Starting phenix.real_space_refine on Fri Mar 6 03:59:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pzp_13735/03_2026/7pzp_13735.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pzp_13735/03_2026/7pzp_13735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pzp_13735/03_2026/7pzp_13735.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pzp_13735/03_2026/7pzp_13735.map" model { file = "/net/cci-nas-00/data/ceres_data/7pzp_13735/03_2026/7pzp_13735.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pzp_13735/03_2026/7pzp_13735.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15333 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 9912 2.51 5 N 2834 2.21 5 O 2758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15602 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7803 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 990, 7798 Classifications: {'peptide': 990} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 68, 'TRANS': 921} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 990, 7798 Classifications: {'peptide': 990} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 68, 'TRANS': 921} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 7981 Chain: "B" Number of atoms: 7799 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 988, 7781 Classifications: {'peptide': 988} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 68, 'TRANS': 919} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 988, 7781 Classifications: {'peptide': 988} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 68, 'TRANS': 919} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 7948 Time building chain proxies: 5.75, per 1000 atoms: 0.37 Number of scatterers: 15602 At special positions: 0 Unit cell: (96.96, 113.12, 150.49, 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 98 16.00 O 2758 8.00 N 2834 7.00 C 9912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 1.4 seconds 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 14 sheets defined 66.9% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 220 through 235 removed outlier: 3.783A pdb=" N GLN A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.568A pdb=" N TYR A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.700A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.099A pdb=" N ARG A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 326 removed outlier: 4.093A pdb=" N ILE A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 340 through 354 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 392 through 410 Processing helix chain 'A' and resid 424 through 463 Processing helix chain 'A' and resid 467 through 474 removed outlier: 4.228A pdb=" N LEU A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 490 Processing helix chain 'A' and resid 496 through 521 Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.674A pdb=" N ALA A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 557 Processing helix chain 'A' and resid 561 through 565 removed outlier: 3.655A pdb=" N GLU A 564 " --> pdb=" O ALA A 561 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A 565 " --> pdb=" O LEU A 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 561 through 565' Processing helix chain 'A' and resid 568 through 587 Processing helix chain 'A' and resid 624 through 635 Processing helix chain 'A' and resid 676 through 687 Processing helix chain 'A' and resid 688 through 705 removed outlier: 3.549A pdb=" N LEU A 692 " --> pdb=" O PRO A 688 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLY A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 removed outlier: 3.640A pdb=" N ALA A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 750 Processing helix chain 'A' and resid 751 through 789 Processing helix chain 'A' and resid 818 through 824 Processing helix chain 'A' and resid 833 through 850 removed outlier: 4.532A pdb=" N LEU A 838 " --> pdb=" O GLY A 834 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP A 839 " --> pdb=" O PRO A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 867 through 877 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.663A pdb=" N GLY A 887 " --> pdb=" O LYS A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 907 removed outlier: 3.963A pdb=" N ASN A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 936 Processing helix chain 'A' and resid 937 through 944 Processing helix chain 'A' and resid 954 through 973 removed outlier: 3.726A pdb=" N GLY A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 986 through 999 Processing helix chain 'A' and resid 1003 through 1017 removed outlier: 3.735A pdb=" N LEU A1017 " --> pdb=" O ARG A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1044 removed outlier: 3.795A pdb=" N GLN A1041 " --> pdb=" O PHE A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1065 removed outlier: 3.868A pdb=" N ARG A1048 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1143 Proline residue: A1120 - end of helix Processing helix chain 'A' and resid 1159 through 1177 removed outlier: 3.636A pdb=" N GLU A1177 " --> pdb=" O ARG A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1191 Processing helix chain 'A' and resid 1197 through 1210 Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.886A pdb=" N ARG A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 Processing helix chain 'B' and resid 238 through 252 Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.666A pdb=" N TYR B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 removed outlier: 3.724A pdb=" N LEU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.869A pdb=" N TYR B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B 308 " --> pdb=" O GLN B 304 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN B 309 " --> pdb=" O CYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 325 removed outlier: 3.556A pdb=" N ILE B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 340 through 354 removed outlier: 3.599A pdb=" N ALA B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 4.282A pdb=" N ASP B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 410 Processing helix chain 'B' and resid 424 through 462 Processing helix chain 'B' and resid 467 through 474 removed outlier: 3.987A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 490 Processing helix chain 'B' and resid 497 through 521 Processing helix chain 'B' and resid 521 through 538 removed outlier: 3.708A pdb=" N ALA B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 536 " --> pdb=" O LYS B 532 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 556 Processing helix chain 'B' and resid 561 through 565 removed outlier: 3.802A pdb=" N GLN B 565 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 587 removed outlier: 3.543A pdb=" N THR B 587 " --> pdb=" O LEU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 635 Processing helix chain 'B' and resid 676 through 687 Processing helix chain 'B' and resid 688 through 705 removed outlier: 3.507A pdb=" N LEU B 692 " --> pdb=" O PRO B 688 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 695 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS B 705 " --> pdb=" O GLN B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 723 Processing helix chain 'B' and resid 751 through 789 Processing helix chain 'B' and resid 818 through 824 Processing helix chain 'B' and resid 836 through 850 Processing helix chain 'B' and resid 856 through 867 removed outlier: 3.614A pdb=" N LEU B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 877 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.618A pdb=" N GLY B 887 " --> pdb=" O LYS B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 907 Processing helix chain 'B' and resid 925 through 936 Processing helix chain 'B' and resid 937 through 944 Processing helix chain 'B' and resid 954 through 973 removed outlier: 3.755A pdb=" N GLY B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 986 through 999 removed outlier: 4.284A pdb=" N GLN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1017 removed outlier: 3.727A pdb=" N ARG B1007 " --> pdb=" O ARG B1003 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU B1017 " --> pdb=" O ARG B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1044 removed outlier: 3.613A pdb=" N GLN B1041 " --> pdb=" O PHE B1037 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU B1042 " --> pdb=" O LYS B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1065 removed outlier: 3.604A pdb=" N ARG B1048 " --> pdb=" O PHE B1044 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP B1053 " --> pdb=" O ALA B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1143 removed outlier: 3.861A pdb=" N LYS B1116 " --> pdb=" O THR B1112 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN B1117 " --> pdb=" O ARG B1113 " (cutoff:3.500A) Proline residue: B1120 - end of helix Processing helix chain 'B' and resid 1159 through 1177 Processing helix chain 'B' and resid 1178 through 1192 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.895A pdb=" N ARG B1224 " --> pdb=" O GLU B1220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 415 Processing sheet with id=AA2, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'A' and resid 607 through 609 Processing sheet with id=AA4, first strand: chain 'A' and resid 794 through 795 Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 800 Processing sheet with id=AA6, first strand: chain 'A' and resid 831 through 832 removed outlier: 4.442A pdb=" N ARG A 831 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 919 through 921 Processing sheet with id=AA8, first strand: chain 'A' and resid 1069 through 1071 Processing sheet with id=AA9, first strand: chain 'B' and resid 411 through 415 Processing sheet with id=AB1, first strand: chain 'B' and resid 495 through 496 removed outlier: 3.592A pdb=" N LYS B 622 " --> pdb=" O TYR B 607 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 794 through 795 Processing sheet with id=AB3, first strand: chain 'B' and resid 798 through 799 Processing sheet with id=AB4, first strand: chain 'B' and resid 919 through 921 Processing sheet with id=AB5, first strand: chain 'B' and resid 1069 through 1071 957 hydrogen bonds defined for protein. 2825 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: 2.44 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3565 1.33 - 1.45: 3217 1.45 - 1.57: 9055 1.57 - 1.69: 0 1.69 - 1.81: 148 Bond restraints: 15985 Sorted by residual: bond pdb=" N THR B 587 " pdb=" CA THR B 587 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.22e-02 6.72e+03 1.07e+01 bond pdb=" N TYR B 468 " pdb=" CA TYR B 468 " ideal model delta sigma weight residual 1.461 1.491 -0.030 9.20e-03 1.18e+04 1.03e+01 bond pdb=" N CYS B 591 " pdb=" CA CYS B 591 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N LEU B 746 " pdb=" CA LEU B 746 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.72e+00 bond pdb=" N ARG A 601 " pdb=" CA ARG A 601 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.44e+00 ... (remaining 15980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 20115 1.93 - 3.86: 1436 3.86 - 5.78: 131 5.78 - 7.71: 28 7.71 - 9.64: 8 Bond angle restraints: 21718 Sorted by residual: angle pdb=" CA GLY B 881 " pdb=" C GLY B 881 " pdb=" O GLY B 881 " ideal model delta sigma weight residual 122.28 118.28 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" C ARG B 805 " pdb=" N THR B 806 " pdb=" CA THR B 806 " ideal model delta sigma weight residual 120.90 126.49 -5.59 1.41e+00 5.03e-01 1.57e+01 angle pdb=" CG ARG A 598 " pdb=" CD ARG A 598 " pdb=" NE ARG A 598 " ideal model delta sigma weight residual 112.00 120.72 -8.72 2.20e+00 2.07e-01 1.57e+01 angle pdb=" N LEU B 593 " pdb=" CA LEU B 593 " pdb=" C LEU B 593 " ideal model delta sigma weight residual 110.30 104.46 5.84 1.50e+00 4.44e-01 1.52e+01 angle pdb=" N ALA B 750 " pdb=" CA ALA B 750 " pdb=" C ALA B 750 " ideal model delta sigma weight residual 111.28 107.13 4.15 1.09e+00 8.42e-01 1.45e+01 ... (remaining 21713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 8762 17.50 - 34.99: 795 34.99 - 52.49: 168 52.49 - 69.99: 32 69.99 - 87.49: 17 Dihedral angle restraints: 9774 sinusoidal: 3962 harmonic: 5812 Sorted by residual: dihedral pdb=" C THR A1002 " pdb=" N THR A1002 " pdb=" CA THR A1002 " pdb=" CB THR A1002 " ideal model delta harmonic sigma weight residual -122.00 -131.26 9.26 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C GLU B 442 " pdb=" N GLU B 442 " pdb=" CA GLU B 442 " pdb=" CB GLU B 442 " ideal model delta harmonic sigma weight residual -122.60 -114.02 -8.58 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" N LEU B 593 " pdb=" C LEU B 593 " pdb=" CA LEU B 593 " pdb=" CB LEU B 593 " ideal model delta harmonic sigma weight residual 122.80 114.84 7.96 0 2.50e+00 1.60e-01 1.01e+01 ... (remaining 9771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2065 0.090 - 0.181: 299 0.181 - 0.271: 37 0.271 - 0.362: 9 0.362 - 0.452: 1 Chirality restraints: 2411 Sorted by residual: chirality pdb=" CG LEU A 718 " pdb=" CB LEU A 718 " pdb=" CD1 LEU A 718 " pdb=" CD2 LEU A 718 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CA LEU B 593 " pdb=" N LEU B 593 " pdb=" C LEU B 593 " pdb=" CB LEU B 593 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CB VAL B 867 " pdb=" CA VAL B 867 " pdb=" CG1 VAL B 867 " pdb=" CG2 VAL B 867 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 2408 not shown) Planarity restraints: 2829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 434 " -0.022 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C LEU A 434 " 0.075 2.00e-02 2.50e+03 pdb=" O LEU A 434 " -0.028 2.00e-02 2.50e+03 pdb=" N LYS A 435 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 899 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C MET B 899 " 0.064 2.00e-02 2.50e+03 pdb=" O MET B 899 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU B 900 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 680 " -0.016 2.00e-02 2.50e+03 2.79e-02 1.16e+01 pdb=" CG HIS A 680 " 0.057 2.00e-02 2.50e+03 pdb=" ND1 HIS A 680 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS A 680 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 HIS A 680 " 0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 680 " -0.000 2.00e-02 2.50e+03 ... (remaining 2826 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 138 2.68 - 3.24: 14673 3.24 - 3.79: 26172 3.79 - 4.35: 34039 4.35 - 4.90: 54133 Nonbonded interactions: 129155 Sorted by model distance: nonbonded pdb=" CG LEU B 245 " pdb=" NE2 HIS B 249 " model vdw 2.128 3.550 nonbonded pdb=" CD2 LEU B 245 " pdb=" NE2 HIS B 249 " model vdw 2.135 3.540 nonbonded pdb=" CE1 HIS B 249 " pdb=" O GLY B 463 " model vdw 2.146 3.260 nonbonded pdb=" O LEU B 245 " pdb=" CD2 HIS B 249 " model vdw 2.240 3.260 nonbonded pdb=" OG SER A 220 " pdb=" OE1 GLN A 223 " model vdw 2.272 3.040 ... (remaining 129150 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 220 through 994 or resid 996 through 1050 or resid 1052 th \ rough 1062 or resid 1064 through 1230)) selection = (chain 'B' and (resid 220 through 994 or resid 996 through 1050 or resid 1052 th \ rough 1062 or resid 1064 through 1230)) } 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=0.03 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.180 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 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 : 0.007 0.082 15985 Z= 0.426 Angle : 1.022 9.639 21718 Z= 0.664 Chirality : 0.066 0.452 2411 Planarity : 0.007 0.057 2829 Dihedral : 14.297 87.486 5994 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.18), residues: 1974 helix: 2.29 (0.14), residues: 1246 sheet: -0.06 (0.63), residues: 64 loop : 0.24 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG B 450 TYR 0.022 0.002 TYR A 378 PHE 0.045 0.003 PHE A1119 TRP 0.021 0.003 TRP A1154 HIS 0.038 0.003 HIS A 680 Details of bonding type rmsd covalent geometry : bond 0.00671 (15985) covalent geometry : angle 1.02221 (21718) hydrogen bonds : bond 0.15095 ( 957) hydrogen bonds : angle 5.52668 ( 2825) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 LEU cc_start: 0.7497 (tt) cc_final: 0.7183 (mp) REVERT: A 299 TYR cc_start: 0.5476 (m-80) cc_final: 0.5006 (m-80) REVERT: A 436 THR cc_start: 0.8587 (m) cc_final: 0.8021 (p) REVERT: A 572 GLN cc_start: 0.7984 (mt0) cc_final: 0.7549 (mt0) REVERT: B 227 LEU cc_start: 0.5445 (tp) cc_final: 0.4758 (tp) REVERT: B 234 LEU cc_start: 0.5374 (mt) cc_final: 0.5139 (mp) REVERT: B 473 LEU cc_start: 0.7445 (mt) cc_final: 0.7111 (pp) REVERT: B 485 GLN cc_start: 0.5606 (mm-40) cc_final: 0.5382 (mm110) REVERT: B 618 ILE cc_start: 0.6219 (pt) cc_final: 0.5318 (mt) REVERT: B 784 SER cc_start: 0.6877 (m) cc_final: 0.6653 (t) REVERT: B 1043 MET cc_start: 0.6277 (mmm) cc_final: 0.5928 (ttm) REVERT: B 1076 VAL cc_start: 0.8298 (m) cc_final: 0.8022 (p) REVERT: B 1230 SER cc_start: 0.6469 (p) cc_final: 0.6178 (t) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.1585 time to fit residues: 82.6721 Evaluate side-chains 182 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN A 512 HIS A 585 GLN ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS A1035 GLN A1221 GLN B 515 GLN B 527 GLN B 529 HIS ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 HIS ** B 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN B 972 GLN B1125 HIS B1209 GLN B1221 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.171240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.154555 restraints weight = 79671.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.157139 restraints weight = 94906.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.158610 restraints weight = 27479.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.159265 restraints weight = 16280.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.159436 restraints weight = 11092.101| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4204 r_free = 0.4204 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4204 r_free = 0.4204 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15985 Z= 0.167 Angle : 0.638 11.542 21718 Z= 0.331 Chirality : 0.040 0.183 2411 Planarity : 0.005 0.040 2829 Dihedral : 4.012 23.425 2174 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.51 % Allowed : 9.34 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.18), residues: 1974 helix: 2.33 (0.14), residues: 1260 sheet: 0.36 (0.66), residues: 54 loop : 0.12 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 450 TYR 0.017 0.002 TYR B 627 PHE 0.019 0.002 PHE B 721 TRP 0.020 0.002 TRP A1154 HIS 0.020 0.002 HIS B 624 Details of bonding type rmsd covalent geometry : bond 0.00372 (15985) covalent geometry : angle 0.63837 (21718) hydrogen bonds : bond 0.05027 ( 957) hydrogen bonds : angle 4.39220 ( 2825) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 306 MET cc_start: 0.6691 (mtt) cc_final: 0.5970 (mpp) REVERT: B 1043 MET cc_start: 0.5368 (mmm) cc_final: 0.5143 (ttm) outliers start: 25 outliers final: 13 residues processed: 206 average time/residue: 0.1187 time to fit residues: 36.8452 Evaluate side-chains 158 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 774 SER Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 970 ASP Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 187 optimal weight: 7.9990 chunk 115 optimal weight: 0.0270 chunk 134 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 171 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.4244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN A 390 HIS A 585 GLN B 252 GLN B 274 GLN B 515 GLN B 585 GLN ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 HIS ** 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 = 0.4328 r_free = 0.4328 target = 0.164566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.147322 restraints weight = 57194.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.149285 restraints weight = 88354.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.150617 restraints weight = 27404.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.151032 restraints weight = 18410.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.151352 restraints weight = 11957.864| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4108 r_free = 0.4108 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4108 r_free = 0.4108 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 15985 Z= 0.182 Angle : 0.667 19.925 21718 Z= 0.331 Chirality : 0.042 0.274 2411 Planarity : 0.005 0.042 2829 Dihedral : 4.133 20.909 2174 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.81 % Allowed : 11.57 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.18), residues: 1974 helix: 2.07 (0.14), residues: 1253 sheet: -0.03 (0.60), residues: 64 loop : 0.14 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 792 TYR 0.023 0.002 TYR B 627 PHE 0.027 0.002 PHE B 863 TRP 0.074 0.003 TRP B 441 HIS 0.013 0.002 HIS A 844 Details of bonding type rmsd covalent geometry : bond 0.00408 (15985) covalent geometry : angle 0.66676 (21718) hydrogen bonds : bond 0.04622 ( 957) hydrogen bonds : angle 4.26231 ( 2825) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 868 MET cc_start: 0.8265 (tpp) cc_final: 0.7852 (tpt) REVERT: B 227 LEU cc_start: 0.6172 (tp) cc_final: 0.5968 (tp) REVERT: B 306 MET cc_start: 0.6934 (mtt) cc_final: 0.6575 (mtp) REVERT: B 1078 VAL cc_start: 0.5357 (t) cc_final: 0.5147 (t) outliers start: 30 outliers final: 19 residues processed: 182 average time/residue: 0.1219 time to fit residues: 33.3482 Evaluate side-chains 157 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 970 ASP Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 GLN B 369 ASN B 515 GLN B 585 GLN B 588 GLN B 745 HIS B 847 ASN ** B 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.163194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.145546 restraints weight = 63075.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.147700 restraints weight = 90546.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.148971 restraints weight = 27721.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.149526 restraints weight = 17770.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.149805 restraints weight = 11542.759| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4083 r_free = 0.4083 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4083 r_free = 0.4083 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15985 Z= 0.141 Angle : 0.597 10.459 21718 Z= 0.295 Chirality : 0.038 0.151 2411 Planarity : 0.005 0.046 2829 Dihedral : 3.980 17.576 2174 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.63 % Allowed : 12.47 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.18), residues: 1974 helix: 2.16 (0.14), residues: 1254 sheet: -0.21 (0.60), residues: 64 loop : 0.15 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 411 TYR 0.017 0.001 TYR B 461 PHE 0.019 0.002 PHE B 721 TRP 0.051 0.002 TRP B1053 HIS 0.006 0.001 HIS A 680 Details of bonding type rmsd covalent geometry : bond 0.00318 (15985) covalent geometry : angle 0.59696 (21718) hydrogen bonds : bond 0.04176 ( 957) hydrogen bonds : angle 4.11439 ( 2825) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7032 (OUTLIER) cc_final: 0.6271 (ptpp) REVERT: A 970 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7992 (m-30) REVERT: B 286 MET cc_start: 0.4628 (mmt) cc_final: 0.4360 (mpp) REVERT: B 306 MET cc_start: 0.6814 (mtt) cc_final: 0.6344 (mtp) REVERT: B 322 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6499 (pm20) REVERT: B 411 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7131 (ttm-80) outliers start: 27 outliers final: 17 residues processed: 169 average time/residue: 0.1190 time to fit residues: 30.2651 Evaluate side-chains 157 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 970 ASP Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 411 ARG Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 109 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 182 optimal weight: 0.9980 chunk 95 optimal weight: 0.0070 chunk 103 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 145 optimal weight: 0.0050 chunk 37 optimal weight: 0.0970 overall best weight: 0.6212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN B 585 GLN B 608 HIS B 693 HIS B 829 GLN ** B 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.163761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.146743 restraints weight = 61734.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.148825 restraints weight = 89272.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.150136 restraints weight = 26375.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.150541 restraints weight = 17403.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.150862 restraints weight = 10917.461| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15985 Z= 0.117 Angle : 0.564 11.605 21718 Z= 0.277 Chirality : 0.037 0.160 2411 Planarity : 0.004 0.039 2829 Dihedral : 3.816 16.836 2174 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.93 % Allowed : 12.53 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.19), residues: 1974 helix: 2.33 (0.14), residues: 1253 sheet: -0.21 (0.61), residues: 64 loop : 0.14 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1007 TYR 0.018 0.001 TYR B 627 PHE 0.017 0.001 PHE B 721 TRP 0.033 0.002 TRP B1053 HIS 0.013 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00259 (15985) covalent geometry : angle 0.56365 (21718) hydrogen bonds : bond 0.03946 ( 957) hydrogen bonds : angle 3.94578 ( 2825) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6319 (ptpp) REVERT: A 868 MET cc_start: 0.8368 (tpp) cc_final: 0.8031 (tpp) REVERT: B 306 MET cc_start: 0.6749 (mtt) cc_final: 0.6337 (mtp) REVERT: B 1047 THR cc_start: 0.5457 (t) cc_final: 0.5244 (t) REVERT: B 1163 MET cc_start: 0.8337 (ttp) cc_final: 0.8072 (ttp) outliers start: 32 outliers final: 18 residues processed: 163 average time/residue: 0.1042 time to fit residues: 26.6688 Evaluate side-chains 150 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 7 optimal weight: 0.9980 chunk 145 optimal weight: 0.0370 chunk 87 optimal weight: 0.9980 chunk 61 optimal weight: 0.0370 chunk 45 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN B 390 HIS B 515 GLN ** B 920 HIS ** 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 = 0.4306 r_free = 0.4306 target = 0.163081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.145964 restraints weight = 56923.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.147817 restraints weight = 88813.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.148975 restraints weight = 27716.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.149377 restraints weight = 18969.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.149642 restraints weight = 12242.154| |-----------------------------------------------------------------------------| r_work (final): 0.4085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4087 r_free = 0.4087 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15985 Z= 0.117 Angle : 0.572 16.872 21718 Z= 0.278 Chirality : 0.037 0.139 2411 Planarity : 0.004 0.040 2829 Dihedral : 3.785 16.946 2174 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.51 % Allowed : 12.95 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.19), residues: 1974 helix: 2.41 (0.14), residues: 1248 sheet: -0.33 (0.55), residues: 74 loop : 0.09 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 464 TYR 0.023 0.001 TYR B 282 PHE 0.016 0.001 PHE B 721 TRP 0.031 0.002 TRP B1053 HIS 0.010 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00261 (15985) covalent geometry : angle 0.57206 (21718) hydrogen bonds : bond 0.03846 ( 957) hydrogen bonds : angle 3.91846 ( 2825) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6371 (ptpp) REVERT: B 306 MET cc_start: 0.6769 (mtt) cc_final: 0.6366 (mtp) REVERT: B 322 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6495 (pm20) REVERT: B 445 LEU cc_start: 0.6625 (mt) cc_final: 0.6331 (mp) REVERT: B 1163 MET cc_start: 0.8317 (ttp) cc_final: 0.8020 (ttp) outliers start: 25 outliers final: 19 residues processed: 154 average time/residue: 0.1059 time to fit residues: 26.4367 Evaluate side-chains 147 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1211 VAL Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 46 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 42 optimal weight: 0.0870 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 113 optimal weight: 0.4980 chunk 102 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 515 GLN ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 HIS ** 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 = 0.4301 r_free = 0.4301 target = 0.162571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.145548 restraints weight = 54752.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.147395 restraints weight = 87263.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.148581 restraints weight = 27697.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.148991 restraints weight = 18639.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.149208 restraints weight = 12378.146| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4091 r_free = 0.4091 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15985 Z= 0.114 Angle : 0.558 10.578 21718 Z= 0.274 Chirality : 0.037 0.160 2411 Planarity : 0.004 0.040 2829 Dihedral : 3.719 16.323 2174 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.39 % Allowed : 13.07 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.19), residues: 1974 helix: 2.44 (0.14), residues: 1248 sheet: -0.36 (0.55), residues: 74 loop : 0.08 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 968 TYR 0.017 0.001 TYR B 461 PHE 0.021 0.001 PHE B 863 TRP 0.028 0.001 TRP B1053 HIS 0.008 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00254 (15985) covalent geometry : angle 0.55760 (21718) hydrogen bonds : bond 0.03778 ( 957) hydrogen bonds : angle 3.90424 ( 2825) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6425 (ptpp) REVERT: B 306 MET cc_start: 0.6786 (mtt) cc_final: 0.6443 (mtp) REVERT: B 322 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6543 (pm20) REVERT: B 1163 MET cc_start: 0.8270 (ttp) cc_final: 0.7956 (ttp) outliers start: 23 outliers final: 17 residues processed: 151 average time/residue: 0.1014 time to fit residues: 25.0607 Evaluate side-chains 147 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 170 optimal weight: 9.9990 chunk 34 optimal weight: 20.0000 chunk 63 optimal weight: 0.0040 chunk 138 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 HIS B 250 HIS B 515 GLN B 585 GLN ** B 920 HIS ** 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 = 0.4301 r_free = 0.4301 target = 0.162418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.145260 restraints weight = 62783.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.147310 restraints weight = 89479.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.148540 restraints weight = 27039.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.148912 restraints weight = 17818.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.150314 restraints weight = 11464.616| |-----------------------------------------------------------------------------| r_work (final): 0.4084 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4086 r_free = 0.4086 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4086 r_free = 0.4086 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15985 Z= 0.113 Angle : 0.569 11.375 21718 Z= 0.281 Chirality : 0.037 0.195 2411 Planarity : 0.004 0.039 2829 Dihedral : 3.714 16.308 2174 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.63 % Allowed : 13.19 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.19), residues: 1974 helix: 2.42 (0.14), residues: 1249 sheet: -0.46 (0.55), residues: 74 loop : 0.09 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B1190 TYR 0.017 0.001 TYR B 282 PHE 0.015 0.001 PHE B 721 TRP 0.027 0.001 TRP B1053 HIS 0.008 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00252 (15985) covalent geometry : angle 0.56946 (21718) hydrogen bonds : bond 0.03724 ( 957) hydrogen bonds : angle 3.94428 ( 2825) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6454 (ptpp) REVERT: B 306 MET cc_start: 0.6842 (mtt) cc_final: 0.6494 (mtp) REVERT: B 322 GLN cc_start: 0.6911 (OUTLIER) cc_final: 0.6482 (pm20) REVERT: B 1047 THR cc_start: 0.5474 (t) cc_final: 0.5252 (t) REVERT: B 1163 MET cc_start: 0.8291 (ttp) cc_final: 0.7974 (ttp) outliers start: 27 outliers final: 21 residues processed: 156 average time/residue: 0.1055 time to fit residues: 25.8692 Evaluate side-chains 154 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 279 GLU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 168 optimal weight: 0.0270 chunk 26 optimal weight: 0.7980 chunk 190 optimal weight: 3.9990 chunk 131 optimal weight: 0.0010 chunk 3 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 192 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.7046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN B 515 GLN ** B 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.161842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.144622 restraints weight = 60201.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.146626 restraints weight = 88087.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.147865 restraints weight = 26920.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.148291 restraints weight = 17814.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.148607 restraints weight = 11482.133| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4067 r_free = 0.4067 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4067 r_free = 0.4067 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6698 moved from start: 0.5480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15985 Z= 0.121 Angle : 0.577 10.286 21718 Z= 0.282 Chirality : 0.037 0.174 2411 Planarity : 0.004 0.039 2829 Dihedral : 3.680 15.561 2174 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.39 % Allowed : 13.86 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.19), residues: 1974 helix: 2.45 (0.14), residues: 1248 sheet: -0.43 (0.55), residues: 74 loop : 0.09 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1190 TYR 0.021 0.001 TYR B 627 PHE 0.022 0.001 PHE B 863 TRP 0.026 0.001 TRP B1053 HIS 0.008 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00276 (15985) covalent geometry : angle 0.57703 (21718) hydrogen bonds : bond 0.03738 ( 957) hydrogen bonds : angle 3.93637 ( 2825) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6453 (ptpp) REVERT: A 1213 LYS cc_start: 0.8156 (mmmt) cc_final: 0.7869 (mmmm) REVERT: B 306 MET cc_start: 0.6840 (mtt) cc_final: 0.6497 (mtp) REVERT: B 322 GLN cc_start: 0.6850 (OUTLIER) cc_final: 0.6277 (pm20) REVERT: B 585 GLN cc_start: 0.4712 (mm-40) cc_final: 0.4467 (mp10) REVERT: B 1047 THR cc_start: 0.5656 (t) cc_final: 0.5444 (t) REVERT: B 1163 MET cc_start: 0.8182 (ttp) cc_final: 0.7875 (ttp) REVERT: B 1190 ARG cc_start: 0.5932 (mmm160) cc_final: 0.5686 (mmm160) outliers start: 23 outliers final: 18 residues processed: 150 average time/residue: 0.0995 time to fit residues: 24.6081 Evaluate side-chains 148 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 143 optimal weight: 0.0770 chunk 8 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 184 optimal weight: 0.0270 chunk 17 optimal weight: 0.6980 chunk 131 optimal weight: 0.0170 chunk 112 optimal weight: 0.0770 chunk 14 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 83 optimal weight: 0.0970 overall best weight: 0.0550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 405 HIS A 829 GLN B 515 GLN B 798 HIS ** B 920 HIS ** 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 = 0.4301 r_free = 0.4301 target = 0.162343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.141789 restraints weight = 78090.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.139258 restraints weight = 68478.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.136718 restraints weight = 45783.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.137375 restraints weight = 38679.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.137066 restraints weight = 29068.805| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3961 r_free = 0.3961 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3961 r_free = 0.3961 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15985 Z= 0.106 Angle : 0.566 10.969 21718 Z= 0.275 Chirality : 0.036 0.171 2411 Planarity : 0.004 0.041 2829 Dihedral : 3.610 22.597 2174 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.02 % Allowed : 14.46 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.19), residues: 1974 helix: 2.50 (0.14), residues: 1250 sheet: -0.40 (0.56), residues: 74 loop : 0.11 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1190 TYR 0.028 0.001 TYR B 461 PHE 0.014 0.001 PHE B 721 TRP 0.024 0.001 TRP B1053 HIS 0.009 0.001 HIS A 405 Details of bonding type rmsd covalent geometry : bond 0.00229 (15985) covalent geometry : angle 0.56645 (21718) hydrogen bonds : bond 0.03547 ( 957) hydrogen bonds : angle 3.87923 ( 2825) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 LEU cc_start: 0.8129 (mp) cc_final: 0.7829 (tp) REVERT: A 1213 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7884 (mmmm) REVERT: B 306 MET cc_start: 0.6837 (mtt) cc_final: 0.6547 (mtp) REVERT: B 322 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6309 (pm20) REVERT: B 1047 THR cc_start: 0.5620 (t) cc_final: 0.5406 (t) REVERT: B 1163 MET cc_start: 0.8336 (ttp) cc_final: 0.8055 (ttp) REVERT: B 1190 ARG cc_start: 0.5944 (mmm160) cc_final: 0.5709 (mmm160) outliers start: 17 outliers final: 12 residues processed: 152 average time/residue: 0.1123 time to fit residues: 26.7312 Evaluate side-chains 142 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 105 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 0.0870 chunk 141 optimal weight: 0.4980 chunk 158 optimal weight: 0.2980 chunk 73 optimal weight: 0.4980 chunk 95 optimal weight: 0.0770 chunk 136 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN B 515 GLN ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.162074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.143709 restraints weight = 67930.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.146048 restraints weight = 90080.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.147447 restraints weight = 26385.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.148029 restraints weight = 16770.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.148155 restraints weight = 11090.696| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4057 r_free = 0.4057 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4057 r_free = 0.4057 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15985 Z= 0.107 Angle : 0.566 11.168 21718 Z= 0.276 Chirality : 0.037 0.162 2411 Planarity : 0.004 0.040 2829 Dihedral : 3.583 19.912 2174 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.02 % Allowed : 14.46 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.19), residues: 1974 helix: 2.50 (0.14), residues: 1252 sheet: -0.34 (0.57), residues: 74 loop : 0.16 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1190 TYR 0.025 0.001 TYR B 461 PHE 0.014 0.001 PHE B 721 TRP 0.027 0.001 TRP A 441 HIS 0.008 0.001 HIS B 249 Details of bonding type rmsd covalent geometry : bond 0.00236 (15985) covalent geometry : angle 0.56561 (21718) hydrogen bonds : bond 0.03525 ( 957) hydrogen bonds : angle 3.89352 ( 2825) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2210.15 seconds wall clock time: 39 minutes 2.23 seconds (2342.23 seconds total)