Starting phenix.real_space_refine on Sun Aug 24 23:56:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v5r_64793/08_2025/9v5r_64793.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v5r_64793/08_2025/9v5r_64793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v5r_64793/08_2025/9v5r_64793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v5r_64793/08_2025/9v5r_64793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v5r_64793/08_2025/9v5r_64793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v5r_64793/08_2025/9v5r_64793.map" } resolution = 2.92 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 14901 2.51 5 N 3808 2.21 5 O 4312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23153 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7638 Classifications: {'peptide': 1016} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 970} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 7732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7732 Classifications: {'peptide': 1018} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 972} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Chain: "C" Number of atoms: 7783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7783 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 979} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 4.74, per 1000 atoms: 0.20 Number of scatterers: 23153 At special positions: 0 Unit cell: (116.55, 122.85, 147, 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 132 16.00 O 4312 8.00 N 3808 7.00 C 14901 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: 1.39 Conformation dependent library (CDL) restraints added in 992.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5610 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 26 sheets defined 57.7% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.595A pdb=" N ILE A 6 " --> pdb=" O ASN A 3 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3 through 7' Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.959A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 67 removed outlier: 3.596A pdb=" N ILE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.668A pdb=" N ALA A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 118 No H-bonds generated for 'chain 'A' and resid 116 through 118' Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.643A pdb=" N ILE A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASP A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ALA A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 197 removed outlier: 3.543A pdb=" N LEU A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 210 Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 299 through 314 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.845A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 386 removed outlier: 4.289A pdb=" N THR A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 424 removed outlier: 5.185A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 424 " --> pdb=" O MET A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 450 removed outlier: 3.505A pdb=" N ALA A 430 " --> pdb=" O PRO A 426 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 488 removed outlier: 3.733A pdb=" N GLY A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 removed outlier: 3.516A pdb=" N MET A 496 " --> pdb=" O LEU A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 538 removed outlier: 4.341A pdb=" N SER A 537 " --> pdb=" O GLY A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 559 removed outlier: 3.798A pdb=" N ILE A 547 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL A 549 " --> pdb=" O TYR A 545 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N MET A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG A 558 " --> pdb=" O TYR A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 602 removed outlier: 3.612A pdb=" N THR A 587 " --> pdb=" O THR A 583 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 602 " --> pdb=" O TYR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 643 through 655 Processing helix chain 'A' and resid 691 through 707 Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 744 through 756 removed outlier: 4.059A pdb=" N THR A 748 " --> pdb=" O ASN A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 780 Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 842 through 849 removed outlier: 4.322A pdb=" N GLN A 846 " --> pdb=" O GLU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 867 removed outlier: 4.149A pdb=" N GLN A 865 " --> pdb=" O GLY A 861 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 867 " --> pdb=" O SER A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 893 Processing helix chain 'A' and resid 898 through 903 removed outlier: 3.904A pdb=" N LEU A 903 " --> pdb=" O PHE A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 920 removed outlier: 3.861A pdb=" N GLY A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 955 removed outlier: 3.618A pdb=" N GLY A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 952 " --> pdb=" O PHE A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 969 Processing helix chain 'A' and resid 971 through 986 removed outlier: 4.332A pdb=" N ILE A 975 " --> pdb=" O ARG A 971 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 986 " --> pdb=" O PHE A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 991 removed outlier: 3.855A pdb=" N ILE A 991 " --> pdb=" O MET A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1017 removed outlier: 3.879A pdb=" N GLN A1000 " --> pdb=" O GLY A 996 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR A1013 " --> pdb=" O GLY A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1032 Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.676A pdb=" N ILE B 6 " --> pdb=" O PRO B 2 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 7' Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.956A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.591A pdb=" N ILE B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 removed outlier: 4.165A pdb=" N ALA B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 167 removed outlier: 3.885A pdb=" N ILE B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASP B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ALA B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 197 removed outlier: 3.571A pdb=" N LEU B 193 " --> pdb=" O ASN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.775A pdb=" N VAL B 203 " --> pdb=" O THR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.583A pdb=" N LYS B 248 " --> pdb=" O GLU B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 303 through 314 Processing helix chain 'B' and resid 329 through 359 Processing helix chain 'B' and resid 365 through 386 removed outlier: 3.807A pdb=" N THR B 369 " --> pdb=" O THR B 365 " (cutoff:3.500A) Proline residue: B 373 - end of helix removed outlier: 3.569A pdb=" N PHE B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 424 removed outlier: 5.061A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 438 Processing helix chain 'B' and resid 440 through 454 removed outlier: 3.568A pdb=" N GLY B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 461 through 496 removed outlier: 3.885A pdb=" N ALA B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE B 466 " --> pdb=" O SER B 462 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 4.262A pdb=" N THR B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Proline residue: B 490 - end of helix Processing helix chain 'B' and resid 517 through 537 removed outlier: 3.895A pdb=" N SER B 537 " --> pdb=" O GLY B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 558 removed outlier: 3.509A pdb=" N LEU B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 removed outlier: 3.592A pdb=" N GLN B 588 " --> pdb=" O GLN B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 602 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 639 through 642 removed outlier: 3.998A pdb=" N ASN B 642 " --> pdb=" O GLY B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 639 through 642' Processing helix chain 'B' and resid 643 through 655 removed outlier: 3.557A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 707 Processing helix chain 'B' and resid 732 through 740 Processing helix chain 'B' and resid 742 through 755 Processing helix chain 'B' and resid 777 through 780 Processing helix chain 'B' and resid 783 through 788 Processing helix chain 'B' and resid 836 through 849 removed outlier: 3.666A pdb=" N GLU B 842 " --> pdb=" O GLY B 838 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU B 843 " --> pdb=" O GLU B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 870 removed outlier: 3.656A pdb=" N GLY B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 892 Processing helix chain 'B' and resid 896 through 903 removed outlier: 4.056A pdb=" N SER B 900 " --> pdb=" O SER B 896 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 920 removed outlier: 3.862A pdb=" N GLY B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 912 " --> pdb=" O GLY B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 957 Processing helix chain 'B' and resid 961 through 986 removed outlier: 4.660A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix Processing helix chain 'B' and resid 986 through 992 removed outlier: 3.568A pdb=" N VAL B 990 " --> pdb=" O VAL B 986 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 991 " --> pdb=" O MET B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1017 removed outlier: 3.900A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL B1007 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR B1013 " --> pdb=" O GLY B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1031 Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.583A pdb=" N ILE C 6 " --> pdb=" O PRO C 2 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP C 7 " --> pdb=" O ASN C 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 7' Processing helix chain 'C' and resid 8 through 25 removed outlier: 3.976A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLY C 23 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU C 25 " --> pdb=" O LEU C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 30 Processing helix chain 'C' and resid 53 through 66 removed outlier: 3.881A pdb=" N VAL C 61 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR C 62 " --> pdb=" O GLN C 58 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL C 64 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 120 through 126 removed outlier: 3.796A pdb=" N GLN C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 162 removed outlier: 3.553A pdb=" N ILE C 154 " --> pdb=" O THR C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 removed outlier: 3.781A pdb=" N ARG C 168 " --> pdb=" O ASP C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'C' and resid 199 through 210 Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.524A pdb=" N PHE C 246 " --> pdb=" O SER C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 314 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 329 through 359 removed outlier: 3.692A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 removed outlier: 3.747A pdb=" N THR C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU C 366 " --> pdb=" O PHE C 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 361 through 366' Processing helix chain 'C' and resid 366 through 386 Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 423 removed outlier: 4.986A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 405 " --> pdb=" O ALA C 401 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 434 Processing helix chain 'C' and resid 439 through 458 removed outlier: 4.400A pdb=" N VAL C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) Proline residue: C 455 - end of helix Processing helix chain 'C' and resid 461 through 496 removed outlier: 4.166A pdb=" N ILE C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE C 474 " --> pdb=" O PHE C 470 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 483 " --> pdb=" O ALA C 479 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) Proline residue: C 490 - end of helix Processing helix chain 'C' and resid 514 through 535 removed outlier: 3.544A pdb=" N MET C 519 " --> pdb=" O TRP C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 559 removed outlier: 3.831A pdb=" N LEU C 542 " --> pdb=" O THR C 538 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N VAL C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 601 removed outlier: 3.686A pdb=" N THR C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 643 through 656 Processing helix chain 'C' and resid 692 through 708 removed outlier: 3.972A pdb=" N ALA C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 742 through 755 removed outlier: 4.193A pdb=" N THR C 748 " --> pdb=" O ASN C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 780 removed outlier: 3.641A pdb=" N ARG C 780 " --> pdb=" O ALA C 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 777 through 780' Processing helix chain 'C' and resid 782 through 788 removed outlier: 3.605A pdb=" N ASP C 788 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 839 Processing helix chain 'C' and resid 840 through 850 removed outlier: 3.872A pdb=" N LYS C 850 " --> pdb=" O GLN C 846 " (cutoff:3.500A) Processing helix chain 'C' and resid 861 through 893 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 896 through 900 Processing helix chain 'C' and resid 901 through 903 No H-bonds generated for 'chain 'C' and resid 901 through 903' Processing helix chain 'C' and resid 904 through 917 removed outlier: 3.847A pdb=" N GLY C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 909 " --> pdb=" O VAL C 905 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C 912 " --> pdb=" O GLY C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 954 removed outlier: 4.067A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 971 Processing helix chain 'C' and resid 972 through 991 removed outlier: 3.547A pdb=" N LEU C 976 " --> pdb=" O LEU C 972 " (cutoff:3.500A) Proline residue: C 988 - end of helix removed outlier: 3.565A pdb=" N ILE C 991 " --> pdb=" O MET C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 999 through 1017 removed outlier: 4.115A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1018 through 1020 No H-bonds generated for 'chain 'C' and resid 1018 through 1020' Processing helix chain 'C' and resid 1021 through 1033 Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.727A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 177 Processing sheet with id=AA3, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.591A pdb=" N TYR A 182 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N TYR A 772 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N MET A 184 " --> pdb=" O TYR A 772 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N MET A 774 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE A 186 " --> pdb=" O MET A 774 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL A 773 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TYR A 758 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 219 removed outlier: 3.570A pdb=" N ALA A 232 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N SER A 233 " --> pdb=" O PHE B 727 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE B 729 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE A 235 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE B 731 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 253 removed outlier: 7.177A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.660A pdb=" N GLN A 284 " --> pdb=" O PHE A 281 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 681 through 682 Processing sheet with id=AA8, first strand: chain 'A' and resid 713 through 714 Processing sheet with id=AA9, first strand: chain 'A' and resid 805 through 812 removed outlier: 4.517A pdb=" N SER C 233 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 790 through 792 Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 132 removed outlier: 4.804A pdb=" N ALA B 42 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.172A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 3.751A pdb=" N ASP B 174 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B 140 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET B 138 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.675A pdb=" N TYR B 182 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N TYR B 772 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N MET B 184 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N MET B 774 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N ILE B 186 " --> pdb=" O MET B 774 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 217 through 219 removed outlier: 4.226A pdb=" N GLY B 217 " --> pdb=" O ILE B 234 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 252 removed outlier: 7.317A pdb=" N VAL B 260 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 284 through 286 removed outlier: 3.502A pdb=" N ALA B 286 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER B 630 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL B 609 " --> pdb=" O PHE B 628 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE B 628 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA B 611 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE B 626 " --> pdb=" O ALA B 611 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASN B 613 " --> pdb=" O THR B 624 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N THR B 624 " --> pdb=" O ASN B 613 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 679 through 680 removed outlier: 3.524A pdb=" N PHE B 680 " --> pdb=" O GLY B 829 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY B 829 " --> pdb=" O PHE B 680 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 131 removed outlier: 3.985A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.088A pdb=" N ASP C 174 " --> pdb=" O LYS C 292 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C 287 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL C 140 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE C 291 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET C 138 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU C 293 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N PHE C 136 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.515A pdb=" N TYR C 182 " --> pdb=" O LYS C 770 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N TYR C 772 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N MET C 184 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N MET C 774 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ILE C 186 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 250 through 253 removed outlier: 7.334A pdb=" N VAL C 260 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.564A pdb=" N GLY C 625 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 284 through 285 removed outlier: 3.710A pdb=" N MET C 573 " --> pdb=" O PHE C 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 824 through 827 Processing sheet with id=AC8, first strand: chain 'C' and resid 790 through 792 1375 hydrogen bonds defined for protein. 3948 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: 4.05 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7461 1.34 - 1.46: 4790 1.46 - 1.58: 11075 1.58 - 1.70: 0 1.70 - 1.82: 258 Bond restraints: 23584 Sorted by residual: bond pdb=" CA ASP C 730 " pdb=" CB ASP C 730 " ideal model delta sigma weight residual 1.531 1.556 -0.025 1.52e-02 4.33e+03 2.77e+00 bond pdb=" CB LYS A 226 " pdb=" CG LYS A 226 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.53e+00 bond pdb=" CB GLN A 197 " pdb=" CG GLN A 197 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.48e+00 bond pdb=" CB GLN C 197 " pdb=" CG GLN C 197 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.48e+00 bond pdb=" CB GLU A 417 " pdb=" CG GLU A 417 " ideal model delta sigma weight residual 1.520 1.567 -0.047 3.00e-02 1.11e+03 2.41e+00 ... (remaining 23579 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 31549 2.84 - 5.68: 399 5.68 - 8.51: 76 8.51 - 11.35: 18 11.35 - 14.19: 7 Bond angle restraints: 32049 Sorted by residual: angle pdb=" N ASN A 3 " pdb=" CA ASN A 3 " pdb=" C ASN A 3 " ideal model delta sigma weight residual 114.56 106.58 7.98 1.27e+00 6.20e-01 3.95e+01 angle pdb=" C VAL B 904 " pdb=" N VAL B 905 " pdb=" CA VAL B 905 " ideal model delta sigma weight residual 120.33 124.02 -3.69 8.00e-01 1.56e+00 2.12e+01 angle pdb=" C VAL C 904 " pdb=" N VAL C 905 " pdb=" CA VAL C 905 " ideal model delta sigma weight residual 120.33 123.95 -3.62 8.00e-01 1.56e+00 2.05e+01 angle pdb=" CA LYS A 428 " pdb=" CB LYS A 428 " pdb=" CG LYS A 428 " ideal model delta sigma weight residual 114.10 122.55 -8.45 2.00e+00 2.50e-01 1.79e+01 angle pdb=" CA LYS C 226 " pdb=" CB LYS C 226 " pdb=" CG LYS C 226 " ideal model delta sigma weight residual 114.10 122.54 -8.44 2.00e+00 2.50e-01 1.78e+01 ... (remaining 32044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12218 17.98 - 35.96: 1396 35.96 - 53.93: 406 53.93 - 71.91: 60 71.91 - 89.89: 28 Dihedral angle restraints: 14108 sinusoidal: 5366 harmonic: 8742 Sorted by residual: dihedral pdb=" CA ASP B 785 " pdb=" C ASP B 785 " pdb=" N ILE B 786 " pdb=" CA ILE B 786 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA GLN C 210 " pdb=" C GLN C 210 " pdb=" N ASN C 211 " pdb=" CA ASN C 211 " ideal model delta harmonic sigma weight residual 180.00 162.21 17.79 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CG ARG B 653 " pdb=" CD ARG B 653 " pdb=" NE ARG B 653 " pdb=" CZ ARG B 653 " ideal model delta sinusoidal sigma weight residual -90.00 -42.62 -47.38 2 1.50e+01 4.44e-03 1.16e+01 ... (remaining 14105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2626 0.040 - 0.080: 843 0.080 - 0.121: 296 0.121 - 0.161: 40 0.161 - 0.201: 4 Chirality restraints: 3809 Sorted by residual: chirality pdb=" CB VAL C 333 " pdb=" CA VAL C 333 " pdb=" CG1 VAL C 333 " pdb=" CG2 VAL C 333 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB VAL C 413 " pdb=" CA VAL C 413 " pdb=" CG1 VAL C 413 " pdb=" CG2 VAL C 413 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CB THR A 648 " pdb=" CA THR A 648 " pdb=" OG1 THR A 648 " pdb=" CG2 THR A 648 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.93e-01 ... (remaining 3806 not shown) Planarity restraints: 4093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 527 " 0.005 2.00e-02 2.50e+03 1.64e-02 5.41e+00 pdb=" CG TYR C 527 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR C 527 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR C 527 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR C 527 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 527 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 527 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 527 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 743 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" C ILE A 743 " -0.037 2.00e-02 2.50e+03 pdb=" O ILE A 743 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN A 744 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 545 " -0.018 2.00e-02 2.50e+03 1.40e-02 3.94e+00 pdb=" CG TYR C 545 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 545 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR C 545 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 545 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 545 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 545 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 545 " -0.002 2.00e-02 2.50e+03 ... (remaining 4090 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 9199 2.90 - 3.40: 23709 3.40 - 3.90: 36281 3.90 - 4.40: 39448 4.40 - 4.90: 67399 Nonbonded interactions: 176036 Sorted by model distance: nonbonded pdb=" O LEU C 937 " pdb=" ND2 ASN C 941 " model vdw 2.403 3.120 nonbonded pdb=" O LEU A 937 " pdb=" OD1 ASN A 941 " model vdw 2.429 3.040 nonbonded pdb=" N GLN A 197 " pdb=" OE1 GLN A 197 " model vdw 2.521 3.120 nonbonded pdb=" N GLU C 962 " pdb=" OE1 GLU C 962 " model vdw 2.542 3.120 nonbonded pdb=" O LEU B 404 " pdb=" OD1 ASP B 407 " model vdw 2.545 3.040 ... (remaining 176031 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 1 through 385 or (resid 386 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 387 through 478 or (resid 479 and (name N or name CA or name C o \ r name CB )) or resid 480 through 500 or resid 516 through 1032)) selection = (chain 'B' and (resid 1 through 421 or (resid 422 through 423 and (name N or nam \ e CA or name C or name O or name CB )) or resid 424 through 449 or (resid 450 an \ d (name N or name CA or name C or name CB or name OG )) or resid 451 through 456 \ or resid 459 through 500 or (resid 516 and (name N or name CA or name C or name \ O or name CB )) or resid 517 through 521 or (resid 522 and (name N or name CA o \ r name C or name O or name CB )) or resid 523 through 526 or (resid 527 and (nam \ e N or name CA or name C or name O or name CB )) or resid 528 through 539 or (re \ sid 540 and (name N or name CA or name C or name O or name CB )) or resid 541 th \ rough 619 or (resid 620 and (name N or name CA or name C or name O or name CB or \ name CG or name CD or name NE or name CZ )) or resid 621 through 682 or (resid \ 683 and (name N or name CA or name C or name O or name CB or name CG or name CD \ or name OE1)) or resid 684 through 849 or (resid 850 and (name N or name CA or n \ ame C or name O or name CB )) or resid 851 through 949 or (resid 950 and (name N \ or name CA or name C or name O or name CB )) or resid 951 through 954 or (resid \ 955 and (name N or name CA or name C or name O or name CB )) or resid 956 throu \ gh 961 or (resid 962 through 963 and (name N or name CA or name C or name O or n \ ame CB )) or resid 964 through 968 or (resid 969 and (name N or name CA or name \ C or name O or name CB )) or resid 970 through 1020 or (resid 1021 and (name N o \ r name CA or name C or name O or name CB )) or resid 1022 through 1028 or (resid \ 1029 through 1032 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 1 through 385 or (resid 386 and (name N or name CA or name \ C or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name \ CZ )) or resid 387 through 421 or (resid 422 through 423 and (name N or name CA \ or name C or name O or name CB )) or resid 424 through 449 or (resid 450 and (n \ ame N or name CA or name C or name CB or name OG )) or resid 451 through 456 or \ resid 459 through 478 or (resid 479 and (name N or name CA or name C or name CB \ )) or resid 480 through 500 or (resid 516 and (name N or name CA or name C or na \ me O or name CB )) or resid 517 through 526 or (resid 527 and (name N or name CA \ or name C or name O or name CB )) or resid 528 through 539 or (resid 540 and (n \ ame N or name CA or name C or name O or name CB )) or resid 541 through 619 or ( \ resid 620 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name NE or name CZ )) or resid 621 through 682 or (resid 683 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name OE1)) \ or resid 684 through 849 or (resid 850 and (name N or name CA or name C or name \ O or name CB )) or resid 851 through 949 or (resid 950 and (name N or name CA or \ name C or name O or name CB )) or resid 951 through 954 or (resid 955 and (name \ N or name CA or name C or name O or name CB )) or resid 956 through 961 or (res \ id 962 through 963 and (name N or name CA or name C or name O or name CB )) or r \ esid 964 through 968 or (resid 969 and (name N or name CA or name C or name O or \ name CB )) or resid 970 through 1020 or (resid 1021 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1022 through 1028 or (resid 1029 through \ 1032 and (name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.530 Find NCS groups from input model: 0.410 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:5.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 23584 Z= 0.158 Angle : 0.827 14.189 32049 Z= 0.414 Chirality : 0.044 0.201 3809 Planarity : 0.004 0.045 4093 Dihedral : 16.966 89.889 8498 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.90 % Allowed : 36.15 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.39 (0.15), residues: 3045 helix: 1.06 (0.14), residues: 1507 sheet: 0.46 (0.28), residues: 383 loop : -0.82 (0.18), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1031 TYR 0.038 0.002 TYR C 527 PHE 0.029 0.001 PHE C 885 TRP 0.016 0.001 TRP B 754 HIS 0.002 0.000 HIS C 525 Details of bonding type rmsd covalent geometry : bond 0.00339 (23584) covalent geometry : angle 0.82676 (32049) hydrogen bonds : bond 0.12726 ( 1363) hydrogen bonds : angle 5.68236 ( 3948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 641 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 SER cc_start: 0.7098 (t) cc_final: 0.6861 (p) REVERT: A 369 THR cc_start: 0.6695 (p) cc_final: 0.6491 (t) REVERT: A 496 MET cc_start: 0.6977 (ppp) cc_final: 0.6589 (ppp) REVERT: A 645 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7191 (tp30) REVERT: A 711 ASP cc_start: 0.7028 (p0) cc_final: 0.6773 (p0) REVERT: A 1017 LEU cc_start: 0.7680 (tp) cc_final: 0.7430 (tp) REVERT: B 1 MET cc_start: 0.6099 (ppp) cc_final: 0.5813 (ppp) REVERT: B 124 GLN cc_start: 0.7709 (tp40) cc_final: 0.7346 (mm110) REVERT: B 149 MET cc_start: 0.6797 (ppp) cc_final: 0.6579 (ppp) REVERT: B 435 MET cc_start: 0.6940 (mmm) cc_final: 0.6450 (tpt) REVERT: B 466 ILE cc_start: 0.7968 (pp) cc_final: 0.7272 (pp) REVERT: B 470 PHE cc_start: 0.6964 (m-80) cc_final: 0.6633 (m-80) REVERT: B 727 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7771 (t80) REVERT: B 781 MET cc_start: 0.7687 (mmm) cc_final: 0.7301 (mmt) REVERT: B 801 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.6259 (t80) REVERT: B 954 ASP cc_start: 0.5231 (OUTLIER) cc_final: 0.4269 (p0) REVERT: B 955 LYS cc_start: 0.6454 (mmtt) cc_final: 0.6225 (mmtt) REVERT: C 21 LEU cc_start: 0.8028 (mm) cc_final: 0.7817 (mm) REVERT: C 177 LEU cc_start: 0.6361 (tp) cc_final: 0.5820 (tp) REVERT: C 204 ILE cc_start: 0.7800 (mt) cc_final: 0.7585 (tt) REVERT: C 307 ARG cc_start: 0.6207 (mmm160) cc_final: 0.5702 (tpm-80) REVERT: C 367 ILE cc_start: 0.8132 (mt) cc_final: 0.7649 (mt) REVERT: C 442 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.6003 (mm) REVERT: C 468 ARG cc_start: 0.7375 (mtm-85) cc_final: 0.7135 (mtm-85) REVERT: C 765 ARG cc_start: 0.8208 (tpp80) cc_final: 0.7871 (mmm-85) REVERT: C 769 LYS cc_start: 0.8413 (mttt) cc_final: 0.8072 (mmtp) REVERT: C 781 MET cc_start: 0.7943 (mmt) cc_final: 0.6830 (mmt) REVERT: C 987 MET cc_start: 0.6891 (tmm) cc_final: 0.6677 (pp-130) REVERT: C 1016 VAL cc_start: 0.7639 (p) cc_final: 0.7438 (p) outliers start: 47 outliers final: 25 residues processed: 667 average time/residue: 0.4736 time to fit residues: 368.6488 Evaluate side-chains 635 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 606 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 727 PHE Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 1024 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 730 ASP Chi-restraints excluded: chain C residue 952 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.0020 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 70 ASN A 338 HIS ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 830 GLN C 125 GLN C 231 ASN C 941 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.158241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.139875 restraints weight = 40021.040| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.97 r_work: 0.3906 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23584 Z= 0.148 Angle : 0.674 10.895 32049 Z= 0.335 Chirality : 0.043 0.160 3809 Planarity : 0.004 0.048 4093 Dihedral : 5.123 56.039 3287 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 7.15 % Allowed : 27.79 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.50 (0.16), residues: 3045 helix: 1.11 (0.13), residues: 1547 sheet: 0.34 (0.27), residues: 392 loop : -0.71 (0.19), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 653 TYR 0.024 0.002 TYR B 545 PHE 0.025 0.001 PHE C 948 TRP 0.014 0.001 TRP B 754 HIS 0.002 0.000 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00328 (23584) covalent geometry : angle 0.67396 (32049) hydrogen bonds : bond 0.04346 ( 1363) hydrogen bonds : angle 4.57871 ( 3948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 639 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7059 (tm-30) cc_final: 0.6749 (tm-30) REVERT: A 128 SER cc_start: 0.7448 (t) cc_final: 0.7113 (p) REVERT: A 314 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7353 (tp30) REVERT: A 328 ASP cc_start: 0.7104 (t0) cc_final: 0.6872 (t0) REVERT: A 342 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7912 (ttmp) REVERT: A 369 THR cc_start: 0.7426 (p) cc_final: 0.7082 (t) REVERT: A 445 ILE cc_start: 0.7382 (tt) cc_final: 0.6937 (tt) REVERT: A 521 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7641 (tp30) REVERT: A 578 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7798 (mt) REVERT: A 615 PHE cc_start: 0.7459 (t80) cc_final: 0.7172 (t80) REVERT: A 645 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7245 (tp30) REVERT: A 649 MET cc_start: 0.7552 (ppp) cc_final: 0.7319 (ppp) REVERT: A 653 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7448 (ttm-80) REVERT: A 711 ASP cc_start: 0.6684 (p0) cc_final: 0.6344 (p0) REVERT: A 712 MET cc_start: 0.5760 (mmm) cc_final: 0.5343 (mmm) REVERT: A 785 ASP cc_start: 0.7214 (m-30) cc_final: 0.6987 (m-30) REVERT: A 807 SER cc_start: 0.7860 (m) cc_final: 0.7526 (p) REVERT: A 940 LYS cc_start: 0.8218 (tmtm) cc_final: 0.7912 (tppt) REVERT: B 156 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7286 (t70) REVERT: B 195 LYS cc_start: 0.8372 (tptp) cc_final: 0.8130 (tptp) REVERT: B 248 LYS cc_start: 0.8109 (mtmm) cc_final: 0.7809 (mtmm) REVERT: B 322 LYS cc_start: 0.7757 (ptpt) cc_final: 0.7432 (pmtt) REVERT: B 342 LYS cc_start: 0.8447 (tptp) cc_final: 0.8212 (tppt) REVERT: B 435 MET cc_start: 0.7194 (mmm) cc_final: 0.6988 (tpp) REVERT: B 437 GLN cc_start: 0.8074 (tp40) cc_final: 0.7812 (tp40) REVERT: B 445 ILE cc_start: 0.8480 (mm) cc_final: 0.8277 (mm) REVERT: B 466 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7604 (pp) REVERT: B 470 PHE cc_start: 0.7468 (m-80) cc_final: 0.6958 (m-80) REVERT: B 496 MET cc_start: 0.7074 (tpp) cc_final: 0.6857 (tpp) REVERT: B 645 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7423 (tp30) REVERT: B 649 MET cc_start: 0.7977 (pmm) cc_final: 0.7686 (pmm) REVERT: B 785 ASP cc_start: 0.6924 (OUTLIER) cc_final: 0.6475 (p0) REVERT: B 801 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6375 (t80) REVERT: B 810 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7443 (mm-30) REVERT: B 940 LYS cc_start: 0.7765 (tptt) cc_final: 0.7381 (tppt) REVERT: B 973 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7706 (ttp-170) REVERT: C 5 PHE cc_start: 0.7219 (m-10) cc_final: 0.6981 (m-10) REVERT: C 21 LEU cc_start: 0.8241 (mm) cc_final: 0.8019 (mm) REVERT: C 102 ILE cc_start: 0.7765 (tp) cc_final: 0.7563 (tt) REVERT: C 149 MET cc_start: 0.6716 (ptp) cc_final: 0.6508 (ptt) REVERT: C 177 LEU cc_start: 0.6733 (tp) cc_final: 0.6426 (tt) REVERT: C 204 ILE cc_start: 0.7743 (mt) cc_final: 0.7419 (tt) REVERT: C 235 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7065 (pt) REVERT: C 307 ARG cc_start: 0.6307 (mmm160) cc_final: 0.5833 (tpm-80) REVERT: C 367 ILE cc_start: 0.8138 (mt) cc_final: 0.7824 (mt) REVERT: C 390 ILE cc_start: 0.8741 (mt) cc_final: 0.8510 (mp) REVERT: C 410 ILE cc_start: 0.7409 (tp) cc_final: 0.6985 (mt) REVERT: C 456 MET cc_start: 0.7397 (ttt) cc_final: 0.7100 (ttp) REVERT: C 468 ARG cc_start: 0.7793 (mtm-85) cc_final: 0.7542 (mtm-85) REVERT: C 478 MET cc_start: 0.6907 (ppp) cc_final: 0.6599 (ppp) REVERT: C 487 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8228 (tt) REVERT: C 521 GLU cc_start: 0.8064 (pp20) cc_final: 0.7430 (tm-30) REVERT: C 632 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.6648 (mtmt) REVERT: C 730 ASP cc_start: 0.7675 (t0) cc_final: 0.7257 (t0) REVERT: C 735 LYS cc_start: 0.8450 (mppt) cc_final: 0.8135 (mppt) REVERT: C 975 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7152 (mp) REVERT: C 1025 PHE cc_start: 0.6891 (m-80) cc_final: 0.6687 (m-80) outliers start: 177 outliers final: 73 residues processed: 743 average time/residue: 0.4220 time to fit residues: 370.6962 Evaluate side-chains 708 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 624 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 556 PHE Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 937 LEU Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 13 TRP Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 727 PHE Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 973 ARG Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 487 ILE Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 632 LYS Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1001 ASN Chi-restraints excluded: chain C residue 1003 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 293 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 222 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 95 optimal weight: 0.0670 chunk 36 optimal weight: 0.1980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 70 ASN A 605 ASN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 194 ASN B 439 GLN B 623 ASN B 830 GLN B 928 GLN C 34 GLN C 623 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.158255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.139807 restraints weight = 40111.871| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 3.01 r_work: 0.3905 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23584 Z= 0.127 Angle : 0.656 11.665 32049 Z= 0.322 Chirality : 0.043 0.181 3809 Planarity : 0.004 0.048 4093 Dihedral : 4.557 56.342 3260 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.98 % Allowed : 29.00 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.57 (0.16), residues: 3045 helix: 1.18 (0.13), residues: 1545 sheet: 0.33 (0.27), residues: 397 loop : -0.67 (0.19), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 653 TYR 0.024 0.002 TYR C 527 PHE 0.018 0.001 PHE A 885 TRP 0.011 0.001 TRP B 754 HIS 0.002 0.000 HIS C 692 Details of bonding type rmsd covalent geometry : bond 0.00281 (23584) covalent geometry : angle 0.65591 (32049) hydrogen bonds : bond 0.04006 ( 1363) hydrogen bonds : angle 4.42110 ( 3948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 662 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7065 (tm-30) cc_final: 0.6678 (tm-30) REVERT: A 128 SER cc_start: 0.7485 (t) cc_final: 0.7137 (p) REVERT: A 156 ASP cc_start: 0.7837 (t70) cc_final: 0.7566 (t70) REVERT: A 162 MET cc_start: 0.7422 (mtt) cc_final: 0.6905 (mpt) REVERT: A 314 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7352 (tp30) REVERT: A 328 ASP cc_start: 0.7135 (t0) cc_final: 0.6877 (t0) REVERT: A 369 THR cc_start: 0.7471 (p) cc_final: 0.7136 (t) REVERT: A 459 PHE cc_start: 0.4013 (OUTLIER) cc_final: 0.2620 (p90) REVERT: A 521 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7567 (tp30) REVERT: A 578 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7789 (mt) REVERT: A 600 THR cc_start: 0.7929 (t) cc_final: 0.7569 (p) REVERT: A 645 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7307 (tp30) REVERT: A 649 MET cc_start: 0.7582 (ppp) cc_final: 0.7275 (ppp) REVERT: A 653 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7477 (ttm-80) REVERT: A 699 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7530 (ptt180) REVERT: A 711 ASP cc_start: 0.6664 (p0) cc_final: 0.6307 (p0) REVERT: A 712 MET cc_start: 0.5828 (mmm) cc_final: 0.5470 (mmm) REVERT: A 735 LYS cc_start: 0.8431 (mtpm) cc_final: 0.8205 (mtpp) REVERT: A 743 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7973 (pt) REVERT: A 785 ASP cc_start: 0.7059 (m-30) cc_final: 0.6827 (m-30) REVERT: A 807 SER cc_start: 0.7904 (m) cc_final: 0.7540 (p) REVERT: A 844 MET cc_start: 0.6230 (mmp) cc_final: 0.5865 (mmt) REVERT: B 156 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7295 (t70) REVERT: B 184 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6789 (ttm) REVERT: B 248 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7863 (mtmm) REVERT: B 267 LYS cc_start: 0.7823 (ttpp) cc_final: 0.7609 (ttpt) REVERT: B 322 LYS cc_start: 0.7769 (ptpt) cc_final: 0.7413 (pmtt) REVERT: B 342 LYS cc_start: 0.8494 (tptp) cc_final: 0.8212 (tppt) REVERT: B 433 LYS cc_start: 0.7763 (mmtt) cc_final: 0.7533 (mmtm) REVERT: B 437 GLN cc_start: 0.8137 (tp40) cc_final: 0.7883 (tp40) REVERT: B 449 LEU cc_start: 0.8213 (mm) cc_final: 0.7962 (mp) REVERT: B 456 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7323 (tpp) REVERT: B 466 ILE cc_start: 0.8348 (pp) cc_final: 0.7679 (pp) REVERT: B 470 PHE cc_start: 0.7504 (m-80) cc_final: 0.7071 (m-80) REVERT: B 496 MET cc_start: 0.7156 (tpp) cc_final: 0.6912 (tpp) REVERT: B 552 MET cc_start: 0.8088 (tmm) cc_final: 0.7846 (tmm) REVERT: B 571 VAL cc_start: 0.8118 (m) cc_final: 0.7916 (p) REVERT: B 600 THR cc_start: 0.8239 (t) cc_final: 0.7780 (p) REVERT: B 645 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7312 (tp30) REVERT: B 754 TRP cc_start: 0.8132 (m100) cc_final: 0.7931 (m-10) REVERT: B 781 MET cc_start: 0.7965 (mmm) cc_final: 0.7677 (mmt) REVERT: B 785 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6517 (p0) REVERT: B 801 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6480 (t80) REVERT: B 810 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7503 (mm-30) REVERT: B 863 SER cc_start: 0.4351 (OUTLIER) cc_final: 0.4003 (m) REVERT: B 913 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6712 (mm) REVERT: B 940 LYS cc_start: 0.7744 (tptt) cc_final: 0.7379 (tppt) REVERT: C 5 PHE cc_start: 0.7379 (m-10) cc_final: 0.6931 (m-10) REVERT: C 78 MET cc_start: 0.5475 (OUTLIER) cc_final: 0.5270 (ptm) REVERT: C 195 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7704 (tptp) REVERT: C 204 ILE cc_start: 0.7760 (mt) cc_final: 0.7407 (tt) REVERT: C 235 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.7151 (pt) REVERT: C 367 ILE cc_start: 0.8141 (mt) cc_final: 0.7839 (mt) REVERT: C 390 ILE cc_start: 0.8744 (mt) cc_final: 0.8491 (mp) REVERT: C 442 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6263 (mm) REVERT: C 456 MET cc_start: 0.7381 (ttt) cc_final: 0.7078 (ttp) REVERT: C 468 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7523 (ttm110) REVERT: C 521 GLU cc_start: 0.8119 (pp20) cc_final: 0.7389 (tm-30) REVERT: C 607 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7372 (tm-30) REVERT: C 632 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7578 (mtmm) REVERT: C 662 MET cc_start: 0.6215 (OUTLIER) cc_final: 0.5969 (tmm) REVERT: C 667 ASN cc_start: 0.8127 (t0) cc_final: 0.7828 (t0) REVERT: C 730 ASP cc_start: 0.7775 (t0) cc_final: 0.7408 (OUTLIER) REVERT: C 781 MET cc_start: 0.8149 (mmt) cc_final: 0.7134 (mmt) REVERT: C 951 ASP cc_start: 0.7807 (m-30) cc_final: 0.7588 (t70) outliers start: 148 outliers final: 69 residues processed: 747 average time/residue: 0.4489 time to fit residues: 394.8158 Evaluate side-chains 723 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 638 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 727 PHE Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 863 SER Chi-restraints excluded: chain B residue 865 GLN Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 662 MET Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 928 GLN Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 953 MET Chi-restraints excluded: chain C residue 976 LEU Chi-restraints excluded: chain C residue 1001 ASN Chi-restraints excluded: chain C residue 1003 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 213 optimal weight: 0.1980 chunk 128 optimal weight: 2.9990 chunk 131 optimal weight: 0.1980 chunk 291 optimal weight: 0.4980 chunk 269 optimal weight: 1.9990 chunk 171 optimal weight: 0.0970 chunk 230 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 196 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 70 ASN A 928 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 ASN B1001 ASN C 588 GLN C 623 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.158645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.140202 restraints weight = 39727.219| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.98 r_work: 0.3907 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23584 Z= 0.125 Angle : 0.666 12.666 32049 Z= 0.325 Chirality : 0.043 0.177 3809 Planarity : 0.004 0.060 4093 Dihedral : 4.515 56.874 3258 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 6.22 % Allowed : 29.40 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.61 (0.16), residues: 3045 helix: 1.22 (0.13), residues: 1548 sheet: 0.37 (0.27), residues: 387 loop : -0.67 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 307 TYR 0.025 0.002 TYR A 892 PHE 0.015 0.001 PHE A 572 TRP 0.014 0.001 TRP A 515 HIS 0.001 0.000 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00281 (23584) covalent geometry : angle 0.66629 (32049) hydrogen bonds : bond 0.03850 ( 1363) hydrogen bonds : angle 4.34721 ( 3948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 651 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7005 (tm-30) cc_final: 0.6572 (tm-30) REVERT: A 128 SER cc_start: 0.7504 (t) cc_final: 0.7152 (p) REVERT: A 156 ASP cc_start: 0.7857 (t70) cc_final: 0.7620 (t70) REVERT: A 162 MET cc_start: 0.7406 (mtt) cc_final: 0.6957 (mpt) REVERT: A 252 LYS cc_start: 0.7603 (tmmm) cc_final: 0.7360 (tptt) REVERT: A 314 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: A 328 ASP cc_start: 0.7151 (t0) cc_final: 0.6915 (t0) REVERT: A 346 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7170 (mp0) REVERT: A 369 THR cc_start: 0.7417 (p) cc_final: 0.7126 (t) REVERT: A 414 GLU cc_start: 0.7067 (tt0) cc_final: 0.6256 (tt0) REVERT: A 445 ILE cc_start: 0.7211 (tt) cc_final: 0.6762 (tt) REVERT: A 459 PHE cc_start: 0.4051 (OUTLIER) cc_final: 0.2644 (p90) REVERT: A 521 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7486 (tp30) REVERT: A 530 SER cc_start: 0.8045 (m) cc_final: 0.7751 (p) REVERT: A 600 THR cc_start: 0.7878 (t) cc_final: 0.7514 (p) REVERT: A 645 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7370 (tp30) REVERT: A 649 MET cc_start: 0.7660 (ppp) cc_final: 0.7393 (ppp) REVERT: A 653 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7551 (ttm-80) REVERT: A 699 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7573 (ptt90) REVERT: A 711 ASP cc_start: 0.6628 (p0) cc_final: 0.6262 (p0) REVERT: A 712 MET cc_start: 0.5867 (mmm) cc_final: 0.5504 (mmm) REVERT: A 735 LYS cc_start: 0.8447 (mtpm) cc_final: 0.8192 (mtpp) REVERT: A 743 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.8001 (pt) REVERT: A 785 ASP cc_start: 0.7011 (m-30) cc_final: 0.6768 (m-30) REVERT: A 844 MET cc_start: 0.6256 (mmp) cc_final: 0.5941 (mmt) REVERT: A 940 LYS cc_start: 0.8218 (tmtm) cc_final: 0.8015 (tppt) REVERT: B 156 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7196 (p0) REVERT: B 195 LYS cc_start: 0.8381 (tptp) cc_final: 0.8178 (tptp) REVERT: B 222 THR cc_start: 0.7207 (p) cc_final: 0.7004 (p) REVERT: B 244 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: B 248 LYS cc_start: 0.8113 (mtmm) cc_final: 0.7791 (pttm) REVERT: B 267 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7423 (ttpt) REVERT: B 269 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6944 (mp0) REVERT: B 322 LYS cc_start: 0.7751 (ptpt) cc_final: 0.7420 (pmtt) REVERT: B 342 LYS cc_start: 0.8502 (tptp) cc_final: 0.8228 (tppt) REVERT: B 351 VAL cc_start: 0.8131 (t) cc_final: 0.7732 (t) REVERT: B 433 LYS cc_start: 0.7812 (mmtt) cc_final: 0.7567 (mmtt) REVERT: B 435 MET cc_start: 0.7267 (tpt) cc_final: 0.6871 (tpp) REVERT: B 466 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7677 (pp) REVERT: B 470 PHE cc_start: 0.7385 (m-80) cc_final: 0.6997 (m-80) REVERT: B 496 MET cc_start: 0.7165 (tpp) cc_final: 0.6863 (tpp) REVERT: B 552 MET cc_start: 0.8008 (tmm) cc_final: 0.7783 (tmm) REVERT: B 600 THR cc_start: 0.8191 (t) cc_final: 0.7694 (p) REVERT: B 645 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7322 (tp30) REVERT: B 649 MET cc_start: 0.7944 (pmm) cc_final: 0.7385 (pmm) REVERT: B 781 MET cc_start: 0.7972 (mmm) cc_final: 0.7676 (mmt) REVERT: B 785 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6511 (p0) REVERT: B 801 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6547 (t80) REVERT: B 810 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7506 (mm-30) REVERT: B 913 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6644 (mm) REVERT: B 940 LYS cc_start: 0.7768 (tptt) cc_final: 0.7377 (tppt) REVERT: B 951 ASP cc_start: 0.7269 (t0) cc_final: 0.6854 (t0) REVERT: B 952 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6942 (tm) REVERT: B 1029 VAL cc_start: 0.7032 (t) cc_final: 0.6781 (t) REVERT: C 5 PHE cc_start: 0.7471 (m-10) cc_final: 0.7017 (m-10) REVERT: C 21 LEU cc_start: 0.8461 (tm) cc_final: 0.8203 (mm) REVERT: C 78 MET cc_start: 0.5554 (OUTLIER) cc_final: 0.5270 (ptm) REVERT: C 123 GLN cc_start: 0.2222 (OUTLIER) cc_final: 0.1699 (mt0) REVERT: C 195 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7699 (tptp) REVERT: C 204 ILE cc_start: 0.7781 (mt) cc_final: 0.7433 (tt) REVERT: C 235 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.7158 (pt) REVERT: C 269 GLU cc_start: 0.7704 (tp30) cc_final: 0.7495 (mm-30) REVERT: C 367 ILE cc_start: 0.8141 (mt) cc_final: 0.7831 (mt) REVERT: C 390 ILE cc_start: 0.8747 (mt) cc_final: 0.8503 (mp) REVERT: C 456 MET cc_start: 0.7374 (ttt) cc_final: 0.7068 (ttp) REVERT: C 468 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7533 (ttm110) REVERT: C 521 GLU cc_start: 0.8125 (pp20) cc_final: 0.7698 (tm-30) REVERT: C 525 HIS cc_start: 0.7650 (m-70) cc_final: 0.7073 (m-70) REVERT: C 575 MET cc_start: 0.8064 (ppp) cc_final: 0.7849 (ptm) REVERT: C 632 LYS cc_start: 0.8056 (mtmt) cc_final: 0.7814 (mtmm) REVERT: C 730 ASP cc_start: 0.7794 (t0) cc_final: 0.7437 (OUTLIER) REVERT: C 735 LYS cc_start: 0.8511 (mppt) cc_final: 0.8006 (mppt) REVERT: C 903 LEU cc_start: 0.7701 (mt) cc_final: 0.7491 (mt) outliers start: 154 outliers final: 73 residues processed: 739 average time/residue: 0.4752 time to fit residues: 410.8612 Evaluate side-chains 718 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 631 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 617 PHE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 727 PHE Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 865 GLN Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 952 LEU Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 976 LEU Chi-restraints excluded: chain C residue 1003 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 287 optimal weight: 0.6980 chunk 283 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 300 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN A 70 ASN A 338 HIS A 569 GLN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN B 623 ASN B1001 ASN C 68 ASN C 124 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.156971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.138626 restraints weight = 39735.139| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.96 r_work: 0.3881 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23584 Z= 0.151 Angle : 0.691 14.950 32049 Z= 0.341 Chirality : 0.044 0.192 3809 Planarity : 0.004 0.054 4093 Dihedral : 4.651 58.241 3258 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 6.83 % Allowed : 28.80 % Favored : 64.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.58 (0.16), residues: 3045 helix: 1.20 (0.13), residues: 1547 sheet: 0.27 (0.27), residues: 399 loop : -0.66 (0.19), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 653 TYR 0.025 0.002 TYR C 527 PHE 0.021 0.001 PHE C 628 TRP 0.018 0.001 TRP B 754 HIS 0.002 0.000 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00344 (23584) covalent geometry : angle 0.69077 (32049) hydrogen bonds : bond 0.04249 ( 1363) hydrogen bonds : angle 4.38811 ( 3948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 643 time to evaluate : 0.554 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7143 (tm-30) cc_final: 0.6730 (tm-30) REVERT: A 128 SER cc_start: 0.7664 (t) cc_final: 0.7313 (p) REVERT: A 162 MET cc_start: 0.7436 (mtt) cc_final: 0.6957 (mpt) REVERT: A 252 LYS cc_start: 0.7559 (tmmm) cc_final: 0.7339 (tptt) REVERT: A 253 VAL cc_start: 0.7299 (OUTLIER) cc_final: 0.7010 (p) REVERT: A 328 ASP cc_start: 0.7081 (t0) cc_final: 0.6854 (t0) REVERT: A 346 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7285 (mm-30) REVERT: A 369 THR cc_start: 0.7497 (p) cc_final: 0.7217 (t) REVERT: A 414 GLU cc_start: 0.6966 (tt0) cc_final: 0.6682 (tt0) REVERT: A 521 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7544 (tm-30) REVERT: A 645 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7414 (tp30) REVERT: A 649 MET cc_start: 0.7659 (ppp) cc_final: 0.7378 (ppp) REVERT: A 653 ARG cc_start: 0.7899 (ttm-80) cc_final: 0.7633 (ttm-80) REVERT: A 699 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7569 (ptt90) REVERT: A 711 ASP cc_start: 0.6590 (p0) cc_final: 0.6181 (p0) REVERT: A 712 MET cc_start: 0.5904 (mmm) cc_final: 0.5540 (mmm) REVERT: A 735 LYS cc_start: 0.8489 (mtpm) cc_final: 0.8218 (mtpp) REVERT: A 743 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8065 (pt) REVERT: A 844 MET cc_start: 0.6400 (mmp) cc_final: 0.6128 (mmt) REVERT: A 940 LYS cc_start: 0.8178 (tmtm) cc_final: 0.7793 (tmmt) REVERT: A 947 GLU cc_start: 0.7853 (tp30) cc_final: 0.7616 (tp30) REVERT: B 108 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.6859 (tm-30) REVERT: B 156 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7267 (p0) REVERT: B 195 LYS cc_start: 0.8414 (tptp) cc_final: 0.8155 (tptp) REVERT: B 244 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6578 (pm20) REVERT: B 248 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7756 (ptpt) REVERT: B 267 LYS cc_start: 0.7877 (ttpp) cc_final: 0.7433 (ttpt) REVERT: B 269 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6955 (mp0) REVERT: B 322 LYS cc_start: 0.7774 (ptpt) cc_final: 0.7446 (pmtt) REVERT: B 342 LYS cc_start: 0.8564 (tptp) cc_final: 0.8294 (tppt) REVERT: B 433 LYS cc_start: 0.7742 (mmtt) cc_final: 0.7499 (mmtt) REVERT: B 435 MET cc_start: 0.7359 (tpt) cc_final: 0.6982 (tpp) REVERT: B 486 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7760 (tt) REVERT: B 496 MET cc_start: 0.7236 (tpp) cc_final: 0.6969 (tpp) REVERT: B 552 MET cc_start: 0.8091 (tmm) cc_final: 0.7878 (tmm) REVERT: B 600 THR cc_start: 0.8240 (t) cc_final: 0.7704 (p) REVERT: B 645 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7326 (tp30) REVERT: B 649 MET cc_start: 0.7955 (pmm) cc_final: 0.7637 (pmm) REVERT: B 653 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8088 (mtm110) REVERT: B 781 MET cc_start: 0.8024 (mmm) cc_final: 0.7522 (mmt) REVERT: B 785 ASP cc_start: 0.6878 (OUTLIER) cc_final: 0.6494 (p0) REVERT: B 801 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6394 (t80) REVERT: B 810 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7546 (mm-30) REVERT: B 863 SER cc_start: 0.4507 (OUTLIER) cc_final: 0.4180 (m) REVERT: B 940 LYS cc_start: 0.7964 (tptt) cc_final: 0.7542 (tppt) REVERT: B 951 ASP cc_start: 0.7447 (t0) cc_final: 0.7024 (t0) REVERT: C 5 PHE cc_start: 0.7626 (m-10) cc_final: 0.7186 (m-10) REVERT: C 78 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.5368 (ptm) REVERT: C 123 GLN cc_start: 0.2306 (OUTLIER) cc_final: 0.1255 (mt0) REVERT: C 131 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8121 (mttm) REVERT: C 195 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7830 (tptp) REVERT: C 204 ILE cc_start: 0.7761 (mt) cc_final: 0.7400 (tt) REVERT: C 235 ILE cc_start: 0.7356 (OUTLIER) cc_final: 0.7108 (pt) REVERT: C 339 GLU cc_start: 0.8180 (tp30) cc_final: 0.7938 (mm-30) REVERT: C 367 ILE cc_start: 0.8288 (mt) cc_final: 0.7976 (mt) REVERT: C 428 LYS cc_start: 0.8363 (tttm) cc_final: 0.7930 (ttpp) REVERT: C 442 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6391 (mm) REVERT: C 468 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7526 (ttm110) REVERT: C 521 GLU cc_start: 0.8153 (pp20) cc_final: 0.7674 (tm-30) REVERT: C 525 HIS cc_start: 0.7701 (m-70) cc_final: 0.7007 (m-70) REVERT: C 561 SER cc_start: 0.6149 (p) cc_final: 0.5565 (m) REVERT: C 573 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7782 (mmm) REVERT: C 607 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7340 (tm-30) REVERT: C 632 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7849 (mtpp) REVERT: C 730 ASP cc_start: 0.7794 (t0) cc_final: 0.7526 (t0) REVERT: C 903 LEU cc_start: 0.7672 (mt) cc_final: 0.7432 (mt) REVERT: C 975 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7341 (mt) outliers start: 169 outliers final: 95 residues processed: 745 average time/residue: 0.4636 time to fit residues: 404.0175 Evaluate side-chains 741 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 628 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 545 TYR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 13 TRP Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 727 PHE Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 863 SER Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 192 GLU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 210 GLN Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 573 MET Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 976 LEU Chi-restraints excluded: chain C residue 1001 ASN Chi-restraints excluded: chain C residue 1003 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 9 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 296 optimal weight: 3.9990 chunk 252 optimal weight: 0.0980 chunk 101 optimal weight: 0.9990 chunk 117 optimal weight: 0.0570 chunk 287 optimal weight: 0.4980 chunk 244 optimal weight: 0.0370 chunk 265 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 overall best weight: 0.2376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 338 HIS A 569 GLN A 605 ASN A 941 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN B 623 ASN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 941 ASN ** 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 = 0.4234 r_free = 0.4234 target = 0.158604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.140309 restraints weight = 39810.122| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.97 r_work: 0.3900 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 23584 Z= 0.129 Angle : 0.702 12.821 32049 Z= 0.340 Chirality : 0.043 0.197 3809 Planarity : 0.004 0.051 4093 Dihedral : 4.551 58.453 3258 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.57 % Allowed : 31.14 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.66 (0.16), residues: 3045 helix: 1.27 (0.13), residues: 1542 sheet: 0.41 (0.28), residues: 379 loop : -0.64 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 307 TYR 0.027 0.002 TYR C 527 PHE 0.025 0.001 PHE B 885 TRP 0.013 0.001 TRP A 515 HIS 0.001 0.000 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00294 (23584) covalent geometry : angle 0.70157 (32049) hydrogen bonds : bond 0.03754 ( 1363) hydrogen bonds : angle 4.31226 ( 3948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 633 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.6943 (tm-30) cc_final: 0.6521 (tm-30) REVERT: A 314 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7412 (tp30) REVERT: A 328 ASP cc_start: 0.7100 (t0) cc_final: 0.6869 (t0) REVERT: A 346 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 369 THR cc_start: 0.7447 (p) cc_final: 0.7167 (t) REVERT: A 390 ILE cc_start: 0.8657 (mt) cc_final: 0.8428 (pp) REVERT: A 414 GLU cc_start: 0.6977 (tt0) cc_final: 0.6750 (tt0) REVERT: A 521 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7581 (tm-30) REVERT: A 645 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7408 (tp30) REVERT: A 649 MET cc_start: 0.7689 (ppp) cc_final: 0.7431 (ppp) REVERT: A 653 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7580 (ttm-80) REVERT: A 699 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7555 (ptt90) REVERT: A 711 ASP cc_start: 0.6602 (p0) cc_final: 0.6164 (p0) REVERT: A 712 MET cc_start: 0.5931 (mmm) cc_final: 0.5565 (mmm) REVERT: A 743 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.8004 (pt) REVERT: B 108 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.6781 (tm-30) REVERT: B 156 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7163 (p0) REVERT: B 195 LYS cc_start: 0.8374 (tptp) cc_final: 0.8101 (tptp) REVERT: B 244 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6416 (pm20) REVERT: B 248 LYS cc_start: 0.8055 (mtmm) cc_final: 0.7615 (ptpt) REVERT: B 267 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7512 (ttpt) REVERT: B 322 LYS cc_start: 0.7757 (ptpt) cc_final: 0.7440 (pmtt) REVERT: B 342 LYS cc_start: 0.8561 (tptp) cc_final: 0.8260 (tppt) REVERT: B 351 VAL cc_start: 0.8099 (t) cc_final: 0.7654 (t) REVERT: B 433 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7534 (mmtt) REVERT: B 435 MET cc_start: 0.7353 (tpt) cc_final: 0.6842 (tpp) REVERT: B 486 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7724 (tt) REVERT: B 496 MET cc_start: 0.7257 (tpp) cc_final: 0.6978 (tpp) REVERT: B 521 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7276 (mm-30) REVERT: B 552 MET cc_start: 0.8096 (tmm) cc_final: 0.7864 (tmm) REVERT: B 600 THR cc_start: 0.8250 (t) cc_final: 0.7750 (p) REVERT: B 645 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7249 (tp30) REVERT: B 649 MET cc_start: 0.7899 (pmm) cc_final: 0.7581 (pmm) REVERT: B 653 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8146 (mtm110) REVERT: B 728 LYS cc_start: 0.7653 (tptp) cc_final: 0.7386 (tptt) REVERT: B 776 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7391 (mm-30) REVERT: B 781 MET cc_start: 0.7888 (mmm) cc_final: 0.7542 (mmt) REVERT: B 785 ASP cc_start: 0.6886 (OUTLIER) cc_final: 0.6469 (p0) REVERT: B 801 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.6403 (t80) REVERT: B 810 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7468 (mm-30) REVERT: B 863 SER cc_start: 0.4447 (OUTLIER) cc_final: 0.4120 (m) REVERT: B 940 LYS cc_start: 0.7866 (tptt) cc_final: 0.7468 (tppt) REVERT: C 5 PHE cc_start: 0.7565 (m-10) cc_final: 0.7149 (m-10) REVERT: C 78 MET cc_start: 0.5530 (OUTLIER) cc_final: 0.5275 (ptm) REVERT: C 195 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7798 (tptp) REVERT: C 204 ILE cc_start: 0.7756 (mt) cc_final: 0.7389 (tt) REVERT: C 235 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.7107 (pt) REVERT: C 314 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7268 (tp30) REVERT: C 339 GLU cc_start: 0.8260 (tp30) cc_final: 0.8026 (mm-30) REVERT: C 367 ILE cc_start: 0.8219 (mt) cc_final: 0.7895 (mt) REVERT: C 428 LYS cc_start: 0.8340 (tttm) cc_final: 0.7904 (ttpp) REVERT: C 468 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7500 (ttm110) REVERT: C 521 GLU cc_start: 0.8163 (pp20) cc_final: 0.7759 (tm-30) REVERT: C 525 HIS cc_start: 0.7628 (m-70) cc_final: 0.7212 (m-70) REVERT: C 561 SER cc_start: 0.6646 (p) cc_final: 0.6313 (m) REVERT: C 632 LYS cc_start: 0.8055 (mtmt) cc_final: 0.7814 (OUTLIER) REVERT: C 683 GLU cc_start: 0.3451 (pt0) cc_final: 0.2817 (pt0) REVERT: C 730 ASP cc_start: 0.7810 (t0) cc_final: 0.7482 (t0) REVERT: C 801 PHE cc_start: 0.7310 (t80) cc_final: 0.7001 (t80) outliers start: 138 outliers final: 72 residues processed: 714 average time/residue: 0.4631 time to fit residues: 387.6644 Evaluate side-chains 705 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 620 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 545 TYR Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 575 MET Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 727 PHE Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 863 SER Chi-restraints excluded: chain B residue 865 GLN Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 1003 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 151 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 282 optimal weight: 0.6980 chunk 194 optimal weight: 0.9990 chunk 267 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 569 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN B1001 ASN C 161 ASN C 210 GLN C 231 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.156363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.138256 restraints weight = 39836.358| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.92 r_work: 0.3872 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23584 Z= 0.158 Angle : 0.731 15.756 32049 Z= 0.359 Chirality : 0.045 0.212 3809 Planarity : 0.004 0.049 4093 Dihedral : 4.650 59.640 3254 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.49 % Allowed : 31.62 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.58 (0.16), residues: 3045 helix: 1.17 (0.13), residues: 1545 sheet: 0.28 (0.27), residues: 391 loop : -0.61 (0.19), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 307 TYR 0.029 0.002 TYR C 527 PHE 0.019 0.001 PHE B 885 TRP 0.018 0.001 TRP B 754 HIS 0.002 0.001 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00363 (23584) covalent geometry : angle 0.73075 (32049) hydrogen bonds : bond 0.04321 ( 1363) hydrogen bonds : angle 4.39425 ( 3948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 637 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 GLN cc_start: 0.7045 (tm-30) cc_final: 0.6655 (tm-30) REVERT: A 369 THR cc_start: 0.7486 (p) cc_final: 0.7230 (t) REVERT: A 521 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 645 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7353 (tp30) REVERT: A 649 MET cc_start: 0.7662 (ppp) cc_final: 0.7402 (ppp) REVERT: A 653 ARG cc_start: 0.7827 (ttm-80) cc_final: 0.7565 (ttm-80) REVERT: A 699 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7629 (ptt180) REVERT: A 711 ASP cc_start: 0.6628 (p0) cc_final: 0.6216 (p0) REVERT: A 712 MET cc_start: 0.5925 (mmm) cc_final: 0.5580 (mmm) REVERT: A 735 LYS cc_start: 0.8493 (mtpm) cc_final: 0.8232 (mtpp) REVERT: A 743 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8080 (pt) REVERT: A 844 MET cc_start: 0.6547 (mmp) cc_final: 0.6029 (mmp) REVERT: A 940 LYS cc_start: 0.8253 (tppt) cc_final: 0.8027 (tppt) REVERT: A 976 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7509 (tm) REVERT: B 130 GLU cc_start: 0.7277 (pm20) cc_final: 0.7070 (pm20) REVERT: B 156 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7201 (p0) REVERT: B 248 LYS cc_start: 0.8136 (mtmm) cc_final: 0.7715 (ptpt) REVERT: B 267 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7692 (ttpt) REVERT: B 317 PHE cc_start: 0.6300 (m-80) cc_final: 0.6098 (m-80) REVERT: B 322 LYS cc_start: 0.7773 (ptpt) cc_final: 0.7485 (pmtt) REVERT: B 342 LYS cc_start: 0.8603 (tptp) cc_final: 0.8344 (tppt) REVERT: B 351 VAL cc_start: 0.8226 (t) cc_final: 0.7874 (t) REVERT: B 433 LYS cc_start: 0.7766 (mmtt) cc_final: 0.7543 (mmtt) REVERT: B 435 MET cc_start: 0.7276 (tpt) cc_final: 0.6761 (tpp) REVERT: B 496 MET cc_start: 0.7318 (tpp) cc_final: 0.7040 (tpp) REVERT: B 521 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7282 (mm-30) REVERT: B 552 MET cc_start: 0.7999 (tmm) cc_final: 0.7759 (tmm) REVERT: B 645 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7223 (tp30) REVERT: B 649 MET cc_start: 0.7933 (pmm) cc_final: 0.7677 (pmm) REVERT: B 653 ARG cc_start: 0.8528 (ttm-80) cc_final: 0.8204 (mtm110) REVERT: B 712 MET cc_start: 0.6268 (tpp) cc_final: 0.5995 (mmm) REVERT: B 728 LYS cc_start: 0.7701 (tptp) cc_final: 0.7404 (tptt) REVERT: B 781 MET cc_start: 0.7998 (mmm) cc_final: 0.7543 (mmt) REVERT: B 801 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.6413 (t80) REVERT: B 810 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7469 (mm-30) REVERT: B 863 SER cc_start: 0.4611 (OUTLIER) cc_final: 0.4307 (m) REVERT: B 940 LYS cc_start: 0.7987 (tptt) cc_final: 0.7557 (tppt) REVERT: B 951 ASP cc_start: 0.7628 (t70) cc_final: 0.7186 (t0) REVERT: B 969 ARG cc_start: 0.7576 (tmm-80) cc_final: 0.7334 (tmm-80) REVERT: C 195 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7882 (tptp) REVERT: C 204 ILE cc_start: 0.7809 (mt) cc_final: 0.7444 (tt) REVERT: C 235 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.7137 (pt) REVERT: C 263 ARG cc_start: 0.7882 (ptt90) cc_final: 0.7380 (mtm-85) REVERT: C 314 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7283 (tp30) REVERT: C 334 LYS cc_start: 0.7781 (pptt) cc_final: 0.7567 (pptt) REVERT: C 339 GLU cc_start: 0.8295 (tp30) cc_final: 0.8064 (mm-30) REVERT: C 428 LYS cc_start: 0.8328 (tttm) cc_final: 0.7882 (ttpp) REVERT: C 459 PHE cc_start: 0.6519 (m-80) cc_final: 0.6120 (m-80) REVERT: C 468 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7482 (ttm110) REVERT: C 521 GLU cc_start: 0.8226 (pp20) cc_final: 0.7795 (tm-30) REVERT: C 525 HIS cc_start: 0.7658 (m-70) cc_final: 0.7191 (m-70) REVERT: C 552 MET cc_start: 0.8040 (tmm) cc_final: 0.7706 (tmm) REVERT: C 561 SER cc_start: 0.6700 (p) cc_final: 0.6355 (m) REVERT: C 632 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7828 (mtpp) REVERT: C 730 ASP cc_start: 0.7835 (t0) cc_final: 0.7523 (t0) REVERT: C 735 LYS cc_start: 0.8529 (mppt) cc_final: 0.8051 (mtmm) outliers start: 136 outliers final: 86 residues processed: 717 average time/residue: 0.4700 time to fit residues: 395.0535 Evaluate side-chains 724 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 630 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 545 TYR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 13 TRP Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 555 LEU Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 727 PHE Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 863 SER Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 953 MET Chi-restraints excluded: chain C residue 1001 ASN Chi-restraints excluded: chain C residue 1003 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 58 optimal weight: 0.3980 chunk 293 optimal weight: 0.6980 chunk 208 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 189 optimal weight: 0.0980 chunk 184 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 266 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 569 GLN A 605 ASN A 928 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 GLN B 569 GLN B 623 ASN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.157452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.139310 restraints weight = 39533.967| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.94 r_work: 0.3885 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23584 Z= 0.145 Angle : 0.764 16.116 32049 Z= 0.371 Chirality : 0.045 0.222 3809 Planarity : 0.004 0.049 4093 Dihedral : 4.625 59.971 3254 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.68 % Allowed : 33.20 % Favored : 62.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.59 (0.16), residues: 3045 helix: 1.17 (0.13), residues: 1543 sheet: 0.36 (0.27), residues: 390 loop : -0.60 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 307 TYR 0.032 0.002 TYR C 527 PHE 0.028 0.001 PHE B 362 TRP 0.023 0.001 TRP B 754 HIS 0.002 0.000 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00335 (23584) covalent geometry : angle 0.76407 (32049) hydrogen bonds : bond 0.04075 ( 1363) hydrogen bonds : angle 4.38925 ( 3948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 631 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6092 (ptt) cc_final: 0.5785 (ptm) REVERT: A 104 GLN cc_start: 0.7007 (tm-30) cc_final: 0.6598 (tm-30) REVERT: A 341 VAL cc_start: 0.8559 (m) cc_final: 0.8186 (p) REVERT: A 342 LYS cc_start: 0.8250 (tppt) cc_final: 0.8038 (tppt) REVERT: A 369 THR cc_start: 0.7456 (p) cc_final: 0.7192 (t) REVERT: A 390 ILE cc_start: 0.8668 (mt) cc_final: 0.8385 (pp) REVERT: A 496 MET cc_start: 0.7224 (ppp) cc_final: 0.6835 (ppp) REVERT: A 521 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 604 ASN cc_start: 0.8407 (m110) cc_final: 0.8207 (m-40) REVERT: A 645 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7375 (tp30) REVERT: A 649 MET cc_start: 0.7664 (ppp) cc_final: 0.7392 (ppp) REVERT: A 653 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7596 (ttm-80) REVERT: A 699 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7559 (ptt180) REVERT: A 711 ASP cc_start: 0.6668 (p0) cc_final: 0.6242 (p0) REVERT: A 712 MET cc_start: 0.5896 (mmm) cc_final: 0.5549 (mmm) REVERT: A 735 LYS cc_start: 0.8489 (mtpm) cc_final: 0.8212 (mtpp) REVERT: A 743 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.8027 (pp) REVERT: A 844 MET cc_start: 0.6578 (mmp) cc_final: 0.6023 (mmp) REVERT: A 940 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8025 (tppt) REVERT: B 149 MET cc_start: 0.7114 (pmm) cc_final: 0.6736 (pmm) REVERT: B 156 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7179 (p0) REVERT: B 244 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6407 (pm20) REVERT: B 248 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7555 (ptpt) REVERT: B 267 LYS cc_start: 0.7951 (ttpp) cc_final: 0.7679 (ttpt) REVERT: B 317 PHE cc_start: 0.6300 (m-80) cc_final: 0.6066 (m-80) REVERT: B 322 LYS cc_start: 0.7763 (ptpt) cc_final: 0.7478 (pmtt) REVERT: B 342 LYS cc_start: 0.8606 (tptp) cc_final: 0.8343 (tppt) REVERT: B 351 VAL cc_start: 0.8211 (t) cc_final: 0.7864 (t) REVERT: B 435 MET cc_start: 0.7259 (tpt) cc_final: 0.6561 (tpp) REVERT: B 439 GLN cc_start: 0.6577 (tp-100) cc_final: 0.6017 (tp40) REVERT: B 445 ILE cc_start: 0.8651 (mm) cc_final: 0.8346 (mt) REVERT: B 496 MET cc_start: 0.7334 (tpp) cc_final: 0.7028 (tpp) REVERT: B 521 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7272 (mm-30) REVERT: B 552 MET cc_start: 0.7995 (tmm) cc_final: 0.7789 (tmm) REVERT: B 645 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7480 (tp30) REVERT: B 648 THR cc_start: 0.8120 (p) cc_final: 0.7843 (p) REVERT: B 728 LYS cc_start: 0.7717 (tptp) cc_final: 0.7480 (tptt) REVERT: B 781 MET cc_start: 0.7963 (mmm) cc_final: 0.7518 (mmt) REVERT: B 785 ASP cc_start: 0.7087 (OUTLIER) cc_final: 0.6818 (p0) REVERT: B 801 PHE cc_start: 0.7383 (OUTLIER) cc_final: 0.6424 (t80) REVERT: B 810 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7445 (mm-30) REVERT: B 863 SER cc_start: 0.4645 (OUTLIER) cc_final: 0.4334 (m) REVERT: B 951 ASP cc_start: 0.7618 (t70) cc_final: 0.7190 (t0) REVERT: B 969 ARG cc_start: 0.7522 (tmm-80) cc_final: 0.7277 (tmm-80) REVERT: C 92 LEU cc_start: 0.7609 (mp) cc_final: 0.7382 (mp) REVERT: C 195 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7835 (tptp) REVERT: C 204 ILE cc_start: 0.7768 (mt) cc_final: 0.7400 (tt) REVERT: C 235 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7130 (pt) REVERT: C 314 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7305 (tp30) REVERT: C 334 LYS cc_start: 0.7708 (pptt) cc_final: 0.7432 (pptt) REVERT: C 339 GLU cc_start: 0.8272 (tp30) cc_final: 0.8055 (mm-30) REVERT: C 456 MET cc_start: 0.7341 (ttt) cc_final: 0.7045 (ttp) REVERT: C 468 ARG cc_start: 0.7718 (mtm-85) cc_final: 0.7406 (ttm110) REVERT: C 521 GLU cc_start: 0.8185 (pp20) cc_final: 0.7677 (tm-30) REVERT: C 525 HIS cc_start: 0.7625 (m-70) cc_final: 0.7041 (m-70) REVERT: C 552 MET cc_start: 0.8042 (tmm) cc_final: 0.7669 (tmm) REVERT: C 632 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7855 (mtpp) REVERT: C 730 ASP cc_start: 0.7848 (t0) cc_final: 0.7414 (OUTLIER) REVERT: C 735 LYS cc_start: 0.8424 (mppt) cc_final: 0.8079 (mppt) REVERT: C 781 MET cc_start: 0.8055 (mmt) cc_final: 0.7203 (mmt) REVERT: C 919 ARG cc_start: 0.7583 (mpp-170) cc_final: 0.7344 (mmp80) REVERT: C 987 MET cc_start: 0.7463 (tmm) cc_final: 0.7204 (pp-130) outliers start: 116 outliers final: 79 residues processed: 695 average time/residue: 0.4806 time to fit residues: 391.3845 Evaluate side-chains 709 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 621 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 545 TYR Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 699 ARG Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 948 PHE Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 138 MET Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 727 PHE Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 863 SER Chi-restraints excluded: chain B residue 921 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 970 MET Chi-restraints excluded: chain C residue 976 LEU Chi-restraints excluded: chain C residue 1001 ASN Chi-restraints excluded: chain C residue 1003 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 200 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 chunk 48 optimal weight: 0.8980 chunk 289 optimal weight: 0.9990 chunk 164 optimal weight: 0.3980 chunk 104 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN A 928 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 GLN B1001 ASN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.157027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.138903 restraints weight = 39677.484| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.92 r_work: 0.3874 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23584 Z= 0.159 Angle : 0.798 18.515 32049 Z= 0.388 Chirality : 0.046 0.311 3809 Planarity : 0.004 0.050 4093 Dihedral : 4.710 59.171 3254 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.85 % Allowed : 33.12 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.49 (0.15), residues: 3045 helix: 1.06 (0.13), residues: 1548 sheet: 0.27 (0.27), residues: 392 loop : -0.61 (0.19), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 307 TYR 0.040 0.002 TYR C 545 PHE 0.023 0.001 PHE A 885 TRP 0.025 0.001 TRP B 754 HIS 0.002 0.000 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00368 (23584) covalent geometry : angle 0.79752 (32049) hydrogen bonds : bond 0.04340 ( 1363) hydrogen bonds : angle 4.46581 ( 3948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 622 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.6139 (ptt) cc_final: 0.5823 (ptm) REVERT: A 104 GLN cc_start: 0.7060 (tm-30) cc_final: 0.6615 (tm-30) REVERT: A 314 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7048 (tp30) REVERT: A 342 LYS cc_start: 0.8279 (tppt) cc_final: 0.8012 (tppt) REVERT: A 369 THR cc_start: 0.7497 (p) cc_final: 0.7242 (t) REVERT: A 521 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7599 (tm-30) REVERT: A 645 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7266 (tp30) REVERT: A 649 MET cc_start: 0.7633 (ppp) cc_final: 0.7361 (ppp) REVERT: A 653 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7528 (ttm-80) REVERT: A 711 ASP cc_start: 0.6643 (p0) cc_final: 0.6183 (p0) REVERT: A 712 MET cc_start: 0.5901 (mmm) cc_final: 0.5553 (mmm) REVERT: A 735 LYS cc_start: 0.8454 (mtpm) cc_final: 0.8162 (mtpp) REVERT: A 743 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8084 (pp) REVERT: A 844 MET cc_start: 0.6584 (mmp) cc_final: 0.6094 (mmp) REVERT: A 940 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7922 (tppt) REVERT: B 149 MET cc_start: 0.7084 (pmm) cc_final: 0.6382 (pmm) REVERT: B 244 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6702 (pm20) REVERT: B 248 LYS cc_start: 0.8042 (mtmm) cc_final: 0.7797 (mtmm) REVERT: B 267 LYS cc_start: 0.7944 (ttpp) cc_final: 0.7577 (ttpt) REVERT: B 317 PHE cc_start: 0.6354 (m-80) cc_final: 0.6143 (m-80) REVERT: B 322 LYS cc_start: 0.7764 (ptpt) cc_final: 0.7497 (pmtt) REVERT: B 342 LYS cc_start: 0.8613 (tptp) cc_final: 0.8361 (tppt) REVERT: B 351 VAL cc_start: 0.8264 (t) cc_final: 0.7909 (t) REVERT: B 355 MET cc_start: 0.8461 (tpp) cc_final: 0.8192 (mtt) REVERT: B 398 MET cc_start: 0.6088 (tmt) cc_final: 0.5771 (tmt) REVERT: B 435 MET cc_start: 0.7370 (tpt) cc_final: 0.6449 (tpp) REVERT: B 439 GLN cc_start: 0.6652 (tp-100) cc_final: 0.6041 (mm110) REVERT: B 445 ILE cc_start: 0.8583 (mm) cc_final: 0.8354 (mt) REVERT: B 496 MET cc_start: 0.7374 (tpp) cc_final: 0.7064 (tpp) REVERT: B 552 MET cc_start: 0.8049 (tmm) cc_final: 0.7804 (tmm) REVERT: B 645 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7657 (tp30) REVERT: B 653 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8213 (mtm110) REVERT: B 683 GLU cc_start: 0.6599 (tt0) cc_final: 0.6394 (mm-30) REVERT: B 712 MET cc_start: 0.6184 (tpp) cc_final: 0.5876 (mmm) REVERT: B 728 LYS cc_start: 0.7737 (tptp) cc_final: 0.7470 (tptt) REVERT: B 776 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7476 (mt-10) REVERT: B 781 MET cc_start: 0.7851 (mmm) cc_final: 0.7411 (mmt) REVERT: B 785 ASP cc_start: 0.6861 (OUTLIER) cc_final: 0.6657 (p0) REVERT: B 801 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6468 (t80) REVERT: B 810 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7467 (mm-30) REVERT: B 863 SER cc_start: 0.4671 (OUTLIER) cc_final: 0.4341 (m) REVERT: B 951 ASP cc_start: 0.7668 (t70) cc_final: 0.7231 (t0) REVERT: C 92 LEU cc_start: 0.7618 (mp) cc_final: 0.7397 (mp) REVERT: C 195 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7850 (tptp) REVERT: C 235 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7035 (pt) REVERT: C 314 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7263 (tp30) REVERT: C 334 LYS cc_start: 0.7700 (pptt) cc_final: 0.7419 (pptt) REVERT: C 339 GLU cc_start: 0.8264 (tp30) cc_final: 0.8062 (mm-30) REVERT: C 342 LYS cc_start: 0.8539 (tppt) cc_final: 0.8277 (ttmt) REVERT: C 417 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6965 (pm20) REVERT: C 468 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7404 (ttm110) REVERT: C 521 GLU cc_start: 0.8196 (pp20) cc_final: 0.7792 (tm-30) REVERT: C 525 HIS cc_start: 0.7615 (m-70) cc_final: 0.7212 (m-70) REVERT: C 552 MET cc_start: 0.8008 (tmm) cc_final: 0.7639 (tmm) REVERT: C 632 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7831 (mtpp) REVERT: C 645 GLU cc_start: 0.7477 (tp30) cc_final: 0.7262 (tp30) REVERT: C 730 ASP cc_start: 0.7793 (t0) cc_final: 0.7465 (t0) REVERT: C 987 MET cc_start: 0.7445 (tmm) cc_final: 0.7216 (pp-130) outliers start: 120 outliers final: 82 residues processed: 689 average time/residue: 0.5036 time to fit residues: 405.7552 Evaluate side-chains 710 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 617 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 545 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 598 TYR Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 727 PHE Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 863 SER Chi-restraints excluded: chain B residue 921 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 417 GLU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 496 MET Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 925 VAL Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 1001 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 95 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 chunk 190 optimal weight: 0.3980 chunk 39 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN A 928 GLN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 GLN B1001 ASN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.156288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.138329 restraints weight = 39521.087| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 2.90 r_work: 0.3870 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23584 Z= 0.169 Angle : 0.822 17.255 32049 Z= 0.402 Chirality : 0.047 0.399 3809 Planarity : 0.004 0.049 4093 Dihedral : 4.740 58.330 3254 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.24 % Allowed : 34.05 % Favored : 61.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.47 (0.15), residues: 3045 helix: 1.03 (0.13), residues: 1546 sheet: 0.31 (0.27), residues: 390 loop : -0.60 (0.19), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 307 TYR 0.038 0.002 TYR C 545 PHE 0.028 0.001 PHE B 362 TRP 0.026 0.001 TRP B 754 HIS 0.002 0.000 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00392 (23584) covalent geometry : angle 0.82167 (32049) hydrogen bonds : bond 0.04479 ( 1363) hydrogen bonds : angle 4.56302 ( 3948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6090 Ramachandran restraints generated. 3045 Oldfield, 0 Emsley, 3045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 619 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "PHE B 386 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6113 (mpp) cc_final: 0.5885 (mpp) REVERT: A 78 MET cc_start: 0.6146 (ptt) cc_final: 0.5884 (ptm) REVERT: A 104 GLN cc_start: 0.7053 (tm-30) cc_final: 0.6620 (tm-30) REVERT: A 346 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7337 (mm-30) REVERT: A 369 THR cc_start: 0.7489 (p) cc_final: 0.7245 (t) REVERT: A 390 ILE cc_start: 0.8608 (pt) cc_final: 0.8375 (pp) REVERT: A 414 GLU cc_start: 0.6975 (tt0) cc_final: 0.6711 (tt0) REVERT: A 496 MET cc_start: 0.7195 (ppp) cc_final: 0.6847 (ppp) REVERT: A 521 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7582 (tm-30) REVERT: A 645 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7226 (tp30) REVERT: A 649 MET cc_start: 0.7594 (ppp) cc_final: 0.7318 (ppp) REVERT: A 653 ARG cc_start: 0.7822 (ttm-80) cc_final: 0.7542 (ttm-80) REVERT: A 711 ASP cc_start: 0.6653 (p0) cc_final: 0.6163 (p0) REVERT: A 712 MET cc_start: 0.5809 (mmm) cc_final: 0.5496 (mmm) REVERT: A 743 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8108 (pp) REVERT: A 844 MET cc_start: 0.6611 (mmp) cc_final: 0.6155 (mmp) REVERT: A 940 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7996 (tppt) REVERT: B 149 MET cc_start: 0.7042 (pmm) cc_final: 0.6372 (pmm) REVERT: B 244 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6487 (pm20) REVERT: B 248 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7640 (ptpt) REVERT: B 267 LYS cc_start: 0.8005 (ttpp) cc_final: 0.7444 (ttpt) REVERT: B 269 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6961 (mp0) REVERT: B 317 PHE cc_start: 0.6395 (m-80) cc_final: 0.6169 (m-80) REVERT: B 342 LYS cc_start: 0.8616 (tptp) cc_final: 0.8375 (tppt) REVERT: B 355 MET cc_start: 0.8517 (tpp) cc_final: 0.8262 (mtt) REVERT: B 398 MET cc_start: 0.6257 (tmt) cc_final: 0.5941 (tmt) REVERT: B 435 MET cc_start: 0.7408 (tpt) cc_final: 0.6477 (tpp) REVERT: B 439 GLN cc_start: 0.6653 (tp-100) cc_final: 0.6023 (mm110) REVERT: B 445 ILE cc_start: 0.8673 (mm) cc_final: 0.8245 (mt) REVERT: B 496 MET cc_start: 0.7430 (tpp) cc_final: 0.7179 (tpp) REVERT: B 552 MET cc_start: 0.8026 (tmm) cc_final: 0.7769 (tmm) REVERT: B 645 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7659 (tp30) REVERT: B 653 ARG cc_start: 0.8384 (ttm-80) cc_final: 0.8145 (mtm110) REVERT: B 683 GLU cc_start: 0.6672 (tt0) cc_final: 0.6348 (mm-30) REVERT: B 712 MET cc_start: 0.6271 (tpp) cc_final: 0.5998 (mmm) REVERT: B 728 LYS cc_start: 0.7745 (tptp) cc_final: 0.7503 (tptt) REVERT: B 776 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7454 (tp30) REVERT: B 781 MET cc_start: 0.7967 (mmm) cc_final: 0.7545 (mmt) REVERT: B 801 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6494 (t80) REVERT: B 810 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7467 (mm-30) REVERT: B 863 SER cc_start: 0.4774 (OUTLIER) cc_final: 0.4443 (m) REVERT: B 940 LYS cc_start: 0.8067 (tptt) cc_final: 0.7614 (tppt) REVERT: B 951 ASP cc_start: 0.7693 (t70) cc_final: 0.7478 (t70) REVERT: C 92 LEU cc_start: 0.7633 (mp) cc_final: 0.7415 (mp) REVERT: C 195 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7860 (tptp) REVERT: C 235 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.7056 (pt) REVERT: C 314 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7269 (tp30) REVERT: C 334 LYS cc_start: 0.7714 (pptt) cc_final: 0.7410 (pptt) REVERT: C 342 LYS cc_start: 0.8565 (tppt) cc_final: 0.8289 (ttmt) REVERT: C 428 LYS cc_start: 0.8302 (tttm) cc_final: 0.7947 (ttpp) REVERT: C 468 ARG cc_start: 0.7712 (mtm-85) cc_final: 0.7376 (ttp80) REVERT: C 521 GLU cc_start: 0.8192 (pp20) cc_final: 0.7802 (tm-30) REVERT: C 525 HIS cc_start: 0.7628 (m-70) cc_final: 0.7219 (m-70) REVERT: C 552 MET cc_start: 0.7995 (tmm) cc_final: 0.7640 (tmm) REVERT: C 632 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7839 (mtpp) REVERT: C 645 GLU cc_start: 0.7462 (tp30) cc_final: 0.7230 (tp30) REVERT: C 730 ASP cc_start: 0.7784 (t0) cc_final: 0.7432 (t0) REVERT: C 735 LYS cc_start: 0.8453 (mtmm) cc_final: 0.8225 (mtmm) REVERT: C 987 MET cc_start: 0.7367 (tmm) cc_final: 0.7154 (pp-130) outliers start: 105 outliers final: 80 residues processed: 680 average time/residue: 0.4704 time to fit residues: 375.6147 Evaluate side-chains 702 residues out of total 2493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 614 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 545 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 697 GLN Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 830 GLN Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 940 LYS Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 ILE Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 695 LEU Chi-restraints excluded: chain B residue 727 PHE Chi-restraints excluded: chain B residue 741 VAL Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 776 GLU Chi-restraints excluded: chain B residue 786 ILE Chi-restraints excluded: chain B residue 801 PHE Chi-restraints excluded: chain B residue 825 MET Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 863 SER Chi-restraints excluded: chain B residue 921 LEU Chi-restraints excluded: chain B residue 948 PHE Chi-restraints excluded: chain B residue 1003 VAL Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain B residue 1017 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 156 ASP Chi-restraints excluded: chain C residue 169 THR Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 355 MET Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 671 ILE Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 729 ILE Chi-restraints excluded: chain C residue 770 LYS Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 909 VAL Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 917 THR Chi-restraints excluded: chain C residue 948 PHE Chi-restraints excluded: chain C residue 952 LEU Chi-restraints excluded: chain C residue 1001 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 270 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 249 optimal weight: 0.7980 chunk 158 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 chunk 264 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 239 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 GLN A 865 GLN A 928 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 ASN B1001 ASN ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.155469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.137267 restraints weight = 39593.169| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.94 r_work: 0.3861 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23584 Z= 0.176 Angle : 0.830 16.615 32049 Z= 0.408 Chirality : 0.047 0.346 3809 Planarity : 0.004 0.048 4093 Dihedral : 4.786 57.243 3253 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.96 % Allowed : 34.73 % Favored : 61.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 aren not related in a simple way. whole: 0.40 (0.15), residues: 3045 helix: 0.96 (0.13), residues: 1542 sheet: 0.32 (0.27), residues: 393 loop : -0.64 (0.19), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 307 TYR 0.037 0.002 TYR C 545 PHE 0.031 0.001 PHE B 885 TRP 0.025 0.002 TRP B 754 HIS 0.002 0.000 HIS A 709 Details of bonding type rmsd covalent geometry : bond 0.00407 (23584) covalent geometry : angle 0.82962 (32049) hydrogen bonds : bond 0.04654 ( 1363) hydrogen bonds : angle 4.64194 ( 3948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7510.59 seconds wall clock time: 128 minutes 22.23 seconds (7702.23 seconds total)