Starting phenix.real_space_refine on Tue Dec 31 14:29:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfn_44501/12_2024/9bfn_44501_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfn_44501/12_2024/9bfn_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_44501/12_2024/9bfn_44501.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfn_44501/12_2024/9bfn_44501.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfn_44501/12_2024/9bfn_44501_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfn_44501/12_2024/9bfn_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-5532/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: 15.98, 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 2.8 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: 3.26 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: 19.23 Time building geometry restraints manager: 11.37 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.320 Construct map_model_manager: 0.610 Extract box with map and model: 1.250 Check model and map are aligned: 0.260 Set scattering table: 0.320 Process input model: 77.840 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:9.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.130 ------------------------------------------------------------------------------- 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 : 2.711 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: 2.5492 time to fit residues: 1167.4972 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 : 2.656 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 667 ASN cc_start: 0.8152 (t0) cc_final: 0.7857 (t0) REVERT: C 20 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8076 (mtt) REVERT: C 76 MET cc_start: 0.8677 (mtp) cc_final: 0.8383 (mtm) REVERT: C 83 ASP cc_start: 0.6514 (t70) cc_final: 0.6263 (t70) REVERT: C 435 MET cc_start: 0.7931 (mmm) cc_final: 0.7714 (mmm) REVERT: C 456 MET cc_start: 0.8803 (ptt) cc_final: 0.8520 (ptt) REVERT: C 673 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: C 686 ASP cc_start: 0.7694 (t0) cc_final: 0.7493 (t0) REVERT: C 714 THR cc_start: 0.9102 (p) cc_final: 0.8884 (p) REVERT: C 868 LEU cc_start: 0.8580 (tp) cc_final: 0.8323 (tp) outliers start: 21 outliers final: 10 residues processed: 338 average time/residue: 2.6002 time to fit residues: 1013.8185 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 : 2.659 ------------------------------------------------------------------------------- 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 155 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 281 optimal weight: 0.0980 chunk 303 optimal weight: 3.9990 chunk 250 optimal weight: 4.9990 chunk 278 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24119 Z= 0.309 Angle : 0.528 5.290 32732 Z= 0.283 Chirality : 0.042 0.171 3842 Planarity : 0.004 0.051 4176 Dihedral : 6.480 84.126 3405 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.07 % Allowed : 8.54 % Favored : 90.39 % 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: 1.74 (0.15), residues: 3094 helix: 2.05 (0.12), residues: 1712 sheet: -0.16 (0.24), residues: 407 loop : 0.24 (0.21), residues: 975 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 0.019 0.001 PHE A 682 TYR 0.024 0.002 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 353 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 326 time to evaluate : 2.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7294 (t0) REVERT: B 667 ASN cc_start: 0.8071 (t0) cc_final: 0.7796 (t0) REVERT: B 962 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: C 20 MET cc_start: 0.8670 (mtt) cc_final: 0.8381 (mtt) REVERT: C 63 GLN cc_start: 0.7220 (mm-40) cc_final: 0.6859 (mm110) REVERT: C 76 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8423 (mtm) REVERT: C 83 ASP cc_start: 0.6625 (t70) cc_final: 0.6406 (t70) REVERT: C 435 MET cc_start: 0.8236 (mmm) cc_final: 0.7951 (mmm) REVERT: C 456 MET cc_start: 0.8779 (ptt) cc_final: 0.8523 (ptt) REVERT: C 673 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6610 (mp0) REVERT: C 714 THR cc_start: 0.9148 (p) cc_final: 0.8925 (p) REVERT: C 868 LEU cc_start: 0.8635 (tp) cc_final: 0.8374 (tp) outliers start: 27 outliers final: 14 residues processed: 338 average time/residue: 2.4529 time to fit residues: 961.3096 Evaluate side-chains 325 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 307 time to evaluate : 2.678 ------------------------------------------------------------------------------- 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 277 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 145 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 chunk 282 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1301 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= 0.250 Angle : 0.505 5.197 32732 Z= 0.270 Chirality : 0.041 0.163 3842 Planarity : 0.004 0.057 4176 Dihedral : 6.439 84.094 3405 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.27 % Allowed : 9.25 % Favored : 89.48 % 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: 1.78 (0.15), residues: 3094 helix: 2.08 (0.12), residues: 1712 sheet: 0.04 (0.25), residues: 374 loop : 0.16 (0.20), residues: 1008 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 0.021 0.002 TYR B 877 ARG 0.005 0.000 ARG B 558 *********************** 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 354 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 322 time to evaluate : 2.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 734 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6004 (tm-30) REVERT: B 962 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: C 63 GLN cc_start: 0.7241 (mm-40) cc_final: 0.6871 (mm-40) REVERT: C 76 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8418 (mtm) REVERT: C 83 ASP cc_start: 0.6571 (t70) cc_final: 0.6330 (t70) REVERT: C 435 MET cc_start: 0.8253 (mmm) cc_final: 0.7967 (mmm) REVERT: C 673 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6569 (mp0) REVERT: C 868 LEU cc_start: 0.8615 (tp) cc_final: 0.8351 (tp) outliers start: 32 outliers final: 15 residues processed: 339 average time/residue: 2.4446 time to fit residues: 957.1315 Evaluate side-chains 329 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 310 time to evaluate : 2.748 ------------------------------------------------------------------------------- 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 732 ASP 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 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 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 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 248 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 24119 Z= 0.286 Angle : 0.518 5.205 32732 Z= 0.277 Chirality : 0.041 0.166 3842 Planarity : 0.004 0.059 4176 Dihedral : 6.527 86.791 3405 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.27 % Allowed : 9.61 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.76 (0.15), residues: 3094 helix: 2.06 (0.12), residues: 1713 sheet: 0.04 (0.25), residues: 374 loop : 0.17 (0.20), residues: 1007 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 0.018 0.001 PHE A 682 TYR 0.022 0.002 TYR B 49 ARG 0.009 0.001 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 354 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 322 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7551 (mp0) REVERT: C 63 GLN cc_start: 0.7306 (mm-40) cc_final: 0.6924 (mm-40) REVERT: C 76 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8407 (mtm) REVERT: C 83 ASP cc_start: 0.6605 (t70) cc_final: 0.6344 (t70) REVERT: C 395 MET cc_start: 0.8351 (mmp) cc_final: 0.7990 (mmp) REVERT: C 422 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: C 435 MET cc_start: 0.8311 (mmm) cc_final: 0.8084 (mmm) REVERT: C 573 MET cc_start: 0.8431 (mmm) cc_final: 0.8221 (tpp) REVERT: C 673 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6585 (mp0) REVERT: C 868 LEU cc_start: 0.8688 (tp) cc_final: 0.8429 (tp) outliers start: 32 outliers final: 13 residues processed: 337 average time/residue: 2.4032 time to fit residues: 943.5335 Evaluate side-chains 332 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 315 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 732 ASP 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 C residue 76 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 24119 Z= 0.315 Angle : 0.529 5.228 32732 Z= 0.283 Chirality : 0.042 0.167 3842 Planarity : 0.005 0.067 4176 Dihedral : 6.609 88.825 3405 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.51 % Allowed : 9.89 % Favored : 88.60 % 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: 1.67 (0.15), residues: 3094 helix: 1.99 (0.12), residues: 1713 sheet: -0.06 (0.25), residues: 385 loop : 0.14 (0.20), residues: 996 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 0.023 0.001 PHE A 615 TYR 0.023 0.002 TYR B 49 ARG 0.010 0.001 ARG C 765 *********************** 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 356 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 318 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7314 (tm-30) REVERT: B 734 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.6004 (tm-30) REVERT: B 962 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7359 (tm-30) REVERT: C 63 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6982 (mm-40) REVERT: C 76 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8473 (mtm) REVERT: C 395 MET cc_start: 0.8426 (mmp) cc_final: 0.8176 (mmp) REVERT: C 422 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: C 615 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7228 (p90) REVERT: C 673 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: C 868 LEU cc_start: 0.8697 (tp) cc_final: 0.8439 (tp) outliers start: 38 outliers final: 20 residues processed: 340 average time/residue: 2.4180 time to fit residues: 958.0645 Evaluate side-chains 339 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 313 time to evaluate : 2.733 ------------------------------------------------------------------------------- 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 993 THR Chi-restraints excluded: chain B residue 148 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 734 GLU 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 615 PHE Chi-restraints excluded: chain C residue 673 GLU Chi-restraints excluded: chain C residue 732 ASP Chi-restraints excluded: chain C residue 807 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 251 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 181 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24119 Z= 0.312 Angle : 0.531 5.207 32732 Z= 0.284 Chirality : 0.042 0.168 3842 Planarity : 0.005 0.074 4176 Dihedral : 6.651 88.615 3405 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.59 % Allowed : 10.41 % Favored : 88.01 % 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: 1.66 (0.15), residues: 3094 helix: 2.00 (0.12), residues: 1707 sheet: -0.06 (0.25), residues: 385 loop : 0.12 (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 0.023 0.001 PHE A 615 TYR 0.021 0.002 TYR B 49 ARG 0.013 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 360 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 320 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 PHE cc_start: 0.8016 (p90) cc_final: 0.7766 (p90) REVERT: B 543 VAL cc_start: 0.8386 (t) cc_final: 0.8111 (t) REVERT: B 734 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5989 (tm-30) REVERT: B 962 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: C 63 GLN cc_start: 0.7305 (mm-40) cc_final: 0.6956 (mm-40) REVERT: C 76 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8474 (mtm) REVERT: C 395 MET cc_start: 0.8408 (mmp) cc_final: 0.8170 (mmp) REVERT: C 422 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: C 615 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7588 (p90) REVERT: C 673 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: C 868 LEU cc_start: 0.8704 (tp) cc_final: 0.8442 (tp) outliers start: 40 outliers final: 24 residues processed: 342 average time/residue: 2.3820 time to fit residues: 944.0790 Evaluate side-chains 345 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 315 time to evaluate : 2.672 ------------------------------------------------------------------------------- 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 977 MET Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 408 ASP Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 544 LEU 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 76 MET Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR 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 807 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24119 Z= 0.323 Angle : 0.537 5.222 32732 Z= 0.287 Chirality : 0.042 0.168 3842 Planarity : 0.005 0.080 4176 Dihedral : 6.677 86.521 3405 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.43 % Allowed : 10.96 % Favored : 87.61 % 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: 1.64 (0.15), residues: 3094 helix: 1.97 (0.12), residues: 1706 sheet: -0.06 (0.25), residues: 384 loop : 0.12 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 789 HIS 0.002 0.001 HIS C 338 PHE 0.021 0.001 PHE A 615 TYR 0.020 0.002 TYR B 877 ARG 0.013 0.001 ARG C 765 *********************** 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 354 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 318 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.8519 (m-10) REVERT: B 589 LYS cc_start: 0.8229 (ptmt) cc_final: 0.7921 (tttt) REVERT: B 734 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6051 (tm-30) REVERT: B 962 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: C 63 GLN cc_start: 0.7321 (mm-40) cc_final: 0.6997 (mm-40) REVERT: C 76 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8482 (mtm) REVERT: C 615 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7777 (p90) REVERT: C 868 LEU cc_start: 0.8718 (tp) cc_final: 0.8425 (tp) outliers start: 36 outliers final: 22 residues processed: 339 average time/residue: 2.4943 time to fit residues: 983.5962 Evaluate side-chains 339 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 312 time to evaluate : 2.723 ------------------------------------------------------------------------------- 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 977 MET Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 148 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 486 LEU Chi-restraints excluded: chain B residue 544 LEU 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 76 MET Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 615 PHE Chi-restraints excluded: chain C residue 732 ASP Chi-restraints excluded: chain C residue 807 SER 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 270 optimal weight: 0.5980 chunk 285 optimal weight: 0.2980 chunk 260 optimal weight: 0.6980 chunk 277 optimal weight: 0.9980 chunk 167 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 217 optimal weight: 3.9990 chunk 85 optimal weight: 0.0870 chunk 250 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1646 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= 0.137 Angle : 0.476 5.940 32732 Z= 0.253 Chirality : 0.040 0.155 3842 Planarity : 0.004 0.090 4176 Dihedral : 6.259 85.308 3405 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.79 % Allowed : 11.91 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.00 (0.15), residues: 3094 helix: 2.31 (0.12), residues: 1704 sheet: 0.03 (0.25), residues: 377 loop : 0.22 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 754 HIS 0.002 0.001 HIS B 338 PHE 0.023 0.001 PHE A 615 TYR 0.017 0.001 TYR B 877 ARG 0.015 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 349 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 329 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 543 VAL cc_start: 0.8367 (t) cc_final: 0.8092 (t) REVERT: B 589 LYS cc_start: 0.8135 (ptmt) cc_final: 0.7844 (tttt) REVERT: B 962 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: C 63 GLN cc_start: 0.7265 (mm-40) cc_final: 0.6956 (mm-40) REVERT: C 76 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8404 (mtm) REVERT: C 435 MET cc_start: 0.7892 (mmm) cc_final: 0.7502 (mmm) REVERT: C 615 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7663 (p90) REVERT: C 868 LEU cc_start: 0.8626 (tp) cc_final: 0.8345 (tp) outliers start: 20 outliers final: 12 residues processed: 339 average time/residue: 2.4125 time to fit residues: 954.1405 Evaluate side-chains 330 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 315 time to evaluate : 2.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 993 THR 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 615 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 0.8980 chunk 293 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 204 optimal weight: 0.0970 chunk 307 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24119 Z= 0.188 Angle : 0.488 5.634 32732 Z= 0.258 Chirality : 0.040 0.156 3842 Planarity : 0.004 0.095 4176 Dihedral : 6.202 85.254 3405 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.71 % Allowed : 12.11 % Favored : 87.17 % 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: 2.05 (0.15), residues: 3094 helix: 2.34 (0.12), residues: 1701 sheet: 0.07 (0.26), residues: 377 loop : 0.24 (0.20), residues: 1016 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 0.030 0.001 PHE A 615 TYR 0.024 0.001 TYR B 182 ARG 0.015 0.000 ARG C 765 ********************** 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 336 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 318 time to evaluate : 2.800 Fit side-chains revert: symmetry clash REVERT: B 543 VAL cc_start: 0.8350 (t) cc_final: 0.8080 (t) REVERT: B 589 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7860 (tttt) REVERT: B 962 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7250 (tm-30) REVERT: C 63 GLN cc_start: 0.7284 (mm-40) cc_final: 0.6974 (mm-40) REVERT: C 76 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8428 (mtm) REVERT: C 435 MET cc_start: 0.7926 (mmm) cc_final: 0.7440 (mmm) REVERT: C 615 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7666 (p90) REVERT: C 765 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.8176 (mtm-85) REVERT: C 868 LEU cc_start: 0.8654 (tp) cc_final: 0.8390 (tp) outliers start: 18 outliers final: 11 residues processed: 325 average time/residue: 2.4639 time to fit residues: 926.1657 Evaluate side-chains 330 residues out of total 2518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 316 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 674 LEU Chi-restraints excluded: chain A residue 732 ASP Chi-restraints excluded: chain A residue 993 THR 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 615 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 3.9990 chunk 261 optimal weight: 0.0570 chunk 75 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 252 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- 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 = 0.3310 r_free = 0.3310 target = 0.117378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.099390 restraints weight = 79177.555| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.27 r_work: 0.2983 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24119 Z= 0.176 Angle : 0.485 5.709 32732 Z= 0.257 Chirality : 0.040 0.154 3842 Planarity : 0.004 0.089 4176 Dihedral : 6.098 83.523 3405 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.71 % Allowed : 12.27 % Favored : 87.01 % 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: 2.38 (0.12), residues: 1702 sheet: -0.01 (0.25), residues: 388 loop : 0.30 (0.21), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 754 HIS 0.002 0.000 HIS C 338 PHE 0.030 0.001 PHE A 615 TYR 0.018 0.001 TYR B 182 ARG 0.015 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: 14047.72 seconds wall clock time: 240 minutes 19.73 seconds (14419.73 seconds total)