Starting phenix.real_space_refine on Sat May 17 16:08:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k9s_62197/05_2025/9k9s_62197.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k9s_62197/05_2025/9k9s_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_62197/05_2025/9k9s_62197.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k9s_62197/05_2025/9k9s_62197.map" model { file = "/net/cci-nas-00/data/ceres_data/9k9s_62197/05_2025/9k9s_62197.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k9s_62197/05_2025/9k9s_62197.cif" } resolution = 2.39 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.37, per 1000 atoms: 0.59 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: 3.66 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.82 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: 5.72 Time building geometry restraints manager: 4.16 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=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 8.92e+00 bond pdb=" N THR C 51 " pdb=" CA THR C 51 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.24e-02 6.50e+03 7.63e+00 bond pdb=" N ASP B 68 " pdb=" CA ASP B 68 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.04e-02 9.25e+03 7.59e+00 bond pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.44e+00 bond pdb=" N VAL C 50 " pdb=" CA VAL C 50 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.43e+00 ... (remaining 14624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 19686 2.43 - 4.85: 228 4.85 - 7.28: 22 7.28 - 9.71: 3 9.71 - 12.14: 2 Bond angle restraints: 19941 Sorted by residual: angle pdb=" CB MET C 184 " pdb=" CG MET C 184 " pdb=" SD MET C 184 " ideal model delta sigma weight residual 112.70 124.84 -12.14 3.00e+00 1.11e-01 1.64e+01 angle pdb=" CA LYS C 349 " pdb=" CB LYS C 349 " pdb=" CG LYS C 349 " ideal model delta sigma weight residual 114.10 121.85 -7.75 2.00e+00 2.50e-01 1.50e+01 angle pdb=" C PHE C 233 " pdb=" N ILE C 234 " pdb=" CA ILE C 234 " ideal model delta sigma weight residual 123.33 119.96 3.37 8.70e-01 1.32e+00 1.50e+01 angle pdb=" C THR C 418 " pdb=" N ASP C 419 " pdb=" CA ASP C 419 " ideal model delta sigma weight residual 121.58 115.06 6.52 1.95e+00 2.63e-01 1.12e+01 angle pdb=" N PRO A 593 " pdb=" CA PRO A 593 " pdb=" C PRO A 593 " ideal model delta sigma weight residual 110.70 114.43 -3.73 1.22e+00 6.72e-01 9.36e+00 ... (remaining 19936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.95: 7985 27.95 - 55.90: 706 55.90 - 83.85: 55 83.85 - 111.80: 5 111.80 - 139.76: 1 Dihedral angle restraints: 8752 sinusoidal: 3875 harmonic: 4877 Sorted by residual: dihedral pdb=" C2 TTP A1102 " pdb=" C1' TTP A1102 " pdb=" N1 TTP A1102 " pdb=" O4' TTP A1102 " ideal model delta sinusoidal sigma weight residual 301.68 161.93 139.76 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" O3B TTP A1102 " pdb=" O3A TTP A1102 " pdb=" PB TTP A1102 " pdb=" PA TTP A1102 " ideal model delta sinusoidal sigma weight residual 180.00 77.53 102.47 1 2.00e+01 2.50e-03 2.92e+01 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 ... (remaining 8749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1563 0.044 - 0.088: 508 0.088 - 0.131: 121 0.131 - 0.175: 11 0.175 - 0.219: 5 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.610 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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 : 0.005 0.058 14631 Z= 0.235 Angle : 0.652 12.137 19941 Z= 0.352 Chirality : 0.045 0.219 2208 Planarity : 0.005 0.087 2393 Dihedral : 18.795 139.756 5606 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (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 TRP 0.015 0.001 TRP A 470 HIS 0.007 0.001 HIS A 170 PHE 0.035 0.002 PHE C 188 TYR 0.019 0.002 TYR A 528 ARG 0.006 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.15250 ( 621) hydrogen bonds : angle 5.71906 ( 1743) covalent geometry : bond 0.00535 (14629) covalent geometry : angle 0.65166 (19941) Misc. bond : bond 0.03915 ( 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 : 1.487 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: 0.7607 (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: 1.2395 time to fit residues: 507.3277 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 : 1.546 ------------------------------------------------------------------------------- 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 139 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 0.0000 chunk 84 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN A 675 ASN A 816 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.161571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126050 restraints weight = 19844.618| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.92 r_work: 0.3467 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.0802 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= 0.141 Angle : 0.566 8.233 19941 Z= 0.303 Chirality : 0.042 0.188 2208 Planarity : 0.005 0.065 2393 Dihedral : 14.884 140.106 2315 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.10 % Favored : 95.59 % Rotamer: Outliers : 3.49 % Allowed : 22.21 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1634 helix: 1.23 (0.21), residues: 598 sheet: 0.60 (0.28), residues: 367 loop : -1.23 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.005 0.001 HIS A 170 PHE 0.032 0.001 PHE C 188 TYR 0.018 0.001 TYR C 363 ARG 0.005 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 621) hydrogen bonds : angle 4.57839 ( 1743) covalent geometry : bond 0.00319 (14629) covalent geometry : angle 0.56554 (19941) Misc. bond : bond 0.00037 ( 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 408 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 355 time to evaluate : 1.681 Fit side-chains revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7793 (t0) cc_final: 0.7449 (t0) REVERT: C 135 ARG cc_start: 0.6402 (tpm-80) cc_final: 0.6037 (tpt90) REVERT: C 157 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6437 (pt0) REVERT: C 181 TYR cc_start: 0.7655 (t80) cc_final: 0.7405 (t80) REVERT: C 183 ILE cc_start: 0.8450 (mt) cc_final: 0.8227 (mt) REVERT: C 224 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6554 (pmmt) REVERT: C 292 ARG cc_start: 0.8053 (tpm170) cc_final: 0.7414 (tpm170) REVERT: C 345 LYS cc_start: 0.7462 (ptpp) cc_final: 0.6975 (ptpp) REVERT: C 349 LYS cc_start: 0.8366 (tptt) cc_final: 0.8155 (tptt) REVERT: C 376 ARG cc_start: 0.6880 (mmt180) cc_final: 0.6551 (mmt180) REVERT: C 381 ASN cc_start: 0.7736 (t0) cc_final: 0.7467 (t0) outliers start: 53 outliers final: 30 residues processed: 375 average time/residue: 1.3491 time to fit residues: 550.0123 Evaluate side-chains 382 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 350 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 143 ASP Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 226 SER 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 540 MET Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 774 LEU 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 96 ILE 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 22 PHE Chi-restraints excluded: chain C residue 30 LYS 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 185 GLU 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 337 GLU Chi-restraints excluded: chain C residue 359 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 34 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 131 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN A 675 ASN A 816 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.159979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.124176 restraints weight = 19899.504| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.69 r_work: 0.3471 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.0894 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= 0.210 Angle : 0.594 8.978 19941 Z= 0.317 Chirality : 0.044 0.189 2208 Planarity : 0.005 0.062 2393 Dihedral : 15.008 138.413 2285 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.28 % Favored : 95.41 % Rotamer: Outliers : 3.96 % Allowed : 22.41 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1634 helix: 1.14 (0.21), residues: 602 sheet: 0.58 (0.27), residues: 373 loop : -1.28 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.007 0.001 HIS A 839 PHE 0.033 0.002 PHE C 188 TYR 0.018 0.002 TYR A 528 ARG 0.005 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.05755 ( 621) hydrogen bonds : angle 4.52205 ( 1743) covalent geometry : bond 0.00505 (14629) covalent geometry : angle 0.59385 (19941) Misc. bond : bond 0.00054 ( 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 421 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 361 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 398 ASP cc_start: 0.7766 (t0) cc_final: 0.7241 (t0) REVERT: C 135 ARG cc_start: 0.6388 (tpm-80) cc_final: 0.6027 (tpt90) REVERT: C 160 LEU cc_start: 0.6490 (tm) cc_final: 0.6057 (tm) REVERT: C 162 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.5915 (tp) REVERT: C 181 TYR cc_start: 0.7621 (t80) cc_final: 0.7288 (t80) REVERT: C 183 ILE cc_start: 0.8450 (mt) cc_final: 0.8240 (mt) REVERT: C 226 ASP cc_start: 0.7421 (t0) cc_final: 0.7118 (t0) REVERT: C 345 LYS cc_start: 0.7510 (ptpp) cc_final: 0.7003 (ptpp) REVERT: C 349 LYS cc_start: 0.8330 (tptt) cc_final: 0.8062 (tptt) REVERT: C 376 ARG cc_start: 0.6832 (mmt180) cc_final: 0.6571 (mmt180) REVERT: C 381 ASN cc_start: 0.7787 (t0) cc_final: 0.7487 (t0) outliers start: 60 outliers final: 43 residues processed: 385 average time/residue: 1.3220 time to fit residues: 555.2467 Evaluate side-chains 393 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 349 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 143 ASP Chi-restraints excluded: chain A residue 207 MET 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 837 LYS Chi-restraints excluded: chain A residue 970 VAL 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 96 ILE Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 169 LYS 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 162 ILE Chi-restraints excluded: chain C residue 185 GLU 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 335 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 359 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 134 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 106 optimal weight: 0.0870 chunk 127 optimal weight: 0.0870 chunk 150 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 362 ASN A 538 GLN A 675 ASN B 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.162067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.126619 restraints weight = 19907.477| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.83 r_work: 0.3481 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1151 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= 0.125 Angle : 0.545 8.728 19941 Z= 0.288 Chirality : 0.042 0.188 2208 Planarity : 0.004 0.056 2393 Dihedral : 14.801 140.318 2285 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.04 % Favored : 95.65 % Rotamer: Outliers : 3.96 % Allowed : 23.20 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.21), residues: 1634 helix: 1.35 (0.21), residues: 600 sheet: 0.65 (0.28), residues: 367 loop : -1.23 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 PHE 0.038 0.001 PHE C 188 TYR 0.017 0.001 TYR A 637 ARG 0.005 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 621) hydrogen bonds : angle 4.32545 ( 1743) covalent geometry : bond 0.00282 (14629) covalent geometry : angle 0.54503 (19941) Misc. bond : bond 0.00024 ( 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 411 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 351 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 551 ASN cc_start: 0.8589 (m-40) cc_final: 0.8355 (m110) REVERT: A 711 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7779 (mmm) REVERT: B 205 ASP cc_start: 0.7809 (t0) cc_final: 0.7565 (t0) REVERT: C 135 ARG cc_start: 0.6411 (tpm-80) cc_final: 0.6091 (tpt90) REVERT: C 157 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6421 (pt0) REVERT: C 160 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.5916 (tm) REVERT: C 162 ILE cc_start: 0.6863 (OUTLIER) cc_final: 0.5817 (tp) REVERT: C 181 TYR cc_start: 0.7599 (t80) cc_final: 0.7279 (t80) REVERT: C 226 ASP cc_start: 0.7461 (t0) cc_final: 0.7066 (t0) REVERT: C 345 LYS cc_start: 0.7643 (ptpp) cc_final: 0.7155 (ptpp) REVERT: C 376 ARG cc_start: 0.6856 (mmt180) cc_final: 0.6565 (mmt180) REVERT: C 381 ASN cc_start: 0.7799 (t0) cc_final: 0.7463 (t0) outliers start: 60 outliers final: 34 residues processed: 379 average time/residue: 1.3298 time to fit residues: 548.1037 Evaluate side-chains 390 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 352 time to evaluate : 1.554 ------------------------------------------------------------------------------- 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 165 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 292 LYS Chi-restraints excluded: chain A residue 340 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 724 MET Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 979 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 130 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 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 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 337 GLU Chi-restraints excluded: chain C residue 359 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 18 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 88 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 538 GLN A 675 ASN B 52 GLN C 397 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.160169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.124617 restraints weight = 19957.524| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.79 r_work: 0.3465 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14631 Z= 0.196 Angle : 0.592 9.854 19941 Z= 0.313 Chirality : 0.044 0.189 2208 Planarity : 0.005 0.057 2393 Dihedral : 14.927 138.074 2283 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.28 % Favored : 95.41 % Rotamer: Outliers : 4.35 % Allowed : 23.20 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1634 helix: 1.24 (0.21), residues: 602 sheet: 0.57 (0.27), residues: 373 loop : -1.28 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 470 HIS 0.007 0.001 HIS A 839 PHE 0.036 0.002 PHE C 188 TYR 0.018 0.001 TYR A 528 ARG 0.005 0.000 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.05466 ( 621) hydrogen bonds : angle 4.41454 ( 1743) covalent geometry : bond 0.00471 (14629) covalent geometry : angle 0.59178 (19941) Misc. bond : bond 0.00051 ( 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 419 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 353 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8795 (m-40) cc_final: 0.8419 (m110) REVERT: A 357 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7844 (mpt) REVERT: A 551 ASN cc_start: 0.8604 (m-40) cc_final: 0.8384 (m110) REVERT: A 711 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7783 (mmm) REVERT: B 205 ASP cc_start: 0.7802 (t0) cc_final: 0.7541 (t0) REVERT: C 135 ARG cc_start: 0.6435 (tpm-80) cc_final: 0.6119 (tpt90) REVERT: C 157 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6414 (pt0) REVERT: C 160 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5756 (tm) REVERT: C 162 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.5867 (tp) REVERT: C 181 TYR cc_start: 0.7585 (t80) cc_final: 0.7271 (t80) REVERT: C 224 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6844 (ptmm) REVERT: C 226 ASP cc_start: 0.7519 (t0) cc_final: 0.7189 (t0) REVERT: C 304 ASN cc_start: 0.7660 (t0) cc_final: 0.7365 (t0) REVERT: C 345 LYS cc_start: 0.7660 (ptpp) cc_final: 0.7162 (ptpp) REVERT: C 376 ARG cc_start: 0.6852 (mmt180) cc_final: 0.6508 (mmt180) REVERT: C 381 ASN cc_start: 0.7844 (t0) cc_final: 0.7509 (t0) outliers start: 66 outliers final: 40 residues processed: 385 average time/residue: 1.3356 time to fit residues: 559.4087 Evaluate side-chains 406 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 360 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 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 943 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 980 VAL Chi-restraints excluded: chain B residue 3 SER 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 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 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 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 333 GLU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 375 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 124 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 159 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 107 optimal weight: 0.0970 chunk 47 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 118 optimal weight: 0.0030 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4131 r_free = 0.4131 target = 0.162705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.126938 restraints weight = 20121.540| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.74 r_work: 0.3514 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14631 Z= 0.113 Angle : 0.530 7.321 19941 Z= 0.281 Chirality : 0.041 0.186 2208 Planarity : 0.004 0.056 2393 Dihedral : 14.685 140.417 2280 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.86 % Favored : 95.84 % Rotamer: Outliers : 3.49 % Allowed : 24.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1634 helix: 1.43 (0.22), residues: 602 sheet: 0.62 (0.28), residues: 365 loop : -1.20 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 PHE 0.041 0.001 PHE C 188 TYR 0.017 0.001 TYR A 637 ARG 0.006 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 621) hydrogen bonds : angle 4.23170 ( 1743) covalent geometry : bond 0.00246 (14629) covalent geometry : angle 0.53035 (19941) Misc. bond : bond 0.00018 ( 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 408 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 355 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7733 (mpt) REVERT: A 711 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7695 (mmm) REVERT: A 978 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7873 (tm-30) REVERT: B 1 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8603 (mmt) REVERT: B 205 ASP cc_start: 0.7717 (t0) cc_final: 0.7491 (t0) REVERT: C 135 ARG cc_start: 0.6504 (tpm-80) cc_final: 0.6272 (tpt90) REVERT: C 157 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6385 (pt0) REVERT: C 160 LEU cc_start: 0.6198 (OUTLIER) cc_final: 0.5369 (tm) REVERT: C 162 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.5733 (tp) REVERT: C 181 TYR cc_start: 0.7599 (t80) cc_final: 0.7293 (t80) REVERT: C 183 ILE cc_start: 0.8377 (mt) cc_final: 0.8127 (mt) REVERT: C 226 ASP cc_start: 0.7417 (t0) cc_final: 0.7032 (t0) REVERT: C 345 LYS cc_start: 0.7647 (ptpp) cc_final: 0.7174 (ptpp) REVERT: C 376 ARG cc_start: 0.6850 (mmt180) cc_final: 0.6530 (mmt180) REVERT: C 381 ASN cc_start: 0.7831 (t0) cc_final: 0.7526 (t0) REVERT: C 406 ASN cc_start: 0.7304 (p0) cc_final: 0.7054 (p0) outliers start: 53 outliers final: 32 residues processed: 380 average time/residue: 1.3651 time to fit residues: 567.8837 Evaluate side-chains 389 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 351 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 165 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 280 THR 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 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 724 MET Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 1 MET 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 130 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 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 238 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 333 GLU Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 375 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 154 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 538 GLN A 551 ASN A 675 ASN B 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.161109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125197 restraints weight = 19974.042| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.72 r_work: 0.3487 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14631 Z= 0.161 Angle : 0.579 11.407 19941 Z= 0.304 Chirality : 0.043 0.188 2208 Planarity : 0.004 0.055 2393 Dihedral : 14.783 138.347 2280 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.92 % Favored : 95.78 % Rotamer: Outliers : 3.69 % Allowed : 24.26 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1634 helix: 1.41 (0.22), residues: 602 sheet: 0.59 (0.27), residues: 373 loop : -1.23 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 PHE 0.041 0.001 PHE C 188 TYR 0.017 0.001 TYR A 637 ARG 0.006 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.04878 ( 621) hydrogen bonds : angle 4.29899 ( 1743) covalent geometry : bond 0.00381 (14629) covalent geometry : angle 0.57850 (19941) Misc. bond : bond 0.00040 ( 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 412 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 356 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ASN cc_start: 0.8755 (m-40) cc_final: 0.8465 (m110) REVERT: A 357 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7757 (mpt) REVERT: A 711 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7738 (mmm) REVERT: B 1 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8578 (mmt) REVERT: B 205 ASP cc_start: 0.7758 (t0) cc_final: 0.7518 (t0) REVERT: C 135 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.6307 (tpt90) REVERT: C 157 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.6426 (pt0) REVERT: C 160 LEU cc_start: 0.6192 (OUTLIER) cc_final: 0.5694 (tm) REVERT: C 162 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.5611 (tp) REVERT: C 181 TYR cc_start: 0.7630 (t80) cc_final: 0.7318 (t80) REVERT: C 183 ILE cc_start: 0.8400 (mt) cc_final: 0.8145 (mt) REVERT: C 226 ASP cc_start: 0.7489 (t0) cc_final: 0.7079 (t0) REVERT: C 345 LYS cc_start: 0.7643 (ptpp) cc_final: 0.7158 (ptpp) REVERT: C 376 ARG cc_start: 0.6870 (mmt180) cc_final: 0.6533 (mmt180) REVERT: C 381 ASN cc_start: 0.7874 (t0) cc_final: 0.7556 (t0) REVERT: C 406 ASN cc_start: 0.7273 (p0) cc_final: 0.7024 (p0) outliers start: 56 outliers final: 37 residues processed: 381 average time/residue: 1.3828 time to fit residues: 571.6843 Evaluate side-chains 402 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 358 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 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 357 MET 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 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 844 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 1 MET 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 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 82 TYR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 ARG 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 333 GLU Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 375 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 115 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 156 optimal weight: 0.0050 chunk 19 optimal weight: 0.0470 chunk 99 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 overall best weight: 0.7094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 538 GLN A 675 ASN B 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.161732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.125302 restraints weight = 19868.621| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.79 r_work: 0.3496 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1380 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= 0.142 Angle : 0.565 7.998 19941 Z= 0.298 Chirality : 0.042 0.188 2208 Planarity : 0.004 0.055 2393 Dihedral : 14.750 138.931 2280 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.86 % Favored : 95.84 % Rotamer: Outliers : 3.69 % Allowed : 24.92 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1634 helix: 1.43 (0.22), residues: 602 sheet: 0.57 (0.27), residues: 373 loop : -1.23 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.006 0.001 HIS A 839 PHE 0.040 0.001 PHE C 188 TYR 0.017 0.001 TYR A 637 ARG 0.006 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 621) hydrogen bonds : angle 4.27248 ( 1743) covalent geometry : bond 0.00329 (14629) covalent geometry : angle 0.56513 (19941) Misc. bond : bond 0.00033 ( 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 418 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 362 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7747 (mpt) REVERT: A 711 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7721 (mmm) REVERT: B 1 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8571 (mmt) REVERT: B 205 ASP cc_start: 0.7765 (t0) cc_final: 0.7528 (t0) REVERT: C 135 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.6318 (tpt90) REVERT: C 157 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6383 (pt0) REVERT: C 160 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5458 (tm) REVERT: C 162 ILE cc_start: 0.6522 (OUTLIER) cc_final: 0.5422 (tp) REVERT: C 181 TYR cc_start: 0.7582 (t80) cc_final: 0.7289 (t80) REVERT: C 183 ILE cc_start: 0.8400 (mt) cc_final: 0.8147 (mt) REVERT: C 226 ASP cc_start: 0.7432 (t0) cc_final: 0.7084 (t0) REVERT: C 227 ARG cc_start: 0.7067 (mtt180) cc_final: 0.6830 (mtt-85) REVERT: C 345 LYS cc_start: 0.7631 (ptpp) cc_final: 0.7138 (ptpp) REVERT: C 349 LYS cc_start: 0.8251 (tptt) cc_final: 0.8011 (tptt) REVERT: C 376 ARG cc_start: 0.6867 (mmt180) cc_final: 0.6510 (mmt180) REVERT: C 381 ASN cc_start: 0.7916 (t0) cc_final: 0.7596 (t0) REVERT: C 406 ASN cc_start: 0.7281 (p0) cc_final: 0.7036 (p0) outliers start: 56 outliers final: 37 residues processed: 384 average time/residue: 1.3062 time to fit residues: 545.9580 Evaluate side-chains 404 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 360 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 165 LEU Chi-restraints excluded: chain A residue 207 MET Chi-restraints excluded: chain A residue 226 SER 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 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 844 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 1 MET 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 106 LYS 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 82 TYR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 ARG 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 335 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 375 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 28 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.0370 chunk 3 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 225 GLN A 538 GLN A 675 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.162220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126107 restraints weight = 19847.738| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.73 r_work: 0.3511 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1454 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= 0.131 Angle : 0.577 9.328 19941 Z= 0.302 Chirality : 0.042 0.188 2208 Planarity : 0.004 0.055 2393 Dihedral : 14.709 139.107 2280 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.04 % Favored : 95.65 % Rotamer: Outliers : 3.43 % Allowed : 25.05 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.21), residues: 1634 helix: 1.49 (0.22), residues: 600 sheet: 0.56 (0.27), residues: 374 loop : -1.22 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 PHE 0.043 0.001 PHE C 188 TYR 0.015 0.001 TYR A 637 ARG 0.006 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 621) hydrogen bonds : angle 4.22842 ( 1743) covalent geometry : bond 0.00300 (14629) covalent geometry : angle 0.57741 (19941) Misc. bond : bond 0.00028 ( 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 412 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 360 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7722 (mpt) REVERT: A 711 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7661 (mmm) REVERT: B 1 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8605 (mmt) REVERT: B 205 ASP cc_start: 0.7766 (t0) cc_final: 0.7538 (t0) REVERT: C 2 THR cc_start: 0.6828 (OUTLIER) cc_final: 0.6501 (m) REVERT: C 157 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6363 (pt0) REVERT: C 162 ILE cc_start: 0.6356 (OUTLIER) cc_final: 0.5244 (tp) REVERT: C 181 TYR cc_start: 0.7589 (t80) cc_final: 0.7292 (t80) REVERT: C 183 ILE cc_start: 0.8385 (mt) cc_final: 0.8127 (mt) REVERT: C 226 ASP cc_start: 0.7456 (t0) cc_final: 0.7088 (t0) REVERT: C 227 ARG cc_start: 0.7041 (mtt180) cc_final: 0.6793 (mtt-85) REVERT: C 304 ASN cc_start: 0.7592 (t0) cc_final: 0.7339 (t0) REVERT: C 345 LYS cc_start: 0.7639 (ptpp) cc_final: 0.7158 (ptpp) REVERT: C 376 ARG cc_start: 0.6855 (mmt180) cc_final: 0.6489 (mmt180) REVERT: C 381 ASN cc_start: 0.7913 (t0) cc_final: 0.7597 (t0) REVERT: C 406 ASN cc_start: 0.7285 (p0) cc_final: 0.7030 (p0) outliers start: 52 outliers final: 38 residues processed: 379 average time/residue: 1.3564 time to fit residues: 558.8034 Evaluate side-chains 395 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 351 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 105 ASP 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 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 844 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 1 MET 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 106 LYS 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 82 TYR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 157 GLU 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 337 GLU Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 375 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 538 GLN A 675 ASN B 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.162178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126021 restraints weight = 19699.275| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.81 r_work: 0.3502 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1488 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= 0.136 Angle : 0.585 8.243 19941 Z= 0.305 Chirality : 0.042 0.188 2208 Planarity : 0.004 0.055 2393 Dihedral : 14.713 138.859 2280 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.04 % Favored : 95.65 % Rotamer: Outliers : 3.16 % Allowed : 25.44 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.21), residues: 1634 helix: 1.46 (0.22), residues: 602 sheet: 0.57 (0.27), residues: 374 loop : -1.23 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.005 0.001 HIS A 839 PHE 0.044 0.001 PHE C 188 TYR 0.018 0.001 TYR A 637 ARG 0.006 0.000 ARG A 407 Details of bonding type rmsd hydrogen bonds : bond 0.04408 ( 621) hydrogen bonds : angle 4.23541 ( 1743) covalent geometry : bond 0.00313 (14629) covalent geometry : angle 0.58519 (19941) Misc. bond : bond 0.00031 ( 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 401 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 353 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.7736 (mpt) REVERT: A 711 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7708 (mmm) REVERT: B 1 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8619 (mmt) REVERT: B 205 ASP cc_start: 0.7790 (t0) cc_final: 0.7556 (t0) REVERT: C 2 THR cc_start: 0.6856 (OUTLIER) cc_final: 0.6506 (m) REVERT: C 157 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6304 (pt0) REVERT: C 162 ILE cc_start: 0.6106 (OUTLIER) cc_final: 0.4897 (tp) REVERT: C 181 TYR cc_start: 0.7573 (t80) cc_final: 0.7292 (t80) REVERT: C 183 ILE cc_start: 0.8422 (mt) cc_final: 0.8160 (mt) REVERT: C 226 ASP cc_start: 0.7490 (t0) cc_final: 0.7163 (t0) REVERT: C 227 ARG cc_start: 0.7077 (mtt180) cc_final: 0.6846 (mtt-85) REVERT: C 304 ASN cc_start: 0.7508 (t0) cc_final: 0.7294 (t0) REVERT: C 345 LYS cc_start: 0.7629 (ptpp) cc_final: 0.7148 (ptpp) REVERT: C 376 ARG cc_start: 0.6857 (mmt180) cc_final: 0.6482 (mmt180) REVERT: C 381 ASN cc_start: 0.7927 (t0) cc_final: 0.7609 (t0) REVERT: C 406 ASN cc_start: 0.7293 (p0) cc_final: 0.7042 (p0) outliers start: 48 outliers final: 37 residues processed: 369 average time/residue: 1.4328 time to fit residues: 577.5521 Evaluate side-chains 396 residues out of total 1517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 353 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 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 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 844 LYS Chi-restraints excluded: chain A residue 943 LYS Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 1 MET 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 106 LYS 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 82 TYR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 135 ARG Chi-restraints excluded: chain C residue 157 GLU 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 337 GLU Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 375 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 106 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 143 optimal weight: 0.0370 chunk 82 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 538 GLN A 675 ASN C 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.162756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.126890 restraints weight = 20011.846| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.77 r_work: 0.3510 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1564 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= 0.128 Angle : 0.583 12.310 19941 Z= 0.303 Chirality : 0.042 0.189 2208 Planarity : 0.004 0.056 2393 Dihedral : 14.654 138.927 2280 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.92 % Favored : 95.78 % Rotamer: Outliers : 3.30 % Allowed : 25.31 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.21), residues: 1634 helix: 1.53 (0.22), residues: 600 sheet: 0.58 (0.27), residues: 373 loop : -1.22 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.006 0.001 HIS A 36 PHE 0.046 0.001 PHE C 188 TYR 0.017 0.001 TYR A 637 ARG 0.008 0.000 ARG A 16 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 621) hydrogen bonds : angle 4.20666 ( 1743) covalent geometry : bond 0.00291 (14629) covalent geometry : angle 0.58294 (19941) Misc. bond : bond 0.00026 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17222.27 seconds wall clock time: 295 minutes 9.15 seconds (17709.15 seconds total)