Starting phenix.real_space_refine on Tue Jan 21 13:21:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfn_44501/01_2025/9bfn_44501_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfn_44501/01_2025/9bfn_44501.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bfn_44501/01_2025/9bfn_44501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfn_44501/01_2025/9bfn_44501.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfn_44501/01_2025/9bfn_44501_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfn_44501/01_2025/9bfn_44501_trim.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 23519 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 2 5.49 5 S 132 5.16 5 C 15249 2.51 5 N 3890 2.21 5 O 4399 1.98 5 F 3 1.80 5 H 24004 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 47679 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 15857 Classifications: {'peptide': 1034} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 988} Chain: "B" Number of atoms: 15850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15850 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "C" Number of atoms: 15850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 15850 Classifications: {'peptide': 1033} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 987} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'3PE': 1, 'A1AOE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 16.28, per 1000 atoms: 0.34 Number of scatterers: 47679 At special positions: 0 Unit cell: (115.56, 123.05, 148.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 132 16.00 P 2 15.00 F 3 9.00 O 4399 8.00 N 3890 7.00 C 15249 6.00 H 24004 1.00 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: 9.43 Conformation dependent library (CDL) restraints added in 3.1 seconds 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5666 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 24 sheets defined 60.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 1 through 7 removed outlier: 3.730A pdb=" N ASP A 7 " --> pdb=" O ASN A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 99 through 115 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 162 Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 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 298 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 Processing helix chain 'A' and resid 361 through 386 Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 424 removed outlier: 4.268A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 5.529A pdb=" N GLY A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.501A pdb=" N PHE A 459 " --> pdb=" O MET A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 497 removed outlier: 3.613A pdb=" N GLY A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 510 through 535 Processing helix chain 'A' and resid 537 through 559 removed outlier: 3.885A pdb=" N TYR A 541 " --> pdb=" O SER A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 601 Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 639 through 642 Processing helix chain 'A' and resid 643 through 656 Processing helix chain 'A' and resid 691 through 708 Processing helix chain 'A' and resid 732 through 739 Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 777 through 780 Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 801 through 804 No H-bonds generated for 'chain 'A' and resid 801 through 804' Processing helix chain 'A' and resid 836 through 850 removed outlier: 3.691A pdb=" N LYS A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 869 removed outlier: 3.520A pdb=" N GLN A 865 " --> pdb=" O GLY A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 893 removed outlier: 3.817A pdb=" N SER A 875 " --> pdb=" O ASN A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 903 removed outlier: 4.191A pdb=" N SER A 900 " --> pdb=" O SER A 896 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 901 " --> pdb=" O ILE A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 920 removed outlier: 3.882A pdb=" N GLY A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 956 Processing helix chain 'A' and resid 959 through 992 removed outlier: 4.747A pdb=" N ARG A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Proline residue: A 974 - end of helix Proline residue: A 988 - end of helix Processing helix chain 'A' and resid 996 through 1033 removed outlier: 4.165A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A1007 " --> pdb=" O VAL A1003 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A1019 " --> pdb=" O THR A1015 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE A1020 " --> pdb=" O VAL A1016 " (cutoff:3.500A) Proline residue: A1023 - end of helix Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 8 through 30 Processing helix chain 'B' and resid 53 through 61 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.784A pdb=" N ASN B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 removed outlier: 4.074A pdb=" N LEU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 114 " --> pdb=" O LYS B 110 " (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 162 Processing helix chain 'B' and resid 162 through 169 Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 298 through 314 Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 329 through 359 Processing helix chain 'B' and resid 361 through 386 removed outlier: 3.983A pdb=" N ILE B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 423 removed outlier: 4.212A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.640A 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 439 through 454 Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.594A pdb=" N PHE B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 497 removed outlier: 3.540A pdb=" N TYR B 467 " --> pdb=" O THR B 463 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.655A 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 511 through 535 Processing helix chain 'B' and resid 537 through 558 removed outlier: 3.530A pdb=" N TYR B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG B 558 " --> pdb=" O TYR B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 601 Processing helix chain 'B' and resid 633 through 637 Processing helix chain 'B' and resid 643 through 655 Processing helix chain 'B' and resid 691 through 707 Processing helix chain 'B' and resid 732 through 739 Processing helix chain 'B' and resid 742 through 756 Processing helix chain 'B' and resid 777 through 780 Processing helix chain 'B' and resid 782 through 788 Processing helix chain 'B' and resid 836 through 850 removed outlier: 3.703A pdb=" N LYS B 850 " --> pdb=" O GLN B 846 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 869 removed outlier: 3.700A pdb=" N GLN B 865 " --> pdb=" O GLY B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 893 Processing helix chain 'B' and resid 896 through 903 removed outlier: 4.113A pdb=" N SER B 900 " --> pdb=" O SER B 896 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 920 removed outlier: 3.779A pdb=" N VAL B 909 " --> pdb=" O VAL B 905 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 957 Processing helix chain 'B' and resid 959 through 992 removed outlier: 4.753A pdb=" N ARG B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Proline residue: B 974 - end of helix Proline residue: B 988 - end of helix Processing helix chain 'B' and resid 998 through 1033 removed outlier: 3.645A pdb=" N GLY B1009 " --> pdb=" O THR B1005 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE B1019 " --> pdb=" O THR B1015 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE B1020 " --> pdb=" O VAL B1016 " (cutoff:3.500A) Proline residue: B1023 - end of helix Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.774A pdb=" N ASP C 7 " --> pdb=" O ASN C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 Processing helix chain 'C' and resid 53 through 61 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.868A pdb=" N ASN C 68 " --> pdb=" O VAL C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 113 removed outlier: 4.078A pdb=" N LEU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 162 Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'C' and resid 242 through 248 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 360 Processing helix chain 'C' and resid 361 through 370 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 370 through 386 Processing helix chain 'C' and resid 391 through 424 removed outlier: 4.218A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ASP C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA C 409 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 452 removed outlier: 5.839A pdb=" N GLY C 440 " --> pdb=" O GLY C 436 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ALA C 441 " --> pdb=" O GLN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 460 through 496 removed outlier: 3.546A pdb=" N GLY C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 4.525A 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 511 through 537 removed outlier: 3.777A pdb=" N TRP C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER C 537 " --> pdb=" O GLY C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 558 removed outlier: 3.613A pdb=" N VAL C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 544 " --> pdb=" O ARG C 540 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 558 " --> pdb=" O TYR C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 601 Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 639 through 642 Processing helix chain 'C' and resid 643 through 656 Processing helix chain 'C' and resid 691 through 708 Processing helix chain 'C' and resid 732 through 740 Processing helix chain 'C' and resid 742 through 755 Processing helix chain 'C' and resid 777 through 780 Processing helix chain 'C' and resid 782 through 788 removed outlier: 3.573A pdb=" N ILE C 786 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY C 787 " --> pdb=" O ASP C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 804 No H-bonds generated for 'chain 'C' and resid 801 through 804' Processing helix chain 'C' and resid 836 through 849 Processing helix chain 'C' and resid 861 through 893 Proline residue: C 874 - end of helix Processing helix chain 'C' and resid 895 through 903 Processing helix chain 'C' and resid 904 through 920 removed outlier: 3.683A pdb=" N GLY C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 956 removed outlier: 3.750A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 991 removed outlier: 5.129A pdb=" N ARG C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Proline residue: C 974 - end of helix Proline residue: C 988 - end of helix Processing helix chain 'C' and resid 996 through 1017 removed outlier: 3.546A pdb=" N GLN C1000 " --> pdb=" O GLY C 996 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1033 Proline residue: C1023 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.810A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.226A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLU A 826 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 828 " --> pdb=" O VAL A 716 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL A 716 " --> pdb=" O LEU A 828 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 131 removed outlier: 3.810A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 12.226A pdb=" N ARG A 815 " --> pdb=" O GLU A 826 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N GLU A 826 " --> pdb=" O ARG A 815 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU A 817 " --> pdb=" O SER A 824 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 178 removed outlier: 3.677A pdb=" N GLY A 288 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 144 " --> pdb=" O PRO A 285 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 178 removed outlier: 3.677A pdb=" N GLY A 288 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ALA A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THR A 624 " --> pdb=" O GLY A 614 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 7.260A pdb=" N TYR A 182 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N TYR A 772 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N MET A 184 " --> pdb=" O TYR A 772 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N MET A 774 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N ILE A 186 " --> pdb=" O MET A 774 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ARG A 767 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ILE A 763 " --> pdb=" O ARG A 767 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS A 769 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP A 761 " --> pdb=" O LYS A 769 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 771 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 219 removed outlier: 4.133A pdb=" N GLY A 217 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A 233 " --> pdb=" O PRO C 725 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 253 removed outlier: 7.153A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 805 through 812 removed outlier: 8.281A pdb=" N ILE B 235 " --> pdb=" O PRO A 725 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N PHE A 727 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 790 through 792 Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 removed outlier: 4.109A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.155A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLN B 830 " --> pdb=" O SER B 715 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N SER B 715 " --> pdb=" O GLN B 830 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 130 removed outlier: 4.109A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 12.155A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.283A 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: 6.729A pdb=" N VAL B 172 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA B 294 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N GLY B 141 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N SER B 287 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N VAL B 139 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 11.285A pdb=" N LEU B 289 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU B 137 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 291 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N SER B 135 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N LEU B 293 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N LEU B 137 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASP B 328 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 177 removed outlier: 6.729A pdb=" N VAL B 172 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA B 294 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 7.476A pdb=" N TYR B 182 " --> pdb=" O LYS B 770 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N TYR B 772 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N MET B 184 " --> pdb=" O TYR B 772 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N MET B 774 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE B 186 " --> pdb=" O MET B 774 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASN B 760 " --> pdb=" O VAL B 771 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 773 " --> pdb=" O TYR B 758 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N TYR B 758 " --> pdb=" O VAL B 773 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 253 removed outlier: 3.501A pdb=" N LYS B 252 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 805 through 812 removed outlier: 8.615A pdb=" N ILE C 235 " --> pdb=" O PRO B 725 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE B 727 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.371A pdb=" N ALA C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLN C 830 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N SER C 715 " --> pdb=" O GLN C 830 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 132 removed outlier: 4.371A pdb=" N ALA C 42 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N ARG C 815 " --> pdb=" O GLU C 826 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N GLU C 826 " --> pdb=" O ARG C 815 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY C 829 " --> pdb=" O PHE C 680 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.167A pdb=" N ASP C 174 " --> pdb=" O LYS C 292 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU C 293 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N PHE C 136 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N LEU C 137 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ASP C 328 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.167A pdb=" N ASP C 174 " --> pdb=" O LYS C 292 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N THR C 624 " --> pdb=" O GLY C 614 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 270 removed outlier: 5.875A pdb=" N MET C 184 " --> pdb=" O TYR C 772 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N MET C 774 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE C 186 " --> pdb=" O MET C 774 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 253 Processing sheet with id=AC6, first strand: chain 'C' and resid 790 through 792 1660 hydrogen bonds defined for protein. 4800 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: 19.29 Time building geometry restraints manager: 11.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 23998 1.02 - 1.21: 25 1.21 - 1.41: 9501 1.41 - 1.61: 14337 1.61 - 1.81: 262 Bond restraints: 48123 Sorted by residual: bond pdb=" C06 A1AOE A1102 " pdb=" N05 A1AOE A1102 " ideal model delta sigma weight residual 1.452 1.222 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" CA SER B 875 " pdb=" C SER B 875 " ideal model delta sigma weight residual 1.524 1.455 0.069 1.29e-02 6.01e+03 2.85e+01 bond pdb=" C SER A 875 " pdb=" O SER A 875 " ideal model delta sigma weight residual 1.237 1.179 0.058 1.17e-02 7.31e+03 2.45e+01 bond pdb=" C ALA A 878 " pdb=" O ALA A 878 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.22e-02 6.72e+03 2.40e+01 bond pdb=" C02 A1AOE A1102 " pdb=" C22 A1AOE A1102 " ideal model delta sigma weight residual 1.527 1.431 0.096 2.00e-02 2.50e+03 2.28e+01 ... (remaining 48118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 86760 2.16 - 4.32: 418 4.32 - 6.48: 29 6.48 - 8.63: 6 8.63 - 10.79: 2 Bond angle restraints: 87215 Sorted by residual: angle pdb=" N ALA A 878 " pdb=" CA ALA A 878 " pdb=" C ALA A 878 " ideal model delta sigma weight residual 111.69 104.18 7.51 1.23e+00 6.61e-01 3.73e+01 angle pdb=" C ALA A 873 " pdb=" N PRO A 874 " pdb=" CA PRO A 874 " ideal model delta sigma weight residual 119.05 112.54 6.51 1.11e+00 8.12e-01 3.43e+01 angle pdb=" C ALA B 873 " pdb=" N PRO B 874 " pdb=" CA PRO B 874 " ideal model delta sigma weight residual 119.05 114.20 4.85 1.11e+00 8.12e-01 1.91e+01 angle pdb=" N ALA B 878 " pdb=" CA ALA B 878 " pdb=" C ALA B 878 " ideal model delta sigma weight residual 112.45 106.44 6.01 1.39e+00 5.18e-01 1.87e+01 angle pdb=" C TYR B 877 " pdb=" CA TYR B 877 " pdb=" CB TYR B 877 " ideal model delta sigma weight residual 110.01 117.61 -7.60 1.80e+00 3.09e-01 1.78e+01 ... (remaining 87210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 20390 17.59 - 35.18: 1657 35.18 - 52.77: 450 52.77 - 70.36: 148 70.36 - 87.95: 18 Dihedral angle restraints: 22663 sinusoidal: 12460 harmonic: 10203 Sorted by residual: dihedral pdb=" C TYR B 877 " pdb=" N TYR B 877 " pdb=" CA TYR B 877 " pdb=" CB TYR B 877 " ideal model delta harmonic sigma weight residual -122.60 -135.15 12.55 0 2.50e+00 1.60e-01 2.52e+01 dihedral pdb=" CA GLN C 437 " pdb=" C GLN C 437 " pdb=" N ILE C 438 " pdb=" CA ILE C 438 " ideal model delta harmonic sigma weight residual -180.00 -160.49 -19.51 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" N TYR B 877 " pdb=" C TYR B 877 " pdb=" CA TYR B 877 " pdb=" CB TYR B 877 " ideal model delta harmonic sigma weight residual 122.80 132.37 -9.57 0 2.50e+00 1.60e-01 1.47e+01 ... (remaining 22660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 3791 0.118 - 0.237: 48 0.237 - 0.355: 1 0.355 - 0.474: 0 0.474 - 0.592: 2 Chirality restraints: 3842 Sorted by residual: chirality pdb=" CA TYR B 877 " pdb=" N TYR B 877 " pdb=" C TYR B 877 " pdb=" CB TYR B 877 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.77e+00 chirality pdb=" CA TYR A 877 " pdb=" N TYR A 877 " pdb=" C TYR A 877 " pdb=" CB TYR A 877 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" CA LEU A 876 " pdb=" N LEU A 876 " pdb=" C LEU A 876 " pdb=" CB LEU A 876 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 3839 not shown) Planarity restraints: 7138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 108 " -0.023 2.00e-02 2.50e+03 2.53e-02 9.57e+00 pdb=" CD GLN A 108 " -0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN A 108 " 0.024 2.00e-02 2.50e+03 pdb=" NE2 GLN A 108 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 108 " 0.037 2.00e-02 2.50e+03 pdb="HE22 GLN A 108 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 877 " -0.034 2.00e-02 2.50e+03 1.57e-02 7.41e+00 pdb=" CG TYR B 877 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 877 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 877 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 877 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 877 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 877 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 877 " -0.019 2.00e-02 2.50e+03 pdb=" HD1 TYR B 877 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 TYR B 877 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR B 877 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR B 877 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 290 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C GLY C 290 " -0.038 2.00e-02 2.50e+03 pdb=" O GLY C 290 " 0.014 2.00e-02 2.50e+03 pdb=" N ILE C 291 " 0.013 2.00e-02 2.50e+03 ... (remaining 7135 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 2239 2.19 - 2.79: 99168 2.79 - 3.40: 138407 3.40 - 4.00: 184949 4.00 - 4.60: 287085 Nonbonded interactions: 711848 Sorted by model distance: nonbonded pdb=" OD1 ASP A 7 " pdb="HH22 ARG A 432 " model vdw 1.590 2.450 nonbonded pdb=" OE1 GLN B 872 " pdb=" H GLN B 872 " model vdw 1.616 2.450 nonbonded pdb=" HH TYR A 758 " pdb=" OD1 ASP A 761 " model vdw 1.619 2.450 nonbonded pdb="HH21 ARG C 818 " pdb=" O GLY C 821 " model vdw 1.630 2.450 nonbonded pdb=" OD2 ASP B 568 " pdb=" H VAL B 644 " model vdw 1.635 2.450 ... (remaining 711843 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 1033) selection = (chain 'B' and (resid 1 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ )) or resid 110 through 1033)) selection = (chain 'C' and (resid 1 through 108 or (resid 109 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ )) or resid 110 through 1033)) } 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.310 Construct map_model_manager: 0.620 Extract box with map and model: 1.290 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 80.220 Find NCS groups from input model: 1.480 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:11.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.004 0.230 24119 Z= 0.252 Angle : 0.548 10.792 32732 Z= 0.300 Chirality : 0.043 0.592 3842 Planarity : 0.004 0.052 4176 Dihedral : 13.361 87.950 8791 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.15), residues: 3094 helix: 2.24 (0.12), residues: 1694 sheet: -0.13 (0.24), residues: 412 loop : 0.44 (0.21), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 13 HIS 0.003 0.001 HIS B 526 PHE 0.016 0.001 PHE A 682 TYR 0.036 0.002 TYR B 877 ARG 0.005 0.000 ARG C 919 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 2.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 420 MET cc_start: 0.8367 (ttp) cc_final: 0.8149 (ttm) REVERT: C 83 ASP cc_start: 0.6563 (t70) cc_final: 0.6338 (t70) REVERT: C 395 MET cc_start: 0.8451 (mmp) cc_final: 0.8240 (mmp) REVERT: C 435 MET cc_start: 0.7825 (mmm) cc_final: 0.7562 (mmm) REVERT: C 456 MET cc_start: 0.8893 (ptt) cc_final: 0.8688 (ptt) REVERT: C 686 ASP cc_start: 0.7762 (t0) cc_final: 0.7555 (t0) REVERT: C 714 THR cc_start: 0.9076 (p) cc_final: 0.8854 (p) outliers start: 0 outliers final: 1 residues processed: 400 average time/residue: 2.5806 time to fit residues: 1183.1758 Evaluate side-chains 322 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 321 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 0.8980 chunk 234 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 0.2980 chunk 93 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.099805 restraints weight = 79350.104| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.27 r_work: 0.2985 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24119 Z= 0.192 Angle : 0.499 5.305 32732 Z= 0.269 Chirality : 0.040 0.162 3842 Planarity : 0.004 0.050 4176 Dihedral : 6.230 83.398 3407 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.83 % Allowed : 7.66 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.15), residues: 3094 helix: 2.24 (0.12), residues: 1709 sheet: -0.08 (0.24), residues: 400 loop : 0.37 (0.21), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 789 HIS 0.002 0.001 HIS C 692 PHE 0.016 0.001 PHE A 682 TYR 0.024 0.001 TYR B 877 ARG 0.004 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 328 time to evaluate : 2.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 GLU cc_start: 0.7857 (mp0) cc_final: 0.7619 (mt-10) REVERT: B 667 ASN cc_start: 0.8420 (t0) cc_final: 0.8141 (t0) REVERT: C 20 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8169 (mtt) REVERT: C 76 MET cc_start: 0.9055 (mtp) cc_final: 0.8789 (mtm) REVERT: C 83 ASP cc_start: 0.7046 (t70) cc_final: 0.6671 (t70) REVERT: C 435 MET cc_start: 0.8108 (mmm) cc_final: 0.7874 (mmm) REVERT: C 456 MET cc_start: 0.8953 (ptt) cc_final: 0.8702 (ptt) REVERT: C 673 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: C 686 ASP cc_start: 0.8065 (t0) cc_final: 0.7861 (t0) REVERT: C 714 THR cc_start: 0.9217 (p) cc_final: 0.9014 (p) REVERT: C 868 LEU cc_start: 0.8680 (tp) cc_final: 0.8431 (tp) outliers start: 21 outliers final: 10 residues processed: 338 average time/residue: 2.5041 time to fit residues: 975.5290 Evaluate side-chains 334 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 322 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 1012 VAL Chi-restraints excluded: chain C residue 20 MET Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 862 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 274 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 159 optimal weight: 0.0060 chunk 221 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 271 optimal weight: 3.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.117180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.099148 restraints weight = 79537.903| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.25 r_work: 0.2959 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24119 Z= 0.241 Angle : 0.502 5.207 32732 Z= 0.268 Chirality : 0.041 0.165 3842 Planarity : 0.004 0.055 4176 Dihedral : 6.280 83.706 3405 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.03 % Allowed : 8.42 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.15), residues: 3094 helix: 2.16 (0.12), residues: 1713 sheet: -0.14 (0.24), residues: 407 loop : 0.30 (0.21), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 754 HIS 0.003 0.001 HIS B 596 PHE 0.017 0.001 PHE A 682 TYR 0.020 0.001 TYR B 49 ARG 0.006 0.001 ARG B 558 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 329 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 566 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.7733 (t0) REVERT: B 667 ASN cc_start: 0.8346 (t0) cc_final: 0.8064 (t0) REVERT: B 962 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7869 (tm-30) REVERT: C 20 MET cc_start: 0.8725 (mtt) cc_final: 0.8322 (mtt) REVERT: C 63 GLN cc_start: 0.7572 (mm-40) cc_final: 0.6954 (mm110) REVERT: C 76 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8772 (mtm) REVERT: C 83 ASP cc_start: 0.7138 (t70) cc_final: 0.6767 (t70) REVERT: C 435 MET cc_start: 0.8302 (mmm) cc_final: 0.8007 (mmm) REVERT: C 673 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6794 (mp0) REVERT: C 714 THR cc_start: 0.9230 (p) cc_final: 0.9019 (p) REVERT: C 868 LEU cc_start: 0.8692 (tp) cc_final: 0.8440 (tp) outliers start: 26 outliers final: 14 residues processed: 341 average time/residue: 2.4772 time to fit residues: 979.5896 Evaluate side-chains 332 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 314 time to evaluate : 2.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 566 ASP Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 962 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 993 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 259 optimal weight: 4.9990 chunk 306 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 295 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097664 restraints weight = 79757.215| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.28 r_work: 0.2967 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24119 Z= 0.257 Angle : 0.506 5.184 32732 Z= 0.271 Chirality : 0.041 0.162 3842 Planarity : 0.004 0.065 4176 Dihedral : 6.354 83.974 3405 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.43 % Allowed : 8.90 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.15), residues: 3094 helix: 2.13 (0.12), residues: 1714 sheet: 0.04 (0.25), residues: 378 loop : 0.19 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 789 HIS 0.003 0.001 HIS B 596 PHE 0.017 0.001 PHE A 682 TYR 0.023 0.002 TYR B 49 ARG 0.006 0.001 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 325 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 601 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8425 (mptm) REVERT: B 667 ASN cc_start: 0.8483 (t0) cc_final: 0.8219 (t0) REVERT: B 734 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6331 (tm-30) REVERT: B 962 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7932 (tm-30) REVERT: C 63 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7113 (mm-40) REVERT: C 76 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8811 (mtm) REVERT: C 83 ASP cc_start: 0.7171 (t70) cc_final: 0.6807 (t70) REVERT: C 395 MET cc_start: 0.8893 (mmp) cc_final: 0.8637 (mmp) REVERT: C 435 MET cc_start: 0.8408 (mmm) cc_final: 0.8097 (mmm) REVERT: C 673 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: C 868 LEU cc_start: 0.8716 (tp) cc_final: 0.8467 (tp) outliers start: 36 outliers final: 18 residues processed: 341 average time/residue: 2.4770 time to fit residues: 981.0679 Evaluate side-chains 335 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 312 time to evaluate : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 962 GLU Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 993 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 92 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 304 optimal weight: 0.6980 chunk 255 optimal weight: 0.8980 chunk 208 optimal weight: 3.9990 chunk 272 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 275 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.115885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097732 restraints weight = 79457.382| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.28 r_work: 0.2967 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24119 Z= 0.246 Angle : 0.498 5.122 32732 Z= 0.266 Chirality : 0.041 0.162 3842 Planarity : 0.004 0.052 4176 Dihedral : 6.348 84.094 3405 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.31 % Allowed : 9.65 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.15), residues: 3094 helix: 2.17 (0.12), residues: 1710 sheet: 0.03 (0.25), residues: 378 loop : 0.18 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 789 HIS 0.003 0.001 HIS C 338 PHE 0.017 0.001 PHE A 682 TYR 0.020 0.002 TYR B 877 ARG 0.007 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 320 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7652 (t0) REVERT: A 339 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: B 429 GLU cc_start: 0.7699 (mp0) cc_final: 0.7429 (mp0) REVERT: C 63 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7090 (mm-40) REVERT: C 76 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8814 (mtm) REVERT: C 83 ASP cc_start: 0.7195 (t70) cc_final: 0.6802 (t70) REVERT: C 435 MET cc_start: 0.8385 (mmm) cc_final: 0.7981 (mmm) REVERT: C 673 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: C 868 LEU cc_start: 0.8761 (tp) cc_final: 0.8516 (tp) outliers start: 33 outliers final: 16 residues processed: 334 average time/residue: 2.4623 time to fit residues: 960.7665 Evaluate side-chains 335 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 315 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 711 ASP Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 993 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 104 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 290 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 178 optimal weight: 4.9990 chunk 79 optimal weight: 0.3980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.116037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.097906 restraints weight = 79568.304| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.28 r_work: 0.2963 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24119 Z= 0.231 Angle : 0.495 5.088 32732 Z= 0.264 Chirality : 0.040 0.160 3842 Planarity : 0.004 0.048 4176 Dihedral : 6.310 84.007 3405 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.35 % Allowed : 9.85 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.15), residues: 3094 helix: 2.20 (0.12), residues: 1710 sheet: 0.04 (0.25), residues: 378 loop : 0.19 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 789 HIS 0.002 0.001 HIS C 338 PHE 0.017 0.001 PHE A 682 TYR 0.019 0.001 TYR B 877 ARG 0.006 0.000 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 324 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7652 (t0) REVERT: A 339 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: B 429 GLU cc_start: 0.7743 (mp0) cc_final: 0.7462 (mp0) REVERT: B 543 VAL cc_start: 0.8488 (t) cc_final: 0.8202 (t) REVERT: B 962 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: C 63 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7196 (mm-40) REVERT: C 76 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8814 (mtm) REVERT: C 83 ASP cc_start: 0.7210 (t70) cc_final: 0.6812 (t70) REVERT: C 422 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: C 435 MET cc_start: 0.8374 (mmm) cc_final: 0.8087 (mmm) REVERT: C 673 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: C 868 LEU cc_start: 0.8753 (tp) cc_final: 0.8508 (tp) outliers start: 34 outliers final: 17 residues processed: 341 average time/residue: 2.4363 time to fit residues: 962.9833 Evaluate side-chains 339 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 316 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 339 GLU Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 962 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 993 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 140 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 289 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.116146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.098220 restraints weight = 79190.599| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.24 r_work: 0.2956 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24119 Z= 0.261 Angle : 0.504 5.110 32732 Z= 0.269 Chirality : 0.041 0.162 3842 Planarity : 0.004 0.048 4176 Dihedral : 6.360 83.881 3405 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.31 % Allowed : 10.05 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.15), residues: 3094 helix: 2.19 (0.12), residues: 1704 sheet: 0.07 (0.25), residues: 374 loop : 0.18 (0.20), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 789 HIS 0.003 0.001 HIS C 338 PHE 0.024 0.001 PHE A 615 TYR 0.020 0.002 TYR B 49 ARG 0.008 0.001 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 324 time to evaluate : 2.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.8635 (m-10) REVERT: B 815 ARG cc_start: 0.8583 (ttp-170) cc_final: 0.8371 (ttp80) REVERT: B 962 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7854 (tm-30) REVERT: C 63 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7244 (mm-40) REVERT: C 76 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8822 (mtm) REVERT: C 83 ASP cc_start: 0.7207 (t70) cc_final: 0.6788 (t70) REVERT: C 422 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: C 615 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7203 (p90) REVERT: C 673 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: C 765 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8390 (mtm-85) REVERT: C 868 LEU cc_start: 0.8755 (tp) cc_final: 0.8509 (tp) outliers start: 33 outliers final: 20 residues processed: 341 average time/residue: 2.4405 time to fit residues: 969.8445 Evaluate side-chains 343 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 317 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 962 GLU Chi-restraints excluded: chain B residue 966 ASP Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 993 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 89 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.111641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.093130 restraints weight = 82304.131| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.31 r_work: 0.2928 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24119 Z= 0.322 Angle : 0.531 5.172 32732 Z= 0.284 Chirality : 0.042 0.166 3842 Planarity : 0.005 0.048 4176 Dihedral : 6.499 87.244 3405 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.27 % Allowed : 10.52 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.15), residues: 3094 helix: 2.07 (0.12), residues: 1709 sheet: 0.05 (0.26), residues: 373 loop : 0.16 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 789 HIS 0.003 0.001 HIS B 596 PHE 0.033 0.002 PHE A 615 TYR 0.023 0.002 TYR B 49 ARG 0.007 0.001 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 325 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 734 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6467 (tp30) REVERT: B 182 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8612 (m-10) REVERT: B 589 LYS cc_start: 0.8569 (ptmt) cc_final: 0.8227 (tttt) REVERT: B 734 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6315 (tm-30) REVERT: B 962 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: B 1008 MET cc_start: 0.8603 (ttp) cc_final: 0.8196 (mtp) REVERT: C 63 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7214 (mm-40) REVERT: C 76 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8846 (mtm) REVERT: C 422 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8071 (mt-10) REVERT: C 615 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.7548 (p90) REVERT: C 673 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6780 (mp0) REVERT: C 868 LEU cc_start: 0.8789 (tp) cc_final: 0.8539 (tp) outliers start: 32 outliers final: 20 residues processed: 343 average time/residue: 2.4457 time to fit residues: 976.7855 Evaluate side-chains 347 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 319 time to evaluate : 2.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 734 GLU Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 862 MET Chi-restraints excluded: chain B residue 962 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 732 ASP Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 896 SER Chi-restraints excluded: chain C residue 993 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 280 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 293 optimal weight: 0.5980 chunk 198 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 224 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.098810 restraints weight = 79244.806| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.27 r_work: 0.2986 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24119 Z= 0.154 Angle : 0.477 5.793 32732 Z= 0.254 Chirality : 0.040 0.155 3842 Planarity : 0.004 0.053 4176 Dihedral : 6.180 82.635 3405 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.03 % Allowed : 11.04 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.15), residues: 3094 helix: 2.32 (0.12), residues: 1704 sheet: 0.04 (0.26), residues: 377 loop : 0.24 (0.21), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 754 HIS 0.002 0.001 HIS C 338 PHE 0.022 0.001 PHE A 615 TYR 0.018 0.001 TYR B 877 ARG 0.010 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 327 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: A 205 THR cc_start: 0.8411 (m) cc_final: 0.8200 (m) REVERT: A 314 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7330 (tm-30) REVERT: B 182 TYR cc_start: 0.8858 (OUTLIER) cc_final: 0.8526 (m-10) REVERT: B 543 VAL cc_start: 0.8452 (t) cc_final: 0.8161 (t) REVERT: B 589 LYS cc_start: 0.8528 (ptmt) cc_final: 0.8203 (tttt) REVERT: B 962 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: B 1008 MET cc_start: 0.8584 (ttp) cc_final: 0.8170 (mtp) REVERT: C 63 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7155 (mm-40) REVERT: C 76 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8777 (mtm) REVERT: C 422 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: C 435 MET cc_start: 0.8181 (mmm) cc_final: 0.7743 (mmm) REVERT: C 615 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7458 (p90) REVERT: C 868 LEU cc_start: 0.8745 (tp) cc_final: 0.8491 (tp) outliers start: 26 outliers final: 12 residues processed: 339 average time/residue: 2.5155 time to fit residues: 999.8510 Evaluate side-chains 343 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 325 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 962 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 993 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 237 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 222 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 273 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.099369 restraints weight = 79308.825| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.28 r_work: 0.2985 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 24119 Z= 0.159 Angle : 0.476 5.818 32732 Z= 0.253 Chirality : 0.040 0.154 3842 Planarity : 0.004 0.065 4176 Dihedral : 6.073 82.532 3405 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.79 % Allowed : 11.52 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.15), residues: 3094 helix: 2.39 (0.12), residues: 1705 sheet: 0.06 (0.26), residues: 371 loop : 0.24 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 754 HIS 0.002 0.000 HIS B 526 PHE 0.032 0.001 PHE A 615 TYR 0.017 0.001 TYR B 877 ARG 0.011 0.000 ARG B 620 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6188 Ramachandran restraints generated. 3094 Oldfield, 0 Emsley, 3094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 331 time to evaluate : 2.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 THR cc_start: 0.8412 (m) cc_final: 0.8210 (m) REVERT: A 314 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7338 (tm-30) REVERT: A 1020 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.6494 (p90) REVERT: B 182 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8515 (m-10) REVERT: B 543 VAL cc_start: 0.8447 (t) cc_final: 0.8160 (t) REVERT: B 589 LYS cc_start: 0.8505 (ptmt) cc_final: 0.8192 (tttt) REVERT: B 962 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7815 (tm-30) REVERT: C 63 GLN cc_start: 0.7662 (mm-40) cc_final: 0.7117 (mm-40) REVERT: C 76 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8780 (mtm) REVERT: C 422 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: C 435 MET cc_start: 0.8151 (mmm) cc_final: 0.7653 (mmm) REVERT: C 615 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7547 (p90) REVERT: C 868 LEU cc_start: 0.8734 (tp) cc_final: 0.8474 (tp) outliers start: 20 outliers final: 13 residues processed: 340 average time/residue: 2.4638 time to fit residues: 974.1833 Evaluate side-chains 346 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 327 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 867 ARG Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1020 PHE Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 962 GLU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 422 GLU Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 862 MET Chi-restraints excluded: chain C residue 896 SER Chi-restraints excluded: chain C residue 993 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 196 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 180 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.112606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.093150 restraints weight = 82915.006| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.47 r_work: 0.2932 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24119 Z= 0.213 Angle : 0.489 5.756 32732 Z= 0.259 Chirality : 0.040 0.157 3842 Planarity : 0.004 0.056 4176 Dihedral : 6.081 82.449 3405 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.91 % Allowed : 11.52 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.15), residues: 3094 helix: 2.36 (0.12), residues: 1704 sheet: 0.09 (0.26), residues: 377 loop : 0.25 (0.21), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 789 HIS 0.002 0.001 HIS C 338 PHE 0.032 0.001 PHE A 615 TYR 0.016 0.001 TYR B 877 ARG 0.010 0.000 ARG C 765 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 24285.62 seconds wall clock time: 413 minutes 34.44 seconds (24814.44 seconds total)