Starting phenix.real_space_refine on Thu Jul 31 15:12:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8isk_35693/07_2025/8isk_35693.cif Found real_map, /net/cci-nas-00/data/ceres_data/8isk_35693/07_2025/8isk_35693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8isk_35693/07_2025/8isk_35693.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8isk_35693/07_2025/8isk_35693.map" model { file = "/net/cci-nas-00/data/ceres_data/8isk_35693/07_2025/8isk_35693.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8isk_35693/07_2025/8isk_35693.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 95 5.16 5 C 8436 2.51 5 N 2282 2.21 5 O 2460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13273 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 845, 6581 Classifications: {'peptide': 845} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 812} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 6606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6606 Classifications: {'peptide': 848} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 815} Chain breaks: 5 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.43, per 1000 atoms: 0.64 Number of scatterers: 13273 At special positions: 0 Unit cell: (110.5, 129.2, 153, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 95 16.00 O 2460 8.00 N 2282 7.00 C 8436 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3170 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 15 sheets defined 41.8% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 103 through 109 Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 151 through 155 removed outlier: 3.954A pdb=" N ASN A 155 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 removed outlier: 3.567A pdb=" N GLU A 190 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 191 " --> pdb=" O PRO A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 191' Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 205 through 213 removed outlier: 3.881A pdb=" N ILE A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 236 removed outlier: 3.688A pdb=" N LEU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 3.508A pdb=" N ARG A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 332 Processing helix chain 'A' and resid 382 through 428 removed outlier: 3.904A pdb=" N ASN A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LYS A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU A 403 " --> pdb=" O HIS A 399 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 482 Processing helix chain 'A' and resid 572 through 591 removed outlier: 3.720A pdb=" N ILE A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 789 Processing helix chain 'A' and resid 791 through 796 Processing helix chain 'A' and resid 816 through 832 Processing helix chain 'A' and resid 878 through 909 removed outlier: 4.204A pdb=" N GLN A 893 " --> pdb=" O GLN A 889 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N THR A 894 " --> pdb=" O ALA A 890 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 895 " --> pdb=" O SER A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 926 removed outlier: 4.185A pdb=" N LEU A 913 " --> pdb=" O ILE A 909 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 915 " --> pdb=" O LYS A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 931 No H-bonds generated for 'chain 'A' and resid 929 through 931' Processing helix chain 'A' and resid 932 through 951 removed outlier: 3.604A pdb=" N ILE A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 950 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 993 removed outlier: 3.821A pdb=" N VAL A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLY A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1006 Processing helix chain 'A' and resid 1013 through 1030 removed outlier: 3.706A pdb=" N PHE A1023 " --> pdb=" O ILE A1019 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE A1030 " --> pdb=" O VAL A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1078 Processing helix chain 'A' and resid 1085 through 1101 removed outlier: 3.656A pdb=" N MET A1101 " --> pdb=" O LEU A1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 103 through 109 removed outlier: 3.501A pdb=" N MET B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 removed outlier: 4.036A pdb=" N ALA B 141 " --> pdb=" O PRO B 137 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE B 148 " --> pdb=" O LYS B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 removed outlier: 3.638A pdb=" N LEU B 154 " --> pdb=" O VAL B 151 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN B 155 " --> pdb=" O SER B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 151 through 155' Processing helix chain 'B' and resid 187 through 194 Proline residue: B 192 - end of helix Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 219 through 236 Processing helix chain 'B' and resid 276 through 286 removed outlier: 3.582A pdb=" N LYS B 285 " --> pdb=" O PHE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 332 Processing helix chain 'B' and resid 382 through 428 removed outlier: 3.958A pdb=" N SER B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE B 415 " --> pdb=" O ARG B 411 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 428 " --> pdb=" O ASP B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 438 removed outlier: 4.094A pdb=" N VAL B 436 " --> pdb=" O PRO B 432 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 437 " --> pdb=" O LEU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 482 removed outlier: 3.740A pdb=" N ARG B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 497 Processing helix chain 'B' and resid 572 through 591 removed outlier: 3.632A pdb=" N ILE B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 789 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 816 through 833 Processing helix chain 'B' and resid 878 through 884 Processing helix chain 'B' and resid 890 through 895 Processing helix chain 'B' and resid 902 through 909 removed outlier: 3.602A pdb=" N ARG B 906 " --> pdb=" O PHE B 902 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS B 907 " --> pdb=" O SER B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 926 removed outlier: 3.547A pdb=" N LEU B 913 " --> pdb=" O ILE B 909 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 926 " --> pdb=" O THR B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 929 through 952 removed outlier: 3.526A pdb=" N GLN B 935 " --> pdb=" O GLU B 931 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP B 952 " --> pdb=" O LYS B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 958 removed outlier: 6.052A pdb=" N ASP B 956 " --> pdb=" O LEU B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 993 removed outlier: 3.984A pdb=" N VAL B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 987 " --> pdb=" O SER B 983 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N GLY B 988 " --> pdb=" O GLN B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1006 Processing helix chain 'B' and resid 1012 through 1031 removed outlier: 3.814A pdb=" N LEU B1016 " --> pdb=" O ASP B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1077 Processing helix chain 'B' and resid 1085 through 1099 Processing helix chain 'B' and resid 1100 through 1102 No H-bonds generated for 'chain 'B' and resid 1100 through 1102' Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 removed outlier: 4.073A pdb=" N ALA A 99 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 87 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 258 removed outlier: 6.608A pdb=" N ALA A 242 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU A 256 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A 240 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP A 368 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 342 " --> pdb=" O TRP A 368 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU A 370 " --> pdb=" O MET A 340 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET A 340 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL A 372 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU A 338 " --> pdb=" O VAL A 372 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS A 374 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA A 336 " --> pdb=" O HIS A 374 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 458 through 463 removed outlier: 3.713A pdb=" N ALA A 452 " --> pdb=" O PHE A 523 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 521 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 514 " --> pdb=" O LEU A 522 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 531 through 535 Processing sheet with id=AA5, first strand: chain 'A' and resid 777 through 780 removed outlier: 6.071A pdb=" N GLY A 770 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TRP A 780 " --> pdb=" O ILE A 768 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE A 768 " --> pdb=" O TRP A 780 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 771 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LYS A 860 " --> pdb=" O THR A 868 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N VAL A 870 " --> pdb=" O ASN A 858 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN A 858 " --> pdb=" O VAL A 870 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N CYS A 872 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER A 856 " --> pdb=" O CYS A 872 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE A 874 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 854 " --> pdb=" O ILE A 874 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL A 857 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLU A 837 " --> pdb=" O VAL A 857 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 970 through 972 removed outlier: 3.670A pdb=" N PHE A 972 " --> pdb=" O VAL A1009 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A1009 " --> pdb=" O PHE A 972 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A1041 " --> pdb=" O ASN A 999 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 970 through 972 removed outlier: 3.670A pdb=" N PHE A 972 " --> pdb=" O VAL A1009 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL A1009 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.888A pdb=" N ILE B 302 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B 100 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 89 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE B 100 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 269 through 270 removed outlier: 5.579A pdb=" N VAL B 253 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS B 244 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 255 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 372 " --> pdb=" O MET B 241 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP B 368 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 342 " --> pdb=" O TRP B 368 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU B 370 " --> pdb=" O MET B 340 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET B 340 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 372 " --> pdb=" O LEU B 338 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU B 338 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 458 through 463 removed outlier: 3.553A pdb=" N ALA B 451 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 531 through 534 removed outlier: 3.773A pdb=" N ALA B 531 " --> pdb=" O VAL B 564 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL B 564 " --> pdb=" O ALA B 531 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 533 " --> pdb=" O GLU B 562 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU B 562 " --> pdb=" O ILE B 533 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 777 through 780 removed outlier: 6.059A pdb=" N GLY B 770 " --> pdb=" O SER B 778 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP B 780 " --> pdb=" O ILE B 768 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE B 768 " --> pdb=" O TRP B 780 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 771 " --> pdb=" O VAL B 870 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS B 875 " --> pdb=" O LEU B 854 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 854 " --> pdb=" O HIS B 875 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 805 through 806 removed outlier: 3.749A pdb=" N ASP B 806 " --> pdb=" O CYS B 812 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 970 through 973 removed outlier: 3.956A pdb=" N SER B1041 " --> pdb=" O ASN B 999 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 970 through 973 665 hydrogen bonds defined for protein. 1881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.40 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4221 1.34 - 1.46: 1744 1.46 - 1.57: 7411 1.57 - 1.69: 0 1.69 - 1.81: 148 Bond restraints: 13524 Sorted by residual: bond pdb=" N ILE B 508 " pdb=" CA ILE B 508 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.84e+00 bond pdb=" CAP O6E B1201 " pdb=" CBL O6E B1201 " ideal model delta sigma weight residual 1.448 1.388 0.060 2.00e-02 2.50e+03 8.92e+00 bond pdb=" CAB O6E A1201 " pdb=" CBI O6E A1201 " ideal model delta sigma weight residual 1.449 1.390 0.059 2.00e-02 2.50e+03 8.68e+00 bond pdb=" CAP O6E A1201 " pdb=" CBL O6E A1201 " ideal model delta sigma weight residual 1.448 1.389 0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" CAB O6E B1201 " pdb=" CBI O6E B1201 " ideal model delta sigma weight residual 1.449 1.392 0.057 2.00e-02 2.50e+03 8.20e+00 ... (remaining 13519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 18014 2.49 - 4.99: 223 4.99 - 7.48: 26 7.48 - 9.98: 3 9.98 - 12.47: 6 Bond angle restraints: 18272 Sorted by residual: angle pdb=" CA GLY B 197 " pdb=" C GLY B 197 " pdb=" O GLY B 197 " ideal model delta sigma weight residual 122.56 118.51 4.05 1.03e+00 9.43e-01 1.55e+01 angle pdb=" C HIS B 250 " pdb=" CA HIS B 250 " pdb=" CB HIS B 250 " ideal model delta sigma weight residual 109.37 116.81 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N ILE B 442 " pdb=" CA ILE B 442 " pdb=" C ILE B 442 " ideal model delta sigma weight residual 112.29 108.89 3.40 9.40e-01 1.13e+00 1.31e+01 angle pdb=" CA LEU A 764 " pdb=" CB LEU A 764 " pdb=" CG LEU A 764 " ideal model delta sigma weight residual 116.30 128.77 -12.47 3.50e+00 8.16e-02 1.27e+01 angle pdb=" CAV O6E B1201 " pdb=" CAO O6E B1201 " pdb=" CBO O6E B1201 " ideal model delta sigma weight residual 125.76 136.44 -10.68 3.00e+00 1.11e-01 1.27e+01 ... (remaining 18267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 7128 17.91 - 35.83: 870 35.83 - 53.74: 197 53.74 - 71.66: 21 71.66 - 89.57: 20 Dihedral angle restraints: 8236 sinusoidal: 3349 harmonic: 4887 Sorted by residual: dihedral pdb=" CD ARG B1082 " pdb=" NE ARG B1082 " pdb=" CZ ARG B1082 " pdb=" NH1 ARG B1082 " ideal model delta sinusoidal sigma weight residual 0.00 -46.34 46.34 1 1.00e+01 1.00e-02 2.97e+01 dihedral pdb=" CD ARG A1082 " pdb=" NE ARG A1082 " pdb=" CZ ARG A1082 " pdb=" NH1 ARG A1082 " ideal model delta sinusoidal sigma weight residual 0.00 -34.97 34.97 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA TYR B 202 " pdb=" C TYR B 202 " pdb=" N LYS B 203 " pdb=" CA LYS B 203 " ideal model delta harmonic sigma weight residual 180.00 160.46 19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 8233 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1680 0.054 - 0.109: 320 0.109 - 0.163: 56 0.163 - 0.218: 6 0.218 - 0.272: 1 Chirality restraints: 2063 Sorted by residual: chirality pdb=" CA TYR B 202 " pdb=" N TYR B 202 " pdb=" C TYR B 202 " pdb=" CB TYR B 202 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA LEU A1092 " pdb=" N LEU A1092 " pdb=" C LEU A1092 " pdb=" CB LEU A1092 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA LEU B1020 " pdb=" N LEU B1020 " pdb=" C LEU B1020 " pdb=" CB LEU B1020 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.84e-01 ... (remaining 2060 not shown) Planarity restraints: 2344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " 0.621 2.00e-02 2.50e+03 3.13e-01 2.45e+03 pdb=" CAP O6E A1201 " -0.059 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " -0.495 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " 0.020 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " -0.120 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " 0.172 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.295 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " -0.096 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " 0.103 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " -0.440 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E A1201 " 0.505 2.00e-02 2.50e+03 2.89e-01 2.09e+03 pdb=" CAO O6E A1201 " -0.138 2.00e-02 2.50e+03 pdb=" CAP O6E A1201 " 0.300 2.00e-02 2.50e+03 pdb=" CAR O6E A1201 " -0.584 2.00e-02 2.50e+03 pdb=" CAV O6E A1201 " 0.032 2.00e-02 2.50e+03 pdb=" CBB O6E A1201 " 0.124 2.00e-02 2.50e+03 pdb=" CBH O6E A1201 " -0.163 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.050 2.00e-02 2.50e+03 pdb=" CBO O6E A1201 " -0.258 2.00e-02 2.50e+03 pdb=" NAE O6E A1201 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " 0.364 2.00e-02 2.50e+03 2.16e-01 1.17e+03 pdb=" CAP O6E B1201 " 0.259 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " -0.303 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " -0.072 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " -0.095 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " 0.088 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " 0.172 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " -0.077 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " -0.343 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " 0.007 2.00e-02 2.50e+03 ... (remaining 2341 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 211 2.67 - 3.23: 12232 3.23 - 3.79: 19462 3.79 - 4.34: 25063 4.34 - 4.90: 42755 Nonbonded interactions: 99723 Sorted by model distance: nonbonded pdb=" OD2 ASP A1022 " pdb=" OG SER A1094 " model vdw 2.116 3.040 nonbonded pdb=" OG1 THR B 517 " pdb=" OD1 ASP B 520 " model vdw 2.138 3.040 nonbonded pdb=" O GLU B 106 " pdb=" OG1 THR B 110 " model vdw 2.189 3.040 nonbonded pdb=" OG SER B 101 " pdb=" OD1 ASN B 103 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 492 " pdb=" OD1 ASP A 495 " model vdw 2.214 3.040 ... (remaining 99718 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 73 through 1045 or resid 1054 through 1125 or resid 1201)) \ selection = (chain 'B' and (resid 73 through 347 or resid 363 through 591 or (resid 745 and \ (name N or name CA or name C or name O or name CB )) or resid 746 through 1125 o \ r resid 1201)) } 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.270 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 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 : 0.008 0.880 13527 Z= 0.785 Angle : 0.689 12.475 18272 Z= 0.373 Chirality : 0.044 0.272 2063 Planarity : 0.015 0.354 2344 Dihedral : 16.319 89.569 5066 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.14 % Allowed : 18.75 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1669 helix: 1.67 (0.22), residues: 624 sheet: 0.50 (0.29), residues: 337 loop : -1.13 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 477 HIS 0.015 0.001 HIS B 325 PHE 0.018 0.001 PHE B 523 TYR 0.017 0.001 TYR A 574 ARG 0.008 0.000 ARG A 937 Details of bonding type rmsd hydrogen bonds : bond 0.13207 ( 655) hydrogen bonds : angle 5.95634 ( 1881) covalent geometry : bond 0.00362 (13524) covalent geometry : angle 0.68896 (18272) Misc. bond : bond 0.50801 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: A 220 MET cc_start: 0.7208 (ttm) cc_final: 0.6943 (tpp) REVERT: A 566 MET cc_start: 0.5745 (mmm) cc_final: 0.5514 (tmm) REVERT: A 900 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8517 (mtpp) REVERT: A 966 ASP cc_start: 0.7478 (t0) cc_final: 0.6981 (p0) REVERT: B 148 PHE cc_start: 0.7846 (p90) cc_final: 0.7483 (p90) REVERT: B 150 ASP cc_start: 0.6754 (t0) cc_final: 0.6328 (t0) REVERT: B 971 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8637 (tp30) outliers start: 2 outliers final: 2 residues processed: 166 average time/residue: 0.2326 time to fit residues: 59.0049 Evaluate side-chains 144 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 142 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain B residue 1083 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS A 580 HIS ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS B 858 ASN B 882 GLN B 883 HIS B 947 ASN ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.195207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.126639 restraints weight = 19037.476| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.43 r_work: 0.3587 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 13527 Z= 0.294 Angle : 0.720 13.493 18272 Z= 0.366 Chirality : 0.047 0.202 2063 Planarity : 0.005 0.052 2344 Dihedral : 7.030 80.809 1890 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.03 % Favored : 94.91 % Rotamer: Outliers : 3.54 % Allowed : 17.22 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 1669 helix: 1.33 (0.21), residues: 641 sheet: 0.09 (0.28), residues: 352 loop : -1.50 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 368 HIS 0.011 0.002 HIS B 325 PHE 0.020 0.002 PHE A 232 TYR 0.035 0.002 TYR A 243 ARG 0.005 0.001 ARG B1082 Details of bonding type rmsd hydrogen bonds : bond 0.06045 ( 655) hydrogen bonds : angle 5.39833 ( 1881) covalent geometry : bond 0.00720 (13524) covalent geometry : angle 0.72041 (18272) Misc. bond : bond 0.00188 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 144 time to evaluate : 1.528 Fit side-chains REVERT: A 478 LEU cc_start: 0.9085 (mt) cc_final: 0.8724 (tt) REVERT: A 574 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6461 (t80) REVERT: A 913 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6891 (mm) REVERT: A 966 ASP cc_start: 0.7798 (t0) cc_final: 0.7058 (p0) REVERT: B 134 PHE cc_start: 0.8196 (m-80) cc_final: 0.7965 (m-80) REVERT: B 148 PHE cc_start: 0.7916 (p90) cc_final: 0.7569 (p90) REVERT: B 150 ASP cc_start: 0.6458 (t0) cc_final: 0.5923 (t0) REVERT: B 332 MET cc_start: 0.6524 (mtm) cc_final: 0.5065 (mtm) REVERT: B 1113 MET cc_start: 0.4648 (mmp) cc_final: 0.4441 (mmp) outliers start: 51 outliers final: 24 residues processed: 185 average time/residue: 0.2177 time to fit residues: 62.9431 Evaluate side-chains 160 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 882 GLN Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 161 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 156 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1007 GLN ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.196903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.128651 restraints weight = 19165.625| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 3.47 r_work: 0.3614 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13527 Z= 0.180 Angle : 0.639 13.441 18272 Z= 0.314 Chirality : 0.044 0.173 2063 Planarity : 0.004 0.051 2344 Dihedral : 6.108 79.743 1887 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 3.33 % Allowed : 18.40 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1669 helix: 1.45 (0.21), residues: 651 sheet: 0.25 (0.28), residues: 347 loop : -1.44 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 368 HIS 0.012 0.001 HIS B 325 PHE 0.015 0.002 PHE B 871 TYR 0.022 0.002 TYR A 243 ARG 0.006 0.000 ARG B 898 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 655) hydrogen bonds : angle 5.10536 ( 1881) covalent geometry : bond 0.00435 (13524) covalent geometry : angle 0.63883 (18272) Misc. bond : bond 0.00066 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 147 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: A 313 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8225 (pp) REVERT: A 329 MET cc_start: 0.7851 (tpt) cc_final: 0.7599 (tpp) REVERT: A 478 LEU cc_start: 0.9118 (mt) cc_final: 0.8772 (tt) REVERT: A 507 MET cc_start: 0.7761 (mmp) cc_final: 0.7365 (ttt) REVERT: A 574 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6267 (t80) REVERT: A 913 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6947 (mm) REVERT: A 933 MET cc_start: 0.7421 (tpp) cc_final: 0.7084 (tpp) REVERT: A 966 ASP cc_start: 0.7866 (t0) cc_final: 0.7104 (p0) REVERT: A 1059 LEU cc_start: 0.8837 (tp) cc_final: 0.8551 (pp) REVERT: B 332 MET cc_start: 0.6428 (mtm) cc_final: 0.6214 (mtt) REVERT: B 574 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6701 (t80) outliers start: 48 outliers final: 22 residues processed: 187 average time/residue: 0.2176 time to fit residues: 62.1336 Evaluate side-chains 162 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 529 THR Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 455 TYR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 123 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 164 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 38 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 882 GLN A 883 HIS A 941 ASN A1081 ASN B 470 GLN ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.198572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.135113 restraints weight = 18292.702| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 3.19 r_work: 0.3687 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13527 Z= 0.114 Angle : 0.581 12.914 18272 Z= 0.280 Chirality : 0.042 0.162 2063 Planarity : 0.004 0.053 2344 Dihedral : 5.432 75.072 1887 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 2.92 % Allowed : 20.21 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.21), residues: 1669 helix: 1.83 (0.21), residues: 640 sheet: 0.37 (0.28), residues: 339 loop : -1.24 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 524 HIS 0.013 0.001 HIS B 325 PHE 0.015 0.001 PHE B 873 TYR 0.013 0.001 TYR A 574 ARG 0.005 0.000 ARG B 898 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 655) hydrogen bonds : angle 4.74373 ( 1881) covalent geometry : bond 0.00258 (13524) covalent geometry : angle 0.58090 (18272) Misc. bond : bond 0.00037 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7913 (mmm160) REVERT: A 313 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8118 (pp) REVERT: A 507 MET cc_start: 0.7695 (mmp) cc_final: 0.7384 (ttt) REVERT: A 566 MET cc_start: 0.5928 (mmm) cc_final: 0.5651 (tmm) REVERT: A 574 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.6226 (t80) REVERT: A 913 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6909 (mm) REVERT: A 933 MET cc_start: 0.7564 (tpp) cc_final: 0.7328 (tpp) REVERT: A 945 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7916 (tm-30) REVERT: A 966 ASP cc_start: 0.7874 (t0) cc_final: 0.7177 (p0) REVERT: A 1059 LEU cc_start: 0.8834 (tp) cc_final: 0.8543 (pp) REVERT: B 150 ASP cc_start: 0.6384 (t0) cc_final: 0.6036 (t0) REVERT: B 574 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6560 (t80) REVERT: B 749 ARG cc_start: 0.7518 (ptp90) cc_final: 0.7314 (ptp90) REVERT: B 971 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8672 (tp30) outliers start: 42 outliers final: 14 residues processed: 190 average time/residue: 0.2135 time to fit residues: 62.4785 Evaluate side-chains 161 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain A residue 1009 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 105 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 0.0170 chunk 68 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 132 optimal weight: 0.1980 chunk 20 optimal weight: 5.9990 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** A 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 HIS B 882 GLN ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.200072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.132318 restraints weight = 18976.432| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 3.50 r_work: 0.3674 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13527 Z= 0.113 Angle : 0.571 12.981 18272 Z= 0.275 Chirality : 0.042 0.164 2063 Planarity : 0.004 0.053 2344 Dihedral : 5.117 73.489 1887 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.29 % Rotamer: Outliers : 2.99 % Allowed : 20.49 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.21), residues: 1669 helix: 1.97 (0.21), residues: 639 sheet: 0.41 (0.28), residues: 339 loop : -1.18 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.013 0.001 HIS B 325 PHE 0.014 0.001 PHE B 873 TYR 0.014 0.001 TYR A 243 ARG 0.002 0.000 ARG A 937 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 655) hydrogen bonds : angle 4.61091 ( 1881) covalent geometry : bond 0.00260 (13524) covalent geometry : angle 0.57101 (18272) Misc. bond : bond 0.00032 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 289 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7612 (mmm160) REVERT: A 313 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8092 (pp) REVERT: A 329 MET cc_start: 0.7804 (tpt) cc_final: 0.7421 (tpp) REVERT: A 507 MET cc_start: 0.7703 (mmp) cc_final: 0.7371 (ttt) REVERT: A 574 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6285 (t80) REVERT: A 913 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6841 (mm) REVERT: A 966 ASP cc_start: 0.7913 (t0) cc_final: 0.7181 (p0) REVERT: A 1059 LEU cc_start: 0.8829 (tp) cc_final: 0.8520 (pp) REVERT: A 1087 GLU cc_start: 0.8281 (pm20) cc_final: 0.8019 (pm20) REVERT: B 574 TYR cc_start: 0.6995 (OUTLIER) cc_final: 0.6597 (t80) REVERT: B 971 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8673 (tp30) REVERT: B 1091 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7419 (mm) outliers start: 43 outliers final: 17 residues processed: 182 average time/residue: 0.2310 time to fit residues: 64.1167 Evaluate side-chains 158 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 105 optimal weight: 9.9990 chunk 153 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 127 optimal weight: 0.4980 chunk 42 optimal weight: 0.3980 chunk 86 optimal weight: 0.2980 chunk 163 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 142 optimal weight: 0.9980 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 883 HIS ** A 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN A1017 GLN B 882 GLN ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.200983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.133654 restraints weight = 19148.836| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 3.51 r_work: 0.3687 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13527 Z= 0.106 Angle : 0.586 13.469 18272 Z= 0.276 Chirality : 0.041 0.161 2063 Planarity : 0.004 0.054 2344 Dihedral : 4.944 70.964 1887 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 3.12 % Allowed : 21.46 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1669 helix: 2.01 (0.21), residues: 645 sheet: 0.50 (0.29), residues: 339 loop : -1.16 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 477 HIS 0.008 0.001 HIS A 907 PHE 0.014 0.001 PHE B 523 TYR 0.014 0.001 TYR A 918 ARG 0.002 0.000 ARG A 920 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 655) hydrogen bonds : angle 4.51575 ( 1881) covalent geometry : bond 0.00240 (13524) covalent geometry : angle 0.58621 (18272) Misc. bond : bond 0.00028 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: A 313 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8062 (pp) REVERT: A 329 MET cc_start: 0.7753 (tpt) cc_final: 0.7388 (tpp) REVERT: A 574 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.6356 (t80) REVERT: A 913 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6790 (mm) REVERT: A 933 MET cc_start: 0.7466 (tpp) cc_final: 0.7157 (tpp) REVERT: A 966 ASP cc_start: 0.7919 (t0) cc_final: 0.7181 (p0) REVERT: A 1059 LEU cc_start: 0.8818 (tp) cc_final: 0.8511 (pp) REVERT: B 158 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7720 (tt) REVERT: B 574 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6612 (t80) REVERT: B 971 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8650 (tp30) REVERT: B 1091 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7511 (mm) outliers start: 45 outliers final: 22 residues processed: 189 average time/residue: 0.2153 time to fit residues: 62.2904 Evaluate side-chains 164 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 6 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 883 HIS ** A 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 GLN B 882 GLN B 886 HIS ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.197922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.129958 restraints weight = 19016.298| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.43 r_work: 0.3639 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13527 Z= 0.162 Angle : 0.622 13.769 18272 Z= 0.300 Chirality : 0.043 0.177 2063 Planarity : 0.004 0.051 2344 Dihedral : 5.175 73.232 1887 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 3.75 % Allowed : 20.97 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1669 helix: 1.93 (0.21), residues: 638 sheet: 0.44 (0.28), residues: 339 loop : -1.16 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 477 HIS 0.007 0.001 HIS A 907 PHE 0.017 0.002 PHE B 523 TYR 0.021 0.002 TYR A 243 ARG 0.003 0.000 ARG A 174 Details of bonding type rmsd hydrogen bonds : bond 0.04343 ( 655) hydrogen bonds : angle 4.71199 ( 1881) covalent geometry : bond 0.00391 (13524) covalent geometry : angle 0.62199 (18272) Misc. bond : bond 0.00038 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 138 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8073 (pp) REVERT: A 574 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.6420 (t80) REVERT: A 913 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6789 (mm) REVERT: A 933 MET cc_start: 0.7476 (tpp) cc_final: 0.7168 (tpp) REVERT: A 966 ASP cc_start: 0.7958 (t0) cc_final: 0.7322 (p0) REVERT: A 1059 LEU cc_start: 0.8844 (tp) cc_final: 0.8510 (pp) REVERT: B 158 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7715 (tt) REVERT: B 574 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.6717 (t80) REVERT: B 971 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8624 (tp30) REVERT: B 994 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8208 (mp) REVERT: B 1091 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7552 (mm) outliers start: 54 outliers final: 27 residues processed: 186 average time/residue: 0.2224 time to fit residues: 64.3465 Evaluate side-chains 167 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 110 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 HIS ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.196665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.130835 restraints weight = 19053.295| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 4.11 r_work: 0.3585 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13527 Z= 0.192 Angle : 0.666 14.420 18272 Z= 0.325 Chirality : 0.044 0.172 2063 Planarity : 0.004 0.050 2344 Dihedral : 5.460 74.354 1887 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 3.82 % Allowed : 20.21 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.21), residues: 1669 helix: 1.75 (0.21), residues: 638 sheet: 0.32 (0.28), residues: 346 loop : -1.27 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 477 HIS 0.008 0.001 HIS A 907 PHE 0.020 0.002 PHE B 523 TYR 0.023 0.002 TYR A 243 ARG 0.003 0.000 ARG B 386 Details of bonding type rmsd hydrogen bonds : bond 0.04771 ( 655) hydrogen bonds : angle 4.88891 ( 1881) covalent geometry : bond 0.00466 (13524) covalent geometry : angle 0.66591 (18272) Misc. bond : bond 0.00039 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 143 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 203 LYS cc_start: 0.9000 (pttt) cc_final: 0.8776 (ptpp) REVERT: A 313 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8100 (pp) REVERT: A 346 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8037 (pt0) REVERT: A 478 LEU cc_start: 0.9140 (mt) cc_final: 0.8791 (tt) REVERT: A 566 MET cc_start: 0.7023 (tpp) cc_final: 0.6426 (tmm) REVERT: A 574 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6460 (t80) REVERT: A 913 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6924 (mm) REVERT: A 933 MET cc_start: 0.7489 (tpp) cc_final: 0.7218 (tpp) REVERT: A 1059 LEU cc_start: 0.8830 (tp) cc_final: 0.8482 (pp) REVERT: B 158 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7776 (tt) REVERT: B 187 LYS cc_start: 0.8024 (mmmt) cc_final: 0.7714 (mmtt) REVERT: B 362 GLN cc_start: 0.5726 (tm-30) cc_final: 0.5447 (tm-30) REVERT: B 574 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6861 (t80) REVERT: B 994 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8233 (mp) REVERT: B 1091 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7593 (mm) outliers start: 55 outliers final: 34 residues processed: 193 average time/residue: 0.2162 time to fit residues: 64.6340 Evaluate side-chains 179 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 795 VAL Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 994 ILE Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 76 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 22 optimal weight: 0.2980 chunk 96 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 ASN ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.199925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.131753 restraints weight = 18946.536| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 3.48 r_work: 0.3670 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13527 Z= 0.116 Angle : 0.620 13.721 18272 Z= 0.296 Chirality : 0.042 0.172 2063 Planarity : 0.004 0.061 2344 Dihedral : 5.116 69.813 1887 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.48 % Favored : 96.46 % Rotamer: Outliers : 2.43 % Allowed : 21.81 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1669 helix: 1.95 (0.21), residues: 638 sheet: 0.45 (0.29), residues: 339 loop : -1.14 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 477 HIS 0.008 0.001 HIS A 907 PHE 0.017 0.001 PHE B 523 TYR 0.014 0.001 TYR B 202 ARG 0.003 0.000 ARG A 937 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 655) hydrogen bonds : angle 4.58936 ( 1881) covalent geometry : bond 0.00264 (13524) covalent geometry : angle 0.62011 (18272) Misc. bond : bond 0.00030 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 LYS cc_start: 0.8866 (pttt) cc_final: 0.8624 (ptpp) REVERT: A 313 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8041 (pp) REVERT: A 346 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8021 (pt0) REVERT: A 478 LEU cc_start: 0.9111 (mt) cc_final: 0.8784 (tt) REVERT: A 574 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.6161 (t80) REVERT: A 913 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6725 (mm) REVERT: A 933 MET cc_start: 0.7581 (tpp) cc_final: 0.7335 (tpp) REVERT: A 1059 LEU cc_start: 0.8824 (tp) cc_final: 0.8487 (pp) REVERT: B 158 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7711 (tt) REVERT: B 187 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7671 (mmtt) REVERT: B 362 GLN cc_start: 0.5740 (tm-30) cc_final: 0.5473 (tm-30) REVERT: B 574 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.6611 (t80) REVERT: B 875 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.8314 (p-80) REVERT: B 971 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8659 (tp30) REVERT: B 1091 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7536 (mm) REVERT: B 1119 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7661 (p) outliers start: 35 outliers final: 19 residues processed: 176 average time/residue: 0.2231 time to fit residues: 60.4588 Evaluate side-chains 169 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 875 HIS Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 9 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 165 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 149 optimal weight: 0.0030 chunk 157 optimal weight: 4.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 HIS ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.200509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.132498 restraints weight = 18965.713| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 3.46 r_work: 0.3677 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13527 Z= 0.116 Angle : 0.634 14.364 18272 Z= 0.299 Chirality : 0.042 0.166 2063 Planarity : 0.004 0.064 2344 Dihedral : 5.008 67.528 1887 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.89 % Favored : 96.05 % Rotamer: Outliers : 2.15 % Allowed : 22.15 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1669 helix: 1.94 (0.21), residues: 639 sheet: 0.47 (0.29), residues: 339 loop : -1.09 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 477 HIS 0.008 0.001 HIS A 907 PHE 0.016 0.001 PHE B 523 TYR 0.013 0.001 TYR A 243 ARG 0.002 0.000 ARG A 174 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 655) hydrogen bonds : angle 4.56755 ( 1881) covalent geometry : bond 0.00269 (13524) covalent geometry : angle 0.63364 (18272) Misc. bond : bond 0.00027 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 LYS cc_start: 0.8869 (pttt) cc_final: 0.8569 (ptpp) REVERT: A 313 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8032 (pp) REVERT: A 346 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8111 (pt0) REVERT: A 478 LEU cc_start: 0.9129 (mt) cc_final: 0.8772 (tt) REVERT: A 574 TYR cc_start: 0.6940 (OUTLIER) cc_final: 0.6355 (t80) REVERT: A 913 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6782 (mm) REVERT: A 933 MET cc_start: 0.7517 (tpp) cc_final: 0.7251 (tpp) REVERT: A 1059 LEU cc_start: 0.8833 (tp) cc_final: 0.8493 (pp) REVERT: B 158 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7745 (tt) REVERT: B 187 LYS cc_start: 0.7963 (mmmt) cc_final: 0.7663 (mmtt) REVERT: B 362 GLN cc_start: 0.5659 (tm-30) cc_final: 0.5410 (tm-30) REVERT: B 574 TYR cc_start: 0.6955 (OUTLIER) cc_final: 0.6624 (t80) REVERT: B 1091 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7542 (mm) REVERT: B 1119 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7618 (p) outliers start: 31 outliers final: 20 residues processed: 167 average time/residue: 0.2298 time to fit residues: 59.3642 Evaluate side-chains 165 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 574 TYR Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 883 HIS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 987 ILE Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 574 TYR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 902 PHE Chi-restraints excluded: chain B residue 1091 LEU Chi-restraints excluded: chain B residue 1119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 121 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 132 optimal weight: 0.0070 chunk 52 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1017 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.196452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.131011 restraints weight = 19085.998| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 4.10 r_work: 0.3583 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13527 Z= 0.198 Angle : 0.688 14.635 18272 Z= 0.334 Chirality : 0.044 0.193 2063 Planarity : 0.004 0.053 2344 Dihedral : 5.339 70.889 1887 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.55 % Favored : 95.39 % Rotamer: Outliers : 2.99 % Allowed : 21.25 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1669 helix: 1.76 (0.21), residues: 638 sheet: 0.36 (0.28), residues: 339 loop : -1.20 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 477 HIS 0.010 0.001 HIS B 875 PHE 0.017 0.002 PHE B 523 TYR 0.025 0.002 TYR A 243 ARG 0.002 0.000 ARG B 898 Details of bonding type rmsd hydrogen bonds : bond 0.04769 ( 655) hydrogen bonds : angle 4.86502 ( 1881) covalent geometry : bond 0.00482 (13524) covalent geometry : angle 0.68804 (18272) Misc. bond : bond 0.00064 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7684.92 seconds wall clock time: 132 minutes 4.33 seconds (7924.33 seconds total)