues: 225.4782 Evaluate side-chains 386 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 346 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 185 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 375 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 146 optimal weight: 8.9990 chunk 140 optimal weight: 0.4980 chunk 59 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 GLN A 675 ASN B 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.161497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.125167 restraints weight = 19953.828| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.81 r_work: 0.3491 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14631 Z= 0.138 Angle : 0.564 7.816 19941 Z= 0.306 Chirality : 0.042 0.187 2208 Planarity : 0.004 0.055 2393 Dihedral : 14.912 86.131 2315 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.16 % Favored : 95.53 % Rotamer: Outliers : 4.28 % Allowed : 22.35 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 are not related in a simple way. whole: 0.16 (0.21), residues: 1634 helix: 1.27 (0.21), residues: 598 sheet: 0.61 (0.28), residues: 368 loop : -1.28 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 16 TYR 0.021 0.001 TYR C 76 PHE 0.042 0.001 PHE C 188 TRP 0.013 0.001 TRP A 470 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (14629) covalent geometry : angle 0.56386 / 0.31 (19941) hydrogen bonds : bond 0.04992 / 3.25 ( 621) hydrogen bonds : angle 4.55973 / 3.13 ( 1743) Misc. bond : bond 0.00002 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 348 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 711 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7769 (mmm) REVERT: B 1 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8571 (mmt) REVERT: C 135 ARG cc_start: 0.6330 (tpm-80) cc_final: 0.5958 (tpt90) REVERT: C 157 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6474 (pt0) REVERT: C 162 ILE cc_start: 0.6894 (OUTLIER) cc_final: 0.5759 (tp) REVERT: C 181 TYR cc_start: 0.7682 (t80) cc_final: 0.7394 (t80) REVERT: C 224 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6575 (ptmm) REVERT: C 322 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6483 (mtmt) REVERT: C 345 LYS cc_start: 0.7459 (ptpp) cc_final: 0.6975 (ptpp) REVERT: C 381 ASN cc_start: 0.7568 (t0) cc_final: 0.7366 (t0) outliers start: 65 outliers final: 44 residues processed: 373 average time/residue: 0.5598 time to fit residues: 227.6937 Evaluate side-chains 391 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 341 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 SER Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 375 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 94 optimal weight: 0.0570 chunk 42 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 108 optimal weight: 0.0000 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 132 optimal weight: 50.0000 chunk 7 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN A 538 GLN A 675 ASN C 304 ASN C 397 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.162380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126212 restraints weight = 19796.484| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.82 r_work: 0.3495 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14631 Z= 0.123 Angle : 0.548 7.563 19941 Z= 0.296 Chirality : 0.042 0.190 2208 Planarity : 0.004 0.054 2393 Dihedral : 14.849 85.338 2310 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.16 % Favored : 95.53 % Rotamer: Outliers : 4.15 % Allowed : 23.20 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 are not related in a simple way. whole: 0.24 (0.21), residues: 1634 helix: 1.35 (0.21), residues: 599 sheet: 0.64 (0.28), residues: 368 loop : -1.23 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 407 TYR 0.016 0.001 TYR C 363 PHE 0.046 0.001 PHE C 188 TRP 0.012 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (14629) covalent geometry : angle 0.54795 / 0.30 (19941) hydrogen bonds : bond 0.04603 / 3.00 ( 621) hydrogen bonds : angle 4.43784 / 3.05 ( 1743) Misc. bond : bond 0.00039 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 347 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 711 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7672 (mpp) REVERT: C 135 ARG cc_start: 0.6385 (tpm-80) cc_final: 0.6017 (tpt90) REVERT: C 157 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6440 (pt0) REVERT: C 160 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6160 (tm) REVERT: C 162 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.5815 (tp) REVERT: C 181 TYR cc_start: 0.7665 (t80) cc_final: 0.7335 (t80) REVERT: C 183 ILE cc_start: 0.8440 (mt) cc_final: 0.8200 (mt) REVERT: C 224 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6585 (ptmm) REVERT: C 322 LYS cc_start: 0.6730 (OUTLIER) cc_final: 0.6409 (mtmt) REVERT: C 345 LYS cc_start: 0.7456 (ptpp) cc_final: 0.6966 (ptpp) REVERT: C 381 ASN cc_start: 0.7599 (t0) cc_final: 0.7344 (t0) outliers start: 63 outliers final: 40 residues processed: 375 average time/residue: 0.5614 time to fit residues: 229.5874 Evaluate side-chains 390 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 344 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 375 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 163 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 0.0570 chunk 12 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 164 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN A 538 GLN A 675 ASN B 59 ASN C 397 ASN 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 = 0.162093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.126119 restraints weight = 19873.416| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.77 r_work: 0.3496 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14631 Z= 0.133 Angle : 0.549 8.308 19941 Z= 0.296 Chirality : 0.042 0.191 2208 Planarity : 0.004 0.053 2393 Dihedral : 14.811 84.591 2309 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.10 % Favored : 95.59 % Rotamer: Outliers : 4.42 % Allowed : 23.01 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 are not related in a simple way. whole: 0.25 (0.21), residues: 1634 helix: 1.37 (0.21), residues: 602 sheet: 0.60 (0.28), residues: 367 loop : -1.22 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 407 TYR 0.016 0.001 TYR A 637 PHE 0.049 0.001 PHE C 188 TRP 0.012 0.001 TRP A 470 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (14629) covalent geometry : angle 0.54857 / 0.30 (19941) hydrogen bonds : bond 0.04643 / 3.04 ( 621) hydrogen bonds : angle 4.38151 / 3.01 ( 1743) Misc. bond : bond 0.00017 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 353 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 711 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7671 (mpp) REVERT: C 135 ARG cc_start: 0.6357 (tpm-80) cc_final: 0.6006 (tpt90) REVERT: C 157 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6428 (pt0) REVERT: C 160 LEU cc_start: 0.6409 (OUTLIER) cc_final: 0.6078 (tm) REVERT: C 162 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.5805 (tp) REVERT: C 181 TYR cc_start: 0.7648 (t80) cc_final: 0.7309 (t80) REVERT: C 183 ILE cc_start: 0.8423 (mt) cc_final: 0.8181 (mt) REVERT: C 224 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6764 (ptmm) REVERT: C 345 LYS cc_start: 0.7457 (ptpp) cc_final: 0.6946 (ptpp) REVERT: C 363 TYR cc_start: 0.7175 (m-80) cc_final: 0.6882 (m-80) REVERT: C 381 ASN cc_start: 0.7641 (t0) cc_final: 0.7344 (t0) REVERT: C 406 ASN cc_start: 0.7202 (p0) cc_final: 0.6866 (p0) outliers start: 67 outliers final: 48 residues processed: 381 average time/residue: 0.5612 time to fit residues: 232.9228 Evaluate side-chains 397 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 344 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 393 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 75 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.0980 chunk 90 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 137 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 GLN A 675 ASN B 52 GLN C 304 ASN C 397 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.159954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.123519 restraints weight = 19754.630| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.81 r_work: 0.3438 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14631 Z= 0.265 Angle : 0.640 10.183 19941 Z= 0.339 Chirality : 0.047 0.193 2208 Planarity : 0.005 0.055 2393 Dihedral : 15.000 85.767 2309 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.22 % Favored : 95.47 % Rotamer: Outliers : 4.28 % Allowed : 23.40 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 are not related in a simple way. whole: 0.07 (0.21), residues: 1634 helix: 1.17 (0.21), residues: 602 sheet: 0.52 (0.27), residues: 373 loop : -1.30 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 407 TYR 0.021 0.002 TYR A 528 PHE 0.047 0.002 PHE C 188 TRP 0.014 0.002 TRP A 470 HIS 0.009 0.002 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.27 (14629) covalent geometry : angle 0.63969 / 0.34 (19941) hydrogen bonds : bond 0.06176 / 4.06 ( 621) hydrogen bonds : angle 4.52406 / 3.10 ( 1743) Misc. bond : bond 0.00070 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 350 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7849 (mpt) REVERT: A 711 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7748 (mpp) REVERT: B 1 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8585 (mmt) REVERT: C 135 ARG cc_start: 0.6432 (tpm-80) cc_final: 0.6037 (tpt90) REVERT: C 157 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6468 (pt0) REVERT: C 160 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6207 (tm) REVERT: C 162 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.5971 (tp) REVERT: C 181 TYR cc_start: 0.7680 (t80) cc_final: 0.7347 (t80) REVERT: C 183 ILE cc_start: 0.8421 (mt) cc_final: 0.8174 (mt) REVERT: C 226 ASP cc_start: 0.7399 (t0) cc_final: 0.7156 (t0) REVERT: C 227 ARG cc_start: 0.7606 (mtt180) cc_final: 0.7378 (mtt180) REVERT: C 345 LYS cc_start: 0.7663 (ptpp) cc_final: 0.7180 (ptpp) REVERT: C 363 TYR cc_start: 0.7261 (m-80) cc_final: 0.6946 (m-80) REVERT: C 381 ASN cc_start: 0.7746 (t0) cc_final: 0.7491 (t0) REVERT: C 406 ASN cc_start: 0.7251 (p0) cc_final: 0.6915 (p0) outliers start: 65 outliers final: 44 residues processed: 377 average time/residue: 0.5667 time to fit residues: 232.1645 Evaluate side-chains 397 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 347 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 421 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 110 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 92 optimal weight: 0.1980 chunk 19 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN A 362 ASN A 538 GLN A 675 ASN B 52 GLN B 59 ASN C 304 ASN C 397 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.161494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.125017 restraints weight = 19775.405| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.78 r_work: 0.3483 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14631 Z= 0.147 Angle : 0.577 9.194 19941 Z= 0.309 Chirality : 0.043 0.200 2208 Planarity : 0.004 0.052 2393 Dihedral : 14.923 86.452 2309 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.35 % Favored : 95.35 % Rotamer: Outliers : 4.15 % Allowed : 23.86 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 are not related in a simple way. whole: 0.15 (0.21), residues: 1634 helix: 1.28 (0.21), residues: 602 sheet: 0.55 (0.27), residues: 368 loop : -1.28 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 407 TYR 0.015 0.001 TYR A 637 PHE 0.048 0.001 PHE C 188 TRP 0.014 0.001 TRP A 470 HIS 0.008 0.001 HIS A 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (14629) covalent geometry : angle 0.57668 / 0.31 (19941) hydrogen bonds : bond 0.04898 / 3.21 ( 621) hydrogen bonds : angle 4.38862 / 3.01 ( 1743) Misc. bond : bond 0.00032 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 348 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7794 (mpt) REVERT: A 711 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7715 (mpp) REVERT: B 205 ASP cc_start: 0.7804 (t0) cc_final: 0.7537 (t0) REVERT: C 135 ARG cc_start: 0.6345 (tpm-80) cc_final: 0.6013 (tpt90) REVERT: C 157 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.6413 (pt0) REVERT: C 160 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6088 (tm) REVERT: C 162 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.5927 (tp) REVERT: C 181 TYR cc_start: 0.7619 (t80) cc_final: 0.7277 (t80) REVERT: C 183 ILE cc_start: 0.8401 (mt) cc_final: 0.8143 (mt) REVERT: C 226 ASP cc_start: 0.7342 (t0) cc_final: 0.7050 (t0) REVERT: C 227 ARG cc_start: 0.7447 (mtt180) cc_final: 0.7195 (mtt180) REVERT: C 345 LYS cc_start: 0.7643 (ptpp) cc_final: 0.7155 (ptpp) REVERT: C 381 ASN cc_start: 0.7766 (t0) cc_final: 0.7453 (t0) REVERT: C 406 ASN cc_start: 0.7208 (p0) cc_final: 0.6965 (p0) outliers start: 63 outliers final: 43 residues processed: 375 average time/residue: 0.5710 time to fit residues: 232.6041 Evaluate side-chains 404 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 356 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 393 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 116 optimal weight: 2.9990 chunk 82 optimal weight: 0.0060 chunk 130 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 102 optimal weight: 0.0670 chunk 128 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 GLN A 675 ASN B 52 GLN C 304 ASN C 397 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.161530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.125372 restraints weight = 19791.924| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.78 r_work: 0.3475 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14631 Z= 0.146 Angle : 0.583 8.936 19941 Z= 0.311 Chirality : 0.043 0.187 2208 Planarity : 0.004 0.053 2393 Dihedral : 14.826 85.720 2306 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.16 % Favored : 95.53 % Rotamer: Outliers : 3.69 % Allowed : 24.65 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 are not related in a simple way. whole: 0.17 (0.21), residues: 1634 helix: 1.31 (0.21), residues: 602 sheet: 0.58 (0.27), residues: 368 loop : -1.29 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 849 TYR 0.015 0.001 TYR A 637 PHE 0.048 0.001 PHE C 188 TRP 0.014 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (14629) covalent geometry : angle 0.58304 / 0.31 (19941) hydrogen bonds : bond 0.04853 / 3.17 ( 621) hydrogen bonds : angle 4.38599 / 3.01 ( 1743) Misc. bond : bond 0.00032 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 352 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7795 (mpt) REVERT: A 711 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7722 (mpp) REVERT: B 205 ASP cc_start: 0.7802 (t0) cc_final: 0.7537 (t0) REVERT: C 135 ARG cc_start: 0.6397 (tpm-80) cc_final: 0.6064 (tpt90) REVERT: C 157 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6439 (pt0) REVERT: C 160 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6106 (tm) REVERT: C 162 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.5887 (tp) REVERT: C 181 TYR cc_start: 0.7624 (t80) cc_final: 0.7286 (t80) REVERT: C 183 ILE cc_start: 0.8407 (mt) cc_final: 0.8149 (mt) REVERT: C 226 ASP cc_start: 0.7365 (t0) cc_final: 0.7062 (t0) REVERT: C 227 ARG cc_start: 0.7359 (mtt180) cc_final: 0.7122 (mtt180) REVERT: C 345 LYS cc_start: 0.7647 (ptpp) cc_final: 0.7154 (ptpp) REVERT: C 381 ASN cc_start: 0.7777 (t0) cc_final: 0.7476 (t0) REVERT: C 397 ASN cc_start: 0.8348 (t0) cc_final: 0.8111 (t0) REVERT: C 406 ASN cc_start: 0.7224 (p0) cc_final: 0.6916 (p0) outliers start: 56 outliers final: 44 residues processed: 375 average time/residue: 0.5588 time to fit residues: 228.0776 Evaluate side-chains 394 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 345 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 393 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 ASN A 538 GLN A 675 ASN B 52 GLN B 59 ASN C 304 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.161042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124878 restraints weight = 20041.916| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.71 r_work: 0.3477 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14631 Z= 0.158 Angle : 0.602 11.926 19941 Z= 0.317 Chirality : 0.043 0.189 2208 Planarity : 0.004 0.053 2393 Dihedral : 14.820 85.419 2306 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.28 % Favored : 95.41 % Rotamer: Outliers : 3.89 % Allowed : 24.52 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 are not related in a simple way. whole: 0.18 (0.21), residues: 1634 helix: 1.32 (0.21), residues: 602 sheet: 0.59 (0.27), residues: 368 loop : -1.30 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 407 TYR 0.016 0.001 TYR A 528 PHE 0.045 0.002 PHE C 188 TRP 0.013 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (14629) covalent geometry : angle 0.60209 / 0.32 (19941) hydrogen bonds : bond 0.04936 / 3.23 ( 621) hydrogen bonds : angle 4.36159 / 2.99 ( 1743) Misc. bond : bond 0.00038 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 346 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.7784 (mpt) REVERT: A 711 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7729 (mpp) REVERT: B 205 ASP cc_start: 0.7791 (t0) cc_final: 0.7524 (t0) REVERT: C 135 ARG cc_start: 0.6417 (tpm-80) cc_final: 0.6050 (tpt90) REVERT: C 157 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6441 (pt0) REVERT: C 160 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6126 (tm) REVERT: C 162 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.5882 (tp) REVERT: C 181 TYR cc_start: 0.7643 (t80) cc_final: 0.7309 (t80) REVERT: C 183 ILE cc_start: 0.8398 (mt) cc_final: 0.8131 (mt) REVERT: C 226 ASP cc_start: 0.7363 (t0) cc_final: 0.6997 (t0) REVERT: C 227 ARG cc_start: 0.7293 (mtt180) cc_final: 0.7024 (mtt180) REVERT: C 345 LYS cc_start: 0.7657 (ptpp) cc_final: 0.7169 (ptpp) REVERT: C 381 ASN cc_start: 0.7798 (t0) cc_final: 0.7477 (t0) REVERT: C 406 ASN cc_start: 0.7231 (p0) cc_final: 0.6929 (p0) REVERT: C 419 ASP cc_start: 0.7160 (p0) cc_final: 0.6926 (p0) outliers start: 59 outliers final: 46 residues processed: 375 average time/residue: 0.5962 time to fit residues: 243.3682 Evaluate side-chains 396 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 345 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 304 ASN Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 337 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 117 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 GLN A 675 ASN B 52 GLN C 304 ASN C 397 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.161270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.125069 restraints weight = 19801.605| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.77 r_work: 0.3467 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14631 Z= 0.193 Angle : 0.814 59.200 19941 Z= 0.458 Chirality : 0.045 0.544 2208 Planarity : 0.004 0.054 2393 Dihedral : 14.823 85.398 2306 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.28 % Favored : 95.41 % Rotamer: Outliers : 3.56 % Allowed : 24.72 % Favored : 71.72 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.33 % 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 are not related in a simple way. whole: 0.17 (0.21), residues: 1634 helix: 1.30 (0.21), residues: 602 sheet: 0.58 (0.27), residues: 374 loop : -1.30 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 376 TYR 0.016 0.001 TYR A 528 PHE 0.042 0.002 PHE C 188 TRP 0.014 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (14629) covalent geometry : angle 0.81360 / 0.46 (19941) hydrogen bonds : bond 0.05025 / 3.30 ( 621) hydrogen bonds : angle 4.35488 / 2.98 ( 1743) Misc. bond : bond 0.00051 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3268 Ramachandran restraints generated. 1634 Oldfield, 0 Emsley, 1634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 348 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 357 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7800 (mpt) REVERT: A 711 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7749 (mpp) REVERT: B 205 ASP cc_start: 0.7817 (t0) cc_final: 0.7548 (t0) REVERT: C 135 ARG cc_start: 0.6416 (tpm-80) cc_final: 0.6055 (tpt90) REVERT: C 157 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6436 (pt0) REVERT: C 160 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6117 (tm) REVERT: C 162 ILE cc_start: 0.6932 (OUTLIER) cc_final: 0.5877 (tp) REVERT: C 181 TYR cc_start: 0.7634 (t80) cc_final: 0.7302 (t80) REVERT: C 183 ILE cc_start: 0.8400 (mt) cc_final: 0.8133 (mt) REVERT: C 226 ASP cc_start: 0.7353 (t0) cc_final: 0.7024 (t0) REVERT: C 227 ARG cc_start: 0.7264 (mtt180) cc_final: 0.7055 (mtt180) REVERT: C 345 LYS cc_start: 0.7659 (ptpp) cc_final: 0.7171 (ptpp) REVERT: C 381 ASN cc_start: 0.7803 (t0) cc_final: 0.7477 (t0) REVERT: C 397 ASN cc_start: 0.8293 (t0) cc_final: 0.8091 (t0) REVERT: C 406 ASN cc_start: 0.7237 (p0) cc_final: 0.6935 (p0) REVERT: C 419 ASP cc_start: 0.7177 (p0) cc_final: 0.6942 (p0) outliers start: 54 outliers final: 46 residues processed: 370 average time/residue: 0.5613 time to fit residues: 225.9010 Evaluate side-chains 399 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 348 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 82 LYS Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 445 LYS Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 642 LYS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 837 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 106 LYS Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 82 TYR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 337 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.6980 chunk 44 optimal weight: 0.0770 chunk 106 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 82 optimal weight: 0.0170 chunk 88 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 538 GLN A 675 ASN B 52 GLN ** C 304 ASN ** 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 = 0.4110 r_free = 0.4110 target = 0.160925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.124736 restraints weight = 19952.928| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.76 r_work: 0.3476 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14631 Z= 0.193 Angle : 0.814 59.200 19941 Z= 0.458 Chirality : 0.045 0.544 2208 Planarity : 0.004 0.054 2393 Dihedral : 14.823 85.398 2306 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.28 % Favored : 95.41 % Rotamer: Outliers : 3.43 % Allowed : 24.79 % Favored : 71.79 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.33 % 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 are not related in a simple way. whole: 0.17 (0.21), residues: 1634 helix: 1.30 (0.21), residues: 602 sheet: 0.58 (0.27), residues: 374 loop : -1.30 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 376 TYR 0.016 0.001 TYR A 528 PHE 0.042 0.002 PHE C 188 TRP 0.014 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (14629) covalent geometry : angle 0.81360 / 0.46 (19941) hydrogen bonds : bond 0.05025 / 3.30 ( 621) hydrogen bonds : angle 4.35488 / 2.98 ( 1743) Misc. bond : bond 0.00051 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7249.69 seconds wall clock time: 123 minutes 22.66 seconds (7402.66 seconds total)