Starting phenix.real_space_refine on Sat Jul 4 21:40:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kge_22867/07_2026/7kge_22867.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kge_22867/07_2026/7kge_22867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kge_22867/07_2026/7kge_22867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kge_22867/07_2026/7kge_22867.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kge_22867/07_2026/7kge_22867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kge_22867/07_2026/7kge_22867.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kge_22867/07_2026/7kge_22867.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kge_22867/07_2026/7kge_22867.cif" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.189 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 135 5.16 5 C 15213 2.51 5 N 3795 2.21 5 O 4332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23478 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "B" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "C" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7785 Classifications: {'peptide': 1020} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 973} Chain breaks: 1 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Time building chain proxies: 4.68, per 1000 atoms: 0.20 Number of scatterers: 23478 At special positions: 0 Unit cell: (124.2, 117.72, 141.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 135 16.00 P 3 15.00 O 4332 8.00 N 3795 7.00 C 15213 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.0 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5706 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 24 sheets defined 61.5% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 8 through 30 removed outlier: 4.331A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Proline residue: A 28 - end of helix Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 61 through 70 removed outlier: 3.647A pdb=" N GLU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 removed outlier: 4.009A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 161 through 169 removed outlier: 3.993A pdb=" N GLU A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) 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 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 removed outlier: 4.146A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.758A pdb=" N ILE A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Proline residue: A 368 - end of helix Processing helix chain 'A' and resid 370 through 387 removed outlier: 3.736A pdb=" N ILE A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 406 removed outlier: 4.323A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 424 Processing helix chain 'A' and resid 426 through 454 removed outlier: 5.479A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.965A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 461 through 497 removed outlier: 3.688A pdb=" N GLN A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 3.747A pdb=" N LEU A 497 " --> pdb=" O CYS A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 534 removed outlier: 3.888A pdb=" N LYS A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS A 534 " --> pdb=" O LYS A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 556 removed outlier: 3.861A pdb=" N MET A 538 " --> pdb=" O HIS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 597 removed outlier: 4.366A pdb=" N ASP A 597 " --> pdb=" O ASN A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 635 through 651 removed outlier: 3.866A pdb=" N ASN A 649 " --> pdb=" O SER A 645 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 651 " --> pdb=" O MET A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 700 removed outlier: 3.658A pdb=" N LYS A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 731 Processing helix chain 'A' and resid 733 through 746 removed outlier: 3.754A pdb=" N VAL A 737 " --> pdb=" O LYS A 733 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N MET A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 771 Processing helix chain 'A' and resid 773 through 778 removed outlier: 3.759A pdb=" N ILE A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 841 removed outlier: 3.656A pdb=" N LYS A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 863 Processing helix chain 'A' and resid 863 through 884 Processing helix chain 'A' and resid 887 through 893 Processing helix chain 'A' and resid 895 through 911 removed outlier: 3.656A pdb=" N GLY A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 946 removed outlier: 3.679A pdb=" N ASN A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 981 removed outlier: 4.969A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 986 through 1027 removed outlier: 3.994A pdb=" N LEU A 993 " --> pdb=" O THR A 989 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE A1009 " --> pdb=" O THR A1005 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE A1010 " --> pdb=" O ILE A1006 " (cutoff:3.500A) Proline residue: A1013 - end of helix Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.767A pdb=" N ILE B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 7 " --> pdb=" O GLN B 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 7' Processing helix chain 'B' and resid 8 through 27 removed outlier: 3.743A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 61 through 71 removed outlier: 4.052A pdb=" N GLY B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.848A pdb=" N ALA B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL 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 161 Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.731A pdb=" N ARG B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 262 through 265 No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 298 through 315 removed outlier: 3.917A pdb=" N LEU B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 360 removed outlier: 3.777A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 370 Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 370 through 387 removed outlier: 3.625A pdb=" N ILE B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 405 removed outlier: 4.498A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 424 Processing helix chain 'B' and resid 426 through 453 removed outlier: 5.639A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 4.228A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 4.005A pdb=" N ALA B 457 " --> pdb=" O PHE B 453 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 458' Processing helix chain 'B' and resid 461 through 496 removed outlier: 3.709A pdb=" N GLN B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.034A 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 509 through 534 removed outlier: 4.048A pdb=" N LYS B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 580 through 595 Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 635 through 651 removed outlier: 4.903A pdb=" N ASN B 649 " --> pdb=" O SER B 645 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR B 651 " --> pdb=" O MET B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 701 Processing helix chain 'B' and resid 723 through 731 Processing helix chain 'B' and resid 733 through 745 removed outlier: 4.444A pdb=" N MET B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 Processing helix chain 'B' and resid 773 through 779 removed outlier: 3.992A pdb=" N ILE B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 787 No H-bonds generated for 'chain 'B' and resid 785 through 787' Processing helix chain 'B' and resid 792 through 795 No H-bonds generated for 'chain 'B' and resid 792 through 795' Processing helix chain 'B' and resid 827 through 840 Processing helix chain 'B' and resid 852 through 883 removed outlier: 3.504A pdb=" N MET B 864 " --> pdb=" O SER B 860 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA B 865 " --> pdb=" O GLU B 861 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N PHE B 866 " --> pdb=" O SER B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 911 removed outlier: 3.583A pdb=" N LEU B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 895 " --> pdb=" O SER B 891 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL B 896 " --> pdb=" O VAL B 892 " (cutoff:3.500A) Proline residue: B 897 - end of helix removed outlier: 3.551A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 947 removed outlier: 3.941A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 939 " --> pdb=" O LEU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 961 Processing helix chain 'B' and resid 961 through 976 removed outlier: 3.718A pdb=" N PHE B 972 " --> pdb=" O THR B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 986 through 1009 removed outlier: 3.805A pdb=" N GLN B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1011 through 1027 Processing helix chain 'C' and resid 2 through 8 removed outlier: 3.521A pdb=" N ILE C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 removed outlier: 4.067A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Proline residue: C 28 - end of helix Processing helix chain 'C' and resid 53 through 61 removed outlier: 3.503A pdb=" N ILE C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 removed outlier: 3.716A pdb=" N GLU C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 114 Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 161 through 169 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 262 through 265 No H-bonds generated for 'chain 'C' and resid 262 through 265' Processing helix chain 'C' and resid 298 through 315 removed outlier: 4.097A pdb=" N LEU C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 360 removed outlier: 3.557A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE C 335 " --> pdb=" O PRO C 331 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 336 " --> pdb=" O PHE C 332 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 357 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE C 358 " --> pdb=" O VAL C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 370 Proline residue: C 368 - end of helix Processing helix chain 'C' and resid 370 through 387 Processing helix chain 'C' and resid 391 through 403 removed outlier: 4.469A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 423 Processing helix chain 'C' and resid 426 through 453 removed outlier: 3.555A pdb=" N THR C 431 " --> pdb=" O PRO C 427 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER C 432 " --> pdb=" O LYS C 428 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 4.080A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 461 through 496 removed outlier: 3.591A pdb=" N VAL C 465 " --> pdb=" O GLY C 461 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 4.380A 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 509 through 534 Processing helix chain 'C' and resid 534 through 556 removed outlier: 4.003A pdb=" N MET C 538 " --> pdb=" O HIS C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 597 removed outlier: 4.062A pdb=" N ASP C 597 " --> pdb=" O ASN C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 648 Processing helix chain 'C' and resid 683 through 701 Processing helix chain 'C' and resid 723 through 731 Processing helix chain 'C' and resid 733 through 743 removed outlier: 3.626A pdb=" N VAL C 737 " --> pdb=" O LYS C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 771 Processing helix chain 'C' and resid 773 through 780 removed outlier: 3.643A pdb=" N ILE C 777 " --> pdb=" O GLN C 773 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C 780 " --> pdb=" O ASP C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 795 No H-bonds generated for 'chain 'C' and resid 792 through 795' Processing helix chain 'C' and resid 827 through 841 removed outlier: 3.635A pdb=" N LYS C 841 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 884 removed outlier: 3.620A pdb=" N MET C 864 " --> pdb=" O SER C 860 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ALA C 865 " --> pdb=" O GLU C 861 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N PHE C 866 " --> pdb=" O SER C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 910 removed outlier: 3.951A pdb=" N VAL C 895 " --> pdb=" O SER C 891 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL C 896 " --> pdb=" O VAL C 892 " (cutoff:3.500A) Proline residue: C 897 - end of helix Processing helix chain 'C' and resid 915 through 946 removed outlier: 4.949A pdb=" N PHE C 939 " --> pdb=" O LEU C 935 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET C 942 " --> pdb=" O GLU C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 976 removed outlier: 3.608A pdb=" N ALA C 958 " --> pdb=" O THR C 954 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix Processing helix chain 'C' and resid 976 through 981 Processing helix chain 'C' and resid 986 through 1007 removed outlier: 3.649A pdb=" N GLN C 990 " --> pdb=" O SER C 986 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL C 997 " --> pdb=" O LEU C 993 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1027 Proline residue: C1013 - end of helix removed outlier: 4.459A pdb=" N PHE C1018 " --> pdb=" O VAL C1014 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C1020 " --> pdb=" O PHE C1016 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLY C1021 " --> pdb=" O ILE C1017 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.212A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N SER A 817 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 709 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ALA A 819 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL A 707 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 821 " --> pdb=" O TYR A 705 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.212A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 6.907A pdb=" N LEU A 139 " --> pdb=" O PRO A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.748A pdb=" N ALA A 286 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 603 " --> pdb=" O THR A 625 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.304A pdb=" N LYS A 182 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLN A 761 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ARG A 758 " --> pdb=" O PRO A 754 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLN A 760 " --> pdb=" O ASP A 752 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP A 752 " --> pdb=" O GLN A 760 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 762 " --> pdb=" O ILE A 750 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 219 removed outlier: 8.137A pdb=" N LEU C 720 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER A 235 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE C 722 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 250 through 252 Processing sheet with id=AA8, first strand: chain 'A' and resid 796 through 803 removed outlier: 7.506A pdb=" N ASP A 716 " --> pdb=" O PRO B 233 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N SER B 235 " --> pdb=" O ASP A 716 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE A 718 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLN B 237 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU A 720 " --> pdb=" O GLN B 237 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 781 through 782 Processing sheet with id=AB1, first strand: chain 'B' and resid 127 through 131 removed outlier: 4.347A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER B 817 " --> pdb=" O GLU B 710 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET B 706 " --> pdb=" O ILE B 821 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 127 through 131 removed outlier: 4.347A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 7.260A pdb=" N LEU 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: 3.614A pdb=" N ALA B 286 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ILE 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: 7.664A pdb=" N LYS B 182 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ILE B 763 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N MET B 184 " --> pdb=" O ILE B 763 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLN B 765 " --> pdb=" O MET B 184 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ILE B 186 " --> pdb=" O GLN B 765 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N TYR B 749 " --> pdb=" O VAL B 764 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 250 through 252 Processing sheet with id=AB7, first strand: chain 'B' and resid 796 through 803 removed outlier: 3.548A pdb=" N GLY B 715 " --> pdb=" O ALA B 803 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 781 through 783 Processing sheet with id=AB9, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.224A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE C 821 " --> pdb=" O MET C 706 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET C 706 " --> pdb=" O ILE C 821 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.224A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N SER C 673 " --> pdb=" O THR C 851 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 7.040A pdb=" N LEU 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: 4.147A pdb=" N ILE C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 603 " --> pdb=" O THR C 625 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL C 619 " --> pdb=" O GLY C 609 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 272 removed outlier: 7.985A pdb=" N LYS C 182 " --> pdb=" O GLN C 761 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N ILE C 763 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET C 184 " --> pdb=" O ILE C 763 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLN C 765 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE C 186 " --> pdb=" O GLN C 765 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG C 758 " --> pdb=" O PRO C 754 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLN C 760 " --> pdb=" O ASP C 752 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP C 752 " --> pdb=" O GLN C 760 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL C 762 " --> pdb=" O ILE C 750 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 252 Processing sheet with id=AC6, first strand: chain 'C' and resid 781 through 782 1610 hydrogen bonds defined for protein. 4653 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.52 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 3843 1.26 - 1.39: 5194 1.39 - 1.53: 13776 1.53 - 1.67: 824 1.67 - 1.81: 264 Bond restraints: 23901 Sorted by residual: bond pdb=" C LYS C 931 " pdb=" O LYS C 931 " ideal model delta sigma weight residual 1.237 1.116 0.120 1.19e-02 7.06e+03 1.02e+02 bond pdb=" C MET A 539 " pdb=" O MET A 539 " ideal model delta sigma weight residual 1.237 1.120 0.116 1.19e-02 7.06e+03 9.58e+01 bond pdb=" C SER A 828 " pdb=" O SER A 828 " ideal model delta sigma weight residual 1.237 1.128 0.108 1.19e-02 7.06e+03 8.30e+01 bond pdb=" C LYS B 931 " pdb=" O LYS B 931 " ideal model delta sigma weight residual 1.237 1.134 0.102 1.19e-02 7.06e+03 7.38e+01 bond pdb=" C PHE A 998 " pdb=" O PHE A 998 " ideal model delta sigma weight residual 1.237 1.141 0.096 1.19e-02 7.06e+03 6.46e+01 ... (remaining 23896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 32093 3.44 - 6.88: 267 6.88 - 10.32: 17 10.32 - 13.76: 6 13.76 - 17.20: 2 Bond angle restraints: 32385 Sorted by residual: angle pdb=" CA MET A 539 " pdb=" C MET A 539 " pdb=" O MET A 539 " ideal model delta sigma weight residual 120.42 111.54 8.88 1.06e+00 8.90e-01 7.03e+01 angle pdb=" CA SER A 828 " pdb=" C SER A 828 " pdb=" O SER A 828 " ideal model delta sigma weight residual 120.42 111.54 8.88 1.06e+00 8.90e-01 7.02e+01 angle pdb=" CA MET A 539 " pdb=" C MET A 539 " pdb=" N VAL A 540 " ideal model delta sigma weight residual 117.39 127.76 -10.37 1.24e+00 6.50e-01 6.99e+01 angle pdb=" CA ILE B 21 " pdb=" C ILE B 21 " pdb=" O ILE B 21 " ideal model delta sigma weight residual 120.47 111.79 8.68 1.08e+00 8.57e-01 6.46e+01 angle pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" N ALA B 12 " ideal model delta sigma weight residual 117.30 125.82 -8.52 1.16e+00 7.43e-01 5.39e+01 ... (remaining 32380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 14198 35.29 - 70.57: 263 70.57 - 105.86: 24 105.86 - 141.14: 0 141.14 - 176.43: 5 Dihedral angle restraints: 14490 sinusoidal: 5673 harmonic: 8817 Sorted by residual: dihedral pdb=" N1 PTY B1102 " pdb=" C2 PTY B1102 " pdb=" C3 PTY B1102 " pdb=" O11 PTY B1102 " ideal model delta sinusoidal sigma weight residual 65.33 -118.24 -176.43 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PTY B1101 " pdb=" O11 PTY B1101 " pdb=" P1 PTY B1101 " pdb=" O12 PTY B1101 " ideal model delta sinusoidal sigma weight residual -59.77 102.66 -162.43 1 3.00e+01 1.11e-03 2.08e+01 dihedral pdb=" C ASN C 932 " pdb=" N ASN C 932 " pdb=" CA ASN C 932 " pdb=" CB ASN C 932 " ideal model delta harmonic sigma weight residual -122.60 -111.35 -11.25 0 2.50e+00 1.60e-01 2.03e+01 ... (remaining 14487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.306: 3871 0.306 - 0.613: 1 0.613 - 0.919: 0 0.919 - 1.226: 0 1.226 - 1.532: 1 Chirality restraints: 3873 Sorted by residual: chirality pdb=" CB VAL A1014 " pdb=" CA VAL A1014 " pdb=" CG1 VAL A1014 " pdb=" CG2 VAL A1014 " both_signs ideal model delta sigma weight residual False -2.63 -1.10 -1.53 2.00e-01 2.50e+01 5.87e+01 chirality pdb=" CB ILE B 21 " pdb=" CA ILE B 21 " pdb=" CG1 ILE B 21 " pdb=" CG2 ILE B 21 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" CA ARG B 363 " pdb=" N ARG B 363 " pdb=" C ARG B 363 " pdb=" CB ARG B 363 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 3870 not shown) Planarity restraints: 4062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 704 " 0.023 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C PHE C 704 " -0.075 2.00e-02 2.50e+03 pdb=" O PHE C 704 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR C 705 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 573 " 0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C PHE B 573 " -0.064 2.00e-02 2.50e+03 pdb=" O PHE B 573 " 0.024 2.00e-02 2.50e+03 pdb=" N GLN B 574 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 930 " -0.015 2.00e-02 2.50e+03 3.15e-02 9.93e+00 pdb=" C ALA A 930 " 0.054 2.00e-02 2.50e+03 pdb=" O ALA A 930 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS A 931 " -0.018 2.00e-02 2.50e+03 ... (remaining 4059 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 239 2.66 - 3.22: 22918 3.22 - 3.78: 35727 3.78 - 4.34: 50063 4.34 - 4.90: 83352 Nonbonded interactions: 192299 Sorted by model distance: nonbonded pdb=" O THR A 546 " pdb=" OG1 THR A 549 " model vdw 2.101 3.040 nonbonded pdb=" O VAL C 38 " pdb=" OG SER C 462 " model vdw 2.124 3.040 nonbonded pdb=" O ALA B 52 " pdb=" OG1 THR B 53 " model vdw 2.190 3.040 nonbonded pdb=" O ASN A 161 " pdb=" OE1 GLU A 165 " model vdw 2.197 3.040 nonbonded pdb=" O VAL C 362 " pdb=" OG1 THR C 365 " model vdw 2.209 3.040 ... (remaining 192294 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 1027) selection = (chain 'B' and resid 1 through 1027) selection = chain 'C' } 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.670 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 0.123 23901 Z= 0.298 Angle : 0.768 17.200 32385 Z= 0.477 Chirality : 0.051 1.532 3873 Planarity : 0.006 0.075 4062 Dihedral : 14.696 176.425 8784 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.90 % Allowed : 0.70 % Favored : 98.40 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.16), residues: 3048 helix: 1.85 (0.13), residues: 1683 sheet: 0.53 (0.22), residues: 454 loop : 0.05 (0.22), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 585 TYR 0.024 0.001 TYR A 749 PHE 0.029 0.001 PHE A 569 TRP 0.005 0.001 TRP B 556 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.30 (23901) covalent geometry : angle 0.76761 / 0.48 (32385) hydrogen bonds : bond 0.14685 / 10.04 ( 1529) hydrogen bonds : angle 5.70873 / 4.21 ( 4653) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 558 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 241 SER cc_start: 0.8128 (p) cc_final: 0.7812 (p) REVERT: A 483 LEU cc_start: 0.8335 (tp) cc_final: 0.8040 (tp) REVERT: A 849 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: A 923 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7238 (mt) REVERT: A 931 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7387 (ttpt) REVERT: A 948 MET cc_start: 0.7445 (ttm) cc_final: 0.6979 (ttp) REVERT: B 252 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7583 (mtmt) REVERT: B 264 ASP cc_start: 0.6878 (m-30) cc_final: 0.6634 (m-30) REVERT: B 385 LEU cc_start: 0.8136 (mt) cc_final: 0.7843 (mt) REVERT: B 570 MET cc_start: 0.8024 (ttm) cc_final: 0.7721 (ttm) REVERT: B 656 MET cc_start: 0.8921 (tpt) cc_final: 0.8596 (tpp) REVERT: B 931 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.5174 (pttp) REVERT: B 932 ASN cc_start: 0.8105 (t0) cc_final: 0.7850 (t0) REVERT: B 959 LYS cc_start: 0.6982 (ttpt) cc_final: 0.6597 (tptp) REVERT: B 963 ARG cc_start: 0.7693 (ttp-170) cc_final: 0.7454 (ttp80) REVERT: C 151 GLU cc_start: 0.6361 (pt0) cc_final: 0.6111 (pt0) REVERT: C 570 MET cc_start: 0.8628 (ttp) cc_final: 0.8376 (ttm) REVERT: C 681 ASN cc_start: 0.7280 (t0) cc_final: 0.6892 (t0) REVERT: C 684 MET cc_start: 0.8521 (mmm) cc_final: 0.8077 (mmm) REVERT: C 893 MET cc_start: 0.6519 (mmp) cc_final: 0.6247 (mmm) REVERT: C 931 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6704 (ttpt) outliers start: 23 outliers final: 9 residues processed: 577 average time/residue: 0.1425 time to fit residues: 132.3188 Evaluate side-chains 506 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 492 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 TYR Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain C residue 931 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 74 ASN A 161 ASN A 799 GLN A 859 GLN B 574 GLN B 594 ASN B 691 GLN C 176 GLN C 691 GLN C 714 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.155180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.128194 restraints weight = 26267.063| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.49 r_work: 0.3038 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 23901 Z= 0.225 Angle : 0.644 9.479 32385 Z= 0.338 Chirality : 0.046 0.264 3873 Planarity : 0.006 0.064 4062 Dihedral : 9.318 171.924 3317 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.18 % Allowed : 8.62 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.15), residues: 3048 helix: 1.65 (0.12), residues: 1695 sheet: 0.48 (0.22), residues: 459 loop : -0.05 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 185 TYR 0.021 0.002 TYR B 49 PHE 0.019 0.002 PHE B 672 TRP 0.007 0.001 TRP B 568 HIS 0.003 0.001 HIS A 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (23901) covalent geometry : angle 0.64415 / 0.34 (32385) hydrogen bonds : bond 0.05682 / 3.83 ( 1529) hydrogen bonds : angle 4.55043 / 3.30 ( 4653) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 517 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 241 SER cc_start: 0.8674 (p) cc_final: 0.8376 (p) REVERT: A 483 LEU cc_start: 0.8530 (tp) cc_final: 0.8277 (tp) REVERT: A 550 PHE cc_start: 0.7739 (OUTLIER) cc_final: 0.7515 (t80) REVERT: A 593 ASN cc_start: 0.7849 (m-40) cc_final: 0.7421 (m-40) REVERT: A 642 ASP cc_start: 0.7869 (m-30) cc_final: 0.7614 (m-30) REVERT: A 726 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7705 (tttt) REVERT: A 910 ARG cc_start: 0.9005 (ttt180) cc_final: 0.8703 (tpp80) REVERT: A 931 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7925 (tmmt) REVERT: A 932 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8227 (m-40) REVERT: A 942 MET cc_start: 0.7619 (mtp) cc_final: 0.7183 (ttp) REVERT: A 948 MET cc_start: 0.7581 (ttm) cc_final: 0.6950 (ttp) REVERT: B 110 LYS cc_start: 0.7814 (mttp) cc_final: 0.7091 (mmtp) REVERT: B 252 LYS cc_start: 0.7975 (mtmm) cc_final: 0.7717 (mtmt) REVERT: B 385 LEU cc_start: 0.8498 (mt) cc_final: 0.8264 (mt) REVERT: B 398 MET cc_start: 0.8321 (mtt) cc_final: 0.8119 (mtt) REVERT: B 538 MET cc_start: 0.7362 (mmt) cc_final: 0.6679 (mmm) REVERT: B 627 LYS cc_start: 0.6843 (mttt) cc_final: 0.6535 (mttt) REVERT: B 691 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: B 695 MET cc_start: 0.8492 (mmp) cc_final: 0.8220 (mmp) REVERT: B 706 MET cc_start: 0.8334 (mtt) cc_final: 0.8031 (mtp) REVERT: B 748 MET cc_start: 0.9012 (mtt) cc_final: 0.8749 (mtp) REVERT: B 931 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.5977 (pttp) REVERT: B 959 LYS cc_start: 0.7400 (ttpt) cc_final: 0.6880 (tptp) REVERT: B 1011 PHE cc_start: 0.7992 (m-80) cc_final: 0.7668 (m-80) REVERT: C 402 ILE cc_start: 0.8713 (mm) cc_final: 0.8479 (tp) REVERT: C 408 ASP cc_start: 0.7543 (m-30) cc_final: 0.7212 (m-30) REVERT: C 474 MET cc_start: 0.8494 (mtp) cc_final: 0.8252 (mtp) REVERT: C 681 ASN cc_start: 0.7693 (t0) cc_final: 0.7464 (t0) outliers start: 56 outliers final: 40 residues processed: 550 average time/residue: 0.1438 time to fit residues: 126.6545 Evaluate side-chains 536 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 491 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 448 VAL Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 229 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 36 optimal weight: 0.0570 chunk 188 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 216 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 chunk 55 optimal weight: 0.0270 chunk 201 optimal weight: 6.9990 overall best weight: 3.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN A 799 GLN B 228 GLN B 594 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.151989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.122089 restraints weight = 26551.477| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.58 r_work: 0.3010 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23901 Z= 0.162 Angle : 0.574 9.981 32385 Z= 0.301 Chirality : 0.042 0.224 3873 Planarity : 0.005 0.063 4062 Dihedral : 8.345 171.832 3298 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.14 % Allowed : 11.58 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.15), residues: 3048 helix: 1.72 (0.12), residues: 1699 sheet: 0.28 (0.21), residues: 483 loop : -0.02 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 185 TYR 0.017 0.001 TYR B 49 PHE 0.016 0.001 PHE B 998 TRP 0.007 0.001 TRP C 800 HIS 0.002 0.001 HIS A 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (23901) covalent geometry : angle 0.57382 / 0.30 (32385) hydrogen bonds : bond 0.04980 / 3.35 ( 1529) hydrogen bonds : angle 4.35297 / 3.15 ( 4653) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 502 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6431 (t80) REVERT: A 167 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8390 (mttt) REVERT: A 241 SER cc_start: 0.8689 (p) cc_final: 0.8410 (p) REVERT: A 435 MET cc_start: 0.7451 (mmm) cc_final: 0.7130 (mmm) REVERT: A 483 LEU cc_start: 0.8436 (tp) cc_final: 0.8229 (tp) REVERT: A 527 MET cc_start: 0.8116 (mmm) cc_final: 0.7619 (tpp) REVERT: A 550 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7573 (t80) REVERT: A 593 ASN cc_start: 0.8018 (m-40) cc_final: 0.7815 (m110) REVERT: A 642 ASP cc_start: 0.7951 (m-30) cc_final: 0.7666 (m-30) REVERT: A 726 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7795 (tttt) REVERT: A 910 ARG cc_start: 0.9013 (ttt180) cc_final: 0.8687 (tpp80) REVERT: A 931 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7448 (tmmt) REVERT: A 942 MET cc_start: 0.7516 (mtp) cc_final: 0.7087 (ttp) REVERT: B 110 LYS cc_start: 0.7811 (mttp) cc_final: 0.7072 (mmtp) REVERT: B 252 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7715 (mtmt) REVERT: B 385 LEU cc_start: 0.8532 (mt) cc_final: 0.8326 (mt) REVERT: B 398 MET cc_start: 0.8268 (mtt) cc_final: 0.7787 (mtt) REVERT: B 538 MET cc_start: 0.7314 (mmt) cc_final: 0.6529 (mmm) REVERT: B 627 LYS cc_start: 0.6894 (mttt) cc_final: 0.6563 (mttt) REVERT: B 639 MET cc_start: 0.7972 (mtp) cc_final: 0.7531 (mtp) REVERT: B 642 ASP cc_start: 0.8113 (m-30) cc_final: 0.7901 (m-30) REVERT: B 931 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.6024 (pttp) REVERT: B 959 LYS cc_start: 0.7443 (ttpt) cc_final: 0.6894 (tptp) REVERT: B 1011 PHE cc_start: 0.8041 (m-80) cc_final: 0.7748 (m-80) REVERT: C 334 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7755 (mtpt) REVERT: C 366 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6361 (mm) REVERT: C 408 ASP cc_start: 0.7591 (m-30) cc_final: 0.7313 (m-30) REVERT: C 474 MET cc_start: 0.8464 (mtp) cc_final: 0.8228 (mtp) REVERT: C 681 ASN cc_start: 0.7809 (t0) cc_final: 0.7534 (t0) REVERT: C 965 ILE cc_start: 0.6777 (OUTLIER) cc_final: 0.6305 (mp) REVERT: C 1002 ILE cc_start: 0.7924 (mm) cc_final: 0.7613 (mm) outliers start: 55 outliers final: 36 residues processed: 535 average time/residue: 0.1406 time to fit residues: 120.8878 Evaluate side-chains 527 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 485 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain C residue 980 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 277 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 42 optimal weight: 30.0000 chunk 145 optimal weight: 1.9990 chunk 265 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 266 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 799 GLN ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.151619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.122143 restraints weight = 26579.774| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.57 r_work: 0.3018 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 23901 Z= 0.155 Angle : 0.565 11.998 32385 Z= 0.293 Chirality : 0.042 0.216 3873 Planarity : 0.005 0.061 4062 Dihedral : 7.796 166.488 3296 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.61 % Allowed : 12.75 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.15), residues: 3048 helix: 1.76 (0.12), residues: 1702 sheet: 0.39 (0.22), residues: 461 loop : -0.14 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 515 TYR 0.016 0.001 TYR B 49 PHE 0.019 0.001 PHE B 824 TRP 0.008 0.001 TRP C 556 HIS 0.002 0.000 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (23901) covalent geometry : angle 0.56452 / 0.29 (32385) hydrogen bonds : bond 0.04715 / 3.19 ( 1529) hydrogen bonds : angle 4.25606 / 3.08 ( 4653) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 494 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7682 (mt) cc_final: 0.7280 (mt) REVERT: A 22 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6407 (t80) REVERT: A 167 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8411 (mttt) REVERT: A 241 SER cc_start: 0.8744 (p) cc_final: 0.8481 (p) REVERT: A 435 MET cc_start: 0.7485 (mmm) cc_final: 0.7144 (mmm) REVERT: A 483 LEU cc_start: 0.8437 (tp) cc_final: 0.8236 (tp) REVERT: A 527 MET cc_start: 0.8098 (mmm) cc_final: 0.7624 (tpp) REVERT: A 550 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7588 (t80) REVERT: A 593 ASN cc_start: 0.7975 (m-40) cc_final: 0.7588 (m-40) REVERT: A 642 ASP cc_start: 0.7912 (m-30) cc_final: 0.7602 (m-30) REVERT: A 692 ASP cc_start: 0.8009 (m-30) cc_final: 0.7525 (m-30) REVERT: A 726 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7807 (tttt) REVERT: A 910 ARG cc_start: 0.9004 (ttt180) cc_final: 0.8653 (tpp80) REVERT: A 931 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7400 (tmmt) REVERT: A 942 MET cc_start: 0.7627 (mtp) cc_final: 0.7196 (ttp) REVERT: B 110 LYS cc_start: 0.7844 (mttp) cc_final: 0.7194 (mmtp) REVERT: B 252 LYS cc_start: 0.7969 (mtmm) cc_final: 0.7691 (mtmt) REVERT: B 385 LEU cc_start: 0.8517 (mt) cc_final: 0.8301 (mt) REVERT: B 398 MET cc_start: 0.8281 (mtt) cc_final: 0.7821 (mtt) REVERT: B 538 MET cc_start: 0.7301 (mmt) cc_final: 0.6451 (mmm) REVERT: B 639 MET cc_start: 0.8018 (mtp) cc_final: 0.7533 (mtp) REVERT: B 642 ASP cc_start: 0.8115 (m-30) cc_final: 0.7906 (m-30) REVERT: B 665 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: B 695 MET cc_start: 0.8309 (mmt) cc_final: 0.8073 (mmp) REVERT: B 931 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.6143 (pttp) REVERT: B 959 LYS cc_start: 0.7533 (ttpt) cc_final: 0.6981 (tptp) REVERT: B 1011 PHE cc_start: 0.8016 (m-80) cc_final: 0.7716 (m-80) REVERT: C 110 LYS cc_start: 0.7579 (mmtm) cc_final: 0.6983 (mmtm) REVERT: C 334 LYS cc_start: 0.8136 (ttmm) cc_final: 0.7704 (mtpt) REVERT: C 366 LEU cc_start: 0.6871 (OUTLIER) cc_final: 0.6465 (mm) REVERT: C 402 ILE cc_start: 0.8760 (mm) cc_final: 0.8530 (tp) REVERT: C 408 ASP cc_start: 0.7557 (m-30) cc_final: 0.7238 (m-30) REVERT: C 681 ASN cc_start: 0.7841 (t0) cc_final: 0.7527 (t0) REVERT: C 965 ILE cc_start: 0.6808 (OUTLIER) cc_final: 0.6340 (mp) outliers start: 67 outliers final: 46 residues processed: 536 average time/residue: 0.1358 time to fit residues: 117.3309 Evaluate side-chains 536 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 483 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 960 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 316 ASN Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 965 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 6.9990 chunk 294 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 298 optimal weight: 50.0000 chunk 235 optimal weight: 6.9990 chunk 216 optimal weight: 9.9990 chunk 202 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN A 248 ASN A 799 GLN B 691 GLN C 128 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.148451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.118991 restraints weight = 26430.199| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.51 r_work: 0.2971 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23901 Z= 0.225 Angle : 0.624 11.317 32385 Z= 0.323 Chirality : 0.044 0.226 3873 Planarity : 0.005 0.062 4062 Dihedral : 7.594 166.604 3296 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.20 % Allowed : 14.11 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.15), residues: 3048 helix: 1.60 (0.12), residues: 1701 sheet: 0.07 (0.22), residues: 478 loop : -0.24 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 515 TYR 0.017 0.002 TYR B 49 PHE 0.024 0.002 PHE B 998 TRP 0.009 0.001 TRP A 610 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.22 (23901) covalent geometry : angle 0.62401 / 0.32 (32385) hydrogen bonds : bond 0.05318 / 3.59 ( 1529) hydrogen bonds : angle 4.39646 / 3.19 ( 4653) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 499 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7278 (OUTLIER) cc_final: 0.6307 (t80) REVERT: A 241 SER cc_start: 0.8797 (p) cc_final: 0.8556 (p) REVERT: A 483 LEU cc_start: 0.8548 (tp) cc_final: 0.8248 (tp) REVERT: A 527 MET cc_start: 0.8167 (mmm) cc_final: 0.7692 (tpp) REVERT: A 550 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7737 (t80) REVERT: A 593 ASN cc_start: 0.7995 (m-40) cc_final: 0.7567 (m-40) REVERT: A 726 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7953 (tttt) REVERT: A 931 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7993 (tmmt) REVERT: A 932 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8308 (m-40) REVERT: B 110 LYS cc_start: 0.7877 (mttp) cc_final: 0.7492 (mttp) REVERT: B 252 LYS cc_start: 0.7912 (mtmm) cc_final: 0.7685 (mtmt) REVERT: B 398 MET cc_start: 0.8330 (mtt) cc_final: 0.7869 (mtt) REVERT: B 538 MET cc_start: 0.7380 (mmt) cc_final: 0.6497 (mmm) REVERT: B 639 MET cc_start: 0.8095 (mtp) cc_final: 0.7589 (mtp) REVERT: B 665 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: B 691 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: B 931 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.6286 (pttp) REVERT: B 959 LYS cc_start: 0.7603 (ttpt) cc_final: 0.7083 (tptp) REVERT: B 1011 PHE cc_start: 0.8078 (m-80) cc_final: 0.7773 (m-80) REVERT: C 110 LYS cc_start: 0.7556 (mmtm) cc_final: 0.6983 (mmtm) REVERT: C 147 ASN cc_start: 0.8485 (t0) cc_final: 0.8240 (t0) REVERT: C 334 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7792 (mtpt) REVERT: C 408 ASP cc_start: 0.7593 (m-30) cc_final: 0.7323 (m-30) REVERT: C 681 ASN cc_start: 0.7850 (t0) cc_final: 0.7542 (t0) REVERT: C 693 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7359 (mt-10) REVERT: C 809 ARG cc_start: 0.8931 (ttm-80) cc_final: 0.8552 (ttt-90) REVERT: C 849 GLU cc_start: 0.8680 (mt-10) cc_final: 0.7382 (tt0) REVERT: C 931 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7430 (ttpt) REVERT: C 965 ILE cc_start: 0.7093 (OUTLIER) cc_final: 0.6569 (mp) outliers start: 82 outliers final: 58 residues processed: 550 average time/residue: 0.1321 time to fit residues: 116.8141 Evaluate side-chains 552 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 485 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 337 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 828 SER Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 442 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 717 ASN Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 LYS Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain C residue 980 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 214 optimal weight: 10.0000 chunk 277 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 271 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 254 optimal weight: 50.0000 chunk 233 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 168 optimal weight: 10.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.149985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.120493 restraints weight = 26676.644| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.57 r_work: 0.2995 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23901 Z= 0.159 Angle : 0.569 12.377 32385 Z= 0.295 Chirality : 0.042 0.168 3873 Planarity : 0.005 0.060 4062 Dihedral : 7.194 162.904 3296 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.00 % Allowed : 15.56 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.15), residues: 3048 helix: 1.72 (0.12), residues: 1703 sheet: 0.11 (0.22), residues: 470 loop : -0.20 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 515 TYR 0.018 0.001 TYR C 157 PHE 0.023 0.001 PHE B 998 TRP 0.007 0.001 TRP A 610 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (23901) covalent geometry : angle 0.56884 / 0.30 (32385) hydrogen bonds : bond 0.04765 / 3.23 ( 1529) hydrogen bonds : angle 4.27560 / 3.10 ( 4653) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 490 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7735 (mt) cc_final: 0.7337 (mt) REVERT: A 22 PHE cc_start: 0.7236 (OUTLIER) cc_final: 0.6247 (t80) REVERT: A 167 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8311 (mttt) REVERT: A 241 SER cc_start: 0.8794 (p) cc_final: 0.8549 (p) REVERT: A 435 MET cc_start: 0.7484 (mmm) cc_final: 0.7224 (mmm) REVERT: A 454 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 456 MET cc_start: 0.8907 (ptt) cc_final: 0.8606 (ptm) REVERT: A 483 LEU cc_start: 0.8475 (tp) cc_final: 0.8236 (tp) REVERT: A 527 MET cc_start: 0.8124 (mmm) cc_final: 0.7682 (tpp) REVERT: A 550 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7746 (t80) REVERT: A 593 ASN cc_start: 0.7977 (m-40) cc_final: 0.7556 (m-40) REVERT: A 642 ASP cc_start: 0.7918 (m-30) cc_final: 0.7636 (m-30) REVERT: A 684 MET cc_start: 0.8257 (mmm) cc_final: 0.7886 (mmm) REVERT: A 726 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7862 (tttt) REVERT: A 931 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7883 (tmmt) REVERT: A 932 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8179 (m-40) REVERT: B 110 LYS cc_start: 0.7889 (mttp) cc_final: 0.7468 (mttp) REVERT: B 252 LYS cc_start: 0.7879 (mtmm) cc_final: 0.7651 (mtmt) REVERT: B 398 MET cc_start: 0.8274 (mtt) cc_final: 0.7919 (mtt) REVERT: B 538 MET cc_start: 0.7319 (mmt) cc_final: 0.6425 (mmm) REVERT: B 639 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7514 (mtp) REVERT: B 665 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: B 691 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7742 (tt0) REVERT: B 931 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.6277 (pttp) REVERT: B 959 LYS cc_start: 0.7543 (ttpt) cc_final: 0.6991 (tptp) REVERT: B 1011 PHE cc_start: 0.8029 (m-80) cc_final: 0.7702 (m-80) REVERT: C 110 LYS cc_start: 0.7517 (mmtm) cc_final: 0.6933 (mmtm) REVERT: C 147 ASN cc_start: 0.8491 (t0) cc_final: 0.8237 (t0) REVERT: C 334 LYS cc_start: 0.8111 (ttmm) cc_final: 0.7768 (mtpt) REVERT: C 348 MET cc_start: 0.7324 (OUTLIER) cc_final: 0.6900 (tpp) REVERT: C 366 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6543 (mm) REVERT: C 402 ILE cc_start: 0.8703 (mm) cc_final: 0.8475 (tp) REVERT: C 408 ASP cc_start: 0.7559 (m-30) cc_final: 0.7242 (m-30) REVERT: C 681 ASN cc_start: 0.7883 (t0) cc_final: 0.7622 (t0) REVERT: C 809 ARG cc_start: 0.8889 (ttm-80) cc_final: 0.8528 (ttt-90) REVERT: C 849 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8081 (mt-10) REVERT: C 931 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7468 (ttpt) REVERT: C 965 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6594 (mp) outliers start: 77 outliers final: 52 residues processed: 536 average time/residue: 0.1381 time to fit residues: 119.3742 Evaluate side-chains 549 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 484 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 LYS Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain C residue 986 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 220 optimal weight: 10.0000 chunk 304 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 262 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 302 optimal weight: 5.9990 chunk 292 optimal weight: 5.9990 chunk 176 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN B 3 GLN B 691 GLN C 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.151575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.122803 restraints weight = 26549.218| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.56 r_work: 0.3013 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 23901 Z= 0.131 Angle : 0.549 12.656 32385 Z= 0.284 Chirality : 0.041 0.153 3873 Planarity : 0.005 0.060 4062 Dihedral : 6.900 160.158 3293 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.61 % Allowed : 16.53 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.15), residues: 3048 helix: 1.88 (0.13), residues: 1690 sheet: 0.05 (0.22), residues: 487 loop : -0.06 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 515 TYR 0.023 0.001 TYR A 157 PHE 0.025 0.001 PHE C 901 TRP 0.006 0.001 TRP C 800 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (23901) covalent geometry : angle 0.54912 / 0.28 (32385) hydrogen bonds : bond 0.04357 / 2.95 ( 1529) hydrogen bonds : angle 4.18984 / 3.03 ( 4653) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 504 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7645 (mt) cc_final: 0.7245 (mt) REVERT: A 22 PHE cc_start: 0.7150 (OUTLIER) cc_final: 0.6211 (t80) REVERT: A 167 LYS cc_start: 0.8591 (mtmm) cc_final: 0.8328 (mttt) REVERT: A 241 SER cc_start: 0.8768 (p) cc_final: 0.8523 (p) REVERT: A 435 MET cc_start: 0.7471 (mmm) cc_final: 0.7201 (mmm) REVERT: A 456 MET cc_start: 0.8940 (ptt) cc_final: 0.8649 (ptm) REVERT: A 527 MET cc_start: 0.8109 (mmm) cc_final: 0.7720 (tpp) REVERT: A 550 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7746 (t80) REVERT: A 593 ASN cc_start: 0.7978 (m-40) cc_final: 0.7552 (m-40) REVERT: A 642 ASP cc_start: 0.7945 (m-30) cc_final: 0.7651 (m-30) REVERT: A 684 MET cc_start: 0.8219 (mmm) cc_final: 0.7844 (mmm) REVERT: A 726 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7850 (tttt) REVERT: A 931 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7431 (tmmt) REVERT: B 110 LYS cc_start: 0.7926 (mttp) cc_final: 0.7500 (mttp) REVERT: B 252 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7616 (mtmt) REVERT: B 398 MET cc_start: 0.8246 (mtt) cc_final: 0.7915 (mtt) REVERT: B 538 MET cc_start: 0.7301 (mmt) cc_final: 0.6379 (mmm) REVERT: B 639 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7546 (mtp) REVERT: B 665 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: B 706 MET cc_start: 0.8334 (mtt) cc_final: 0.8097 (mtp) REVERT: B 893 MET cc_start: 0.8454 (mmp) cc_final: 0.8091 (mmp) REVERT: B 959 LYS cc_start: 0.7554 (ttpt) cc_final: 0.7018 (tptp) REVERT: B 1011 PHE cc_start: 0.8031 (m-80) cc_final: 0.7720 (m-80) REVERT: C 110 LYS cc_start: 0.7591 (mmtm) cc_final: 0.6990 (mmtm) REVERT: C 147 ASN cc_start: 0.8477 (t0) cc_final: 0.8217 (t0) REVERT: C 314 LYS cc_start: 0.8415 (ttmt) cc_final: 0.7979 (mttt) REVERT: C 334 LYS cc_start: 0.8042 (ttmm) cc_final: 0.7674 (mtpt) REVERT: C 366 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6514 (mm) REVERT: C 408 ASP cc_start: 0.7493 (m-30) cc_final: 0.7197 (m-30) REVERT: C 681 ASN cc_start: 0.7873 (t0) cc_final: 0.7622 (t0) REVERT: C 794 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: C 849 GLU cc_start: 0.8594 (mt-10) cc_final: 0.7086 (tt0) REVERT: C 931 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7393 (ttpt) REVERT: C 965 ILE cc_start: 0.6993 (OUTLIER) cc_final: 0.6486 (mp) outliers start: 67 outliers final: 52 residues processed: 544 average time/residue: 0.1447 time to fit residues: 126.5065 Evaluate side-chains 553 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 492 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 17 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 794 GLU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 LYS Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain C residue 1020 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 175 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 197 optimal weight: 5.9990 chunk 282 optimal weight: 5.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 GLN B 691 GLN C 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.151702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.122496 restraints weight = 26562.605| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.56 r_work: 0.3008 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23901 Z= 0.132 Angle : 0.549 13.277 32385 Z= 0.284 Chirality : 0.041 0.235 3873 Planarity : 0.005 0.061 4062 Dihedral : 6.690 159.080 3289 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.69 % Allowed : 17.04 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.15), residues: 3048 helix: 1.91 (0.13), residues: 1692 sheet: 0.12 (0.22), residues: 486 loop : -0.05 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 515 TYR 0.019 0.001 TYR A 157 PHE 0.033 0.001 PHE B 866 TRP 0.005 0.001 TRP A 610 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 (23901) covalent geometry : angle 0.54911 / 0.28 (32385) hydrogen bonds : bond 0.04294 / 2.91 ( 1529) hydrogen bonds : angle 4.14819 / 3.00 ( 4653) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 504 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7601 (mt) cc_final: 0.7257 (mt) REVERT: A 22 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6165 (t80) REVERT: A 167 LYS cc_start: 0.8546 (mtmm) cc_final: 0.8282 (mttt) REVERT: A 241 SER cc_start: 0.8771 (p) cc_final: 0.8529 (p) REVERT: A 435 MET cc_start: 0.7467 (mmm) cc_final: 0.7192 (mmm) REVERT: A 454 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8766 (mp) REVERT: A 456 MET cc_start: 0.8928 (ptt) cc_final: 0.8633 (ptm) REVERT: A 527 MET cc_start: 0.8070 (mmm) cc_final: 0.7707 (tpp) REVERT: A 550 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7709 (t80) REVERT: A 593 ASN cc_start: 0.7964 (m-40) cc_final: 0.7538 (m-40) REVERT: A 684 MET cc_start: 0.8220 (mmm) cc_final: 0.7838 (mmm) REVERT: A 726 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7857 (tttt) REVERT: A 931 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7496 (tmmt) REVERT: B 89 GLU cc_start: 0.8407 (tp30) cc_final: 0.8172 (tp30) REVERT: B 110 LYS cc_start: 0.7886 (mttp) cc_final: 0.7447 (mttp) REVERT: B 252 LYS cc_start: 0.7842 (mtmm) cc_final: 0.7619 (mtmt) REVERT: B 398 MET cc_start: 0.8268 (mtt) cc_final: 0.7959 (mtt) REVERT: B 639 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7533 (mtp) REVERT: B 665 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7619 (mt-10) REVERT: B 691 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: B 748 MET cc_start: 0.8958 (mtp) cc_final: 0.8615 (mtm) REVERT: B 893 MET cc_start: 0.8478 (mmp) cc_final: 0.8102 (mmp) REVERT: B 931 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.6239 (pttp) REVERT: B 959 LYS cc_start: 0.7528 (ttpt) cc_final: 0.6981 (tptp) REVERT: B 963 ARG cc_start: 0.7668 (ttp-170) cc_final: 0.7372 (ttp-170) REVERT: B 1011 PHE cc_start: 0.8007 (m-80) cc_final: 0.7704 (m-80) REVERT: C 110 LYS cc_start: 0.7540 (mmtm) cc_final: 0.6894 (mmtm) REVERT: C 147 ASN cc_start: 0.8500 (t0) cc_final: 0.8271 (t0) REVERT: C 314 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8052 (mtmt) REVERT: C 334 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7674 (mtpt) REVERT: C 348 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6966 (mmt) REVERT: C 366 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6501 (mm) REVERT: C 408 ASP cc_start: 0.7448 (m-30) cc_final: 0.7195 (m-30) REVERT: C 681 ASN cc_start: 0.7863 (t0) cc_final: 0.7614 (t0) REVERT: C 794 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: C 849 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8022 (mt-10) REVERT: C 931 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7459 (ttpt) REVERT: C 965 ILE cc_start: 0.6944 (OUTLIER) cc_final: 0.6451 (mp) outliers start: 69 outliers final: 54 residues processed: 546 average time/residue: 0.1445 time to fit residues: 127.0083 Evaluate side-chains 557 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 490 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 468 LYS Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 348 MET Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 794 GLU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 LYS Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain C residue 1020 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 29 optimal weight: 8.9990 chunk 302 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 198 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 240 optimal weight: 0.0370 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 594 ASN B 691 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.151019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.122096 restraints weight = 26742.116| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.51 r_work: 0.3010 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23901 Z= 0.149 Angle : 0.566 13.717 32385 Z= 0.291 Chirality : 0.041 0.208 3873 Planarity : 0.005 0.061 4062 Dihedral : 6.633 158.458 3289 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.73 % Allowed : 17.43 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.15), residues: 3048 helix: 1.89 (0.13), residues: 1692 sheet: 0.10 (0.22), residues: 487 loop : -0.03 (0.22), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 515 TYR 0.018 0.001 TYR A 157 PHE 0.029 0.001 PHE C 939 TRP 0.006 0.001 TRP C 556 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (23901) covalent geometry : angle 0.56647 / 0.29 (32385) hydrogen bonds : bond 0.04420 / 3.00 ( 1529) hydrogen bonds : angle 4.17189 / 3.02 ( 4653) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 497 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7595 (mt) cc_final: 0.7257 (mt) REVERT: A 22 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6125 (t80) REVERT: A 123 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7414 (mtp85) REVERT: A 167 LYS cc_start: 0.8595 (mtmm) cc_final: 0.8344 (mttt) REVERT: A 241 SER cc_start: 0.8781 (p) cc_final: 0.8536 (p) REVERT: A 435 MET cc_start: 0.7467 (mmm) cc_final: 0.7183 (mmm) REVERT: A 454 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8765 (mp) REVERT: A 456 MET cc_start: 0.8919 (ptt) cc_final: 0.8616 (ptm) REVERT: A 527 MET cc_start: 0.8045 (mmm) cc_final: 0.7701 (tpp) REVERT: A 550 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7724 (t80) REVERT: A 593 ASN cc_start: 0.7977 (m-40) cc_final: 0.7549 (m-40) REVERT: A 684 MET cc_start: 0.8256 (mmm) cc_final: 0.7936 (mmm) REVERT: A 726 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7847 (tttt) REVERT: A 931 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7547 (tmmt) REVERT: B 89 GLU cc_start: 0.8350 (tp30) cc_final: 0.8118 (tp30) REVERT: B 110 LYS cc_start: 0.7866 (mttp) cc_final: 0.7541 (mttp) REVERT: B 252 LYS cc_start: 0.7873 (mtmm) cc_final: 0.7648 (mtmt) REVERT: B 398 MET cc_start: 0.8242 (mtt) cc_final: 0.7924 (mtt) REVERT: B 639 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7515 (mtp) REVERT: B 665 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7640 (mt-10) REVERT: B 691 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: B 748 MET cc_start: 0.8958 (mtp) cc_final: 0.8631 (mtm) REVERT: B 893 MET cc_start: 0.8472 (mmp) cc_final: 0.8099 (mmp) REVERT: B 931 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.6243 (pttp) REVERT: B 959 LYS cc_start: 0.7554 (ttpt) cc_final: 0.7002 (tptp) REVERT: B 1011 PHE cc_start: 0.8007 (m-80) cc_final: 0.7693 (m-80) REVERT: C 110 LYS cc_start: 0.7564 (mmtm) cc_final: 0.6904 (mmtm) REVERT: C 147 ASN cc_start: 0.8487 (t0) cc_final: 0.8257 (t0) REVERT: C 314 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8060 (mtmt) REVERT: C 334 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7716 (mtpt) REVERT: C 366 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6523 (mm) REVERT: C 408 ASP cc_start: 0.7436 (m-30) cc_final: 0.7186 (m-30) REVERT: C 681 ASN cc_start: 0.7865 (t0) cc_final: 0.7634 (t0) REVERT: C 794 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: C 849 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7994 (mt-10) REVERT: C 931 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7457 (ttpt) REVERT: C 965 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6476 (mp) outliers start: 70 outliers final: 56 residues processed: 542 average time/residue: 0.1465 time to fit residues: 127.6673 Evaluate side-chains 557 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 489 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 794 GLU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 LYS Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain C residue 1020 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 190 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 287 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 160 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 594 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.151348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.122415 restraints weight = 26758.100| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.53 r_work: 0.3012 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23901 Z= 0.141 Angle : 0.558 13.588 32385 Z= 0.288 Chirality : 0.041 0.206 3873 Planarity : 0.005 0.061 4062 Dihedral : 6.551 157.946 3289 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.81 % Allowed : 17.31 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.15), residues: 3048 helix: 1.90 (0.13), residues: 1692 sheet: 0.13 (0.21), residues: 496 loop : -0.01 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 515 TYR 0.025 0.001 TYR C 157 PHE 0.029 0.001 PHE C 939 TRP 0.005 0.001 TRP A 610 HIS 0.002 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (23901) covalent geometry : angle 0.55804 / 0.29 (32385) hydrogen bonds : bond 0.04339 / 2.94 ( 1529) hydrogen bonds : angle 4.15694 / 3.01 ( 4653) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 495 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7581 (mt) cc_final: 0.7241 (mt) REVERT: A 22 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6114 (t80) REVERT: A 123 ARG cc_start: 0.7604 (mtp85) cc_final: 0.7367 (mtt-85) REVERT: A 167 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8286 (mttt) REVERT: A 241 SER cc_start: 0.8781 (p) cc_final: 0.8539 (p) REVERT: A 435 MET cc_start: 0.7463 (mmm) cc_final: 0.7181 (mmm) REVERT: A 456 MET cc_start: 0.8940 (ptt) cc_final: 0.8646 (ptm) REVERT: A 527 MET cc_start: 0.8044 (mmm) cc_final: 0.7703 (tpp) REVERT: A 550 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7599 (t80) REVERT: A 593 ASN cc_start: 0.7967 (m-40) cc_final: 0.7540 (m-40) REVERT: A 684 MET cc_start: 0.8251 (mmm) cc_final: 0.7936 (mmm) REVERT: A 726 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7888 (tttt) REVERT: A 931 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7534 (tmmt) REVERT: B 89 GLU cc_start: 0.8361 (tp30) cc_final: 0.8139 (tp30) REVERT: B 110 LYS cc_start: 0.7864 (mttp) cc_final: 0.7538 (mttp) REVERT: B 252 LYS cc_start: 0.7871 (mtmm) cc_final: 0.7643 (mtmt) REVERT: B 398 MET cc_start: 0.8259 (mtt) cc_final: 0.7958 (mtt) REVERT: B 639 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7509 (mtp) REVERT: B 665 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: B 674 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8401 (tp) REVERT: B 748 MET cc_start: 0.8956 (mtp) cc_final: 0.8627 (mtm) REVERT: B 893 MET cc_start: 0.8402 (mmp) cc_final: 0.7964 (mmp) REVERT: B 931 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.6202 (pttp) REVERT: B 959 LYS cc_start: 0.7534 (ttpt) cc_final: 0.6987 (tptp) REVERT: C 110 LYS cc_start: 0.7526 (mmtm) cc_final: 0.6873 (mmtm) REVERT: C 147 ASN cc_start: 0.8497 (t0) cc_final: 0.8266 (t0) REVERT: C 314 LYS cc_start: 0.8361 (ttmt) cc_final: 0.8049 (mtmt) REVERT: C 334 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7708 (mtpt) REVERT: C 348 MET cc_start: 0.7272 (tpp) cc_final: 0.6892 (mmt) REVERT: C 366 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6480 (mm) REVERT: C 408 ASP cc_start: 0.7426 (m-30) cc_final: 0.7173 (m-30) REVERT: C 639 MET cc_start: 0.8635 (mmm) cc_final: 0.8245 (tpp) REVERT: C 681 ASN cc_start: 0.7881 (t0) cc_final: 0.7659 (t0) REVERT: C 794 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: C 849 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8001 (mt-10) REVERT: C 931 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7380 (ttpt) REVERT: C 965 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6512 (mp) outliers start: 72 outliers final: 58 residues processed: 541 average time/residue: 0.1473 time to fit residues: 128.4836 Evaluate side-chains 556 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 487 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 550 PHE Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LYS Chi-restraints excluded: chain A residue 932 ASN Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 639 MET Chi-restraints excluded: chain B residue 665 GLU Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 796 VAL Chi-restraints excluded: chain B residue 870 LEU Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 923 ILE Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 MET Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 439 THR Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 758 ARG Chi-restraints excluded: chain C residue 777 ILE Chi-restraints excluded: chain C residue 794 GLU Chi-restraints excluded: chain C residue 882 LEU Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 931 LYS Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain C residue 1020 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 129 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 166 optimal weight: 0.4980 chunk 282 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 229 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 ASN B 594 ASN B 691 GLN C 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.150981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.121275 restraints weight = 26673.965| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.47 r_work: 0.3002 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23901 Z= 0.145 Angle : 0.561 13.865 32385 Z= 0.289 Chirality : 0.041 0.199 3873 Planarity : 0.005 0.061 4062 Dihedral : 6.477 157.436 3289 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.88 % Allowed : 17.35 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.15), residues: 3048 helix: 1.91 (0.13), residues: 1692 sheet: 0.12 (0.21), residues: 496 loop : -0.00 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 515 TYR 0.023 0.001 TYR A 157 PHE 0.029 0.001 PHE C 939 TRP 0.005 0.001 TRP A 610 HIS 0.002 0.000 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (23901) covalent geometry : angle 0.56141 / 0.29 (32385) hydrogen bonds : bond 0.04358 / 2.96 ( 1529) hydrogen bonds : angle 4.15743 / 3.01 ( 4653) =============================================================================== Job complete usr+sys time: 5803.56 seconds wall clock time: 99 minutes 58.61 seconds (5998.61 seconds total)