Starting phenix.real_space_refine on Tue Apr 7 00:46:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kge_22867/04_2026/7kge_22867.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kge_22867/04_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_22867/04_2026/7kge_22867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kge_22867/04_2026/7kge_22867.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kge_22867/04_2026/7kge_22867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kge_22867/04_2026/7kge_22867.map" } 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-2.1rc1-6017/lib/python3.9/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: 5.85, per 1000 atoms: 0.25 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: 2.11 Conformation dependent library (CDL) restraints added in 997.7 milliseconds 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: 0.95 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: 5.54 Time building geometry restraints manager: 2.78 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: 14208 35.29 - 70.57: 271 70.57 - 105.86: 24 105.86 - 141.14: 0 141.14 - 176.43: 5 Dihedral angle restraints: 14508 sinusoidal: 5691 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 14505 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: 0.090 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.790 Find NCS groups from input model: 0.550 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 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 : 14.747 176.425 8802 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 covalent geometry : bond 0.00441 (23901) covalent geometry : angle 0.76761 (32385) hydrogen bonds : bond 0.14685 ( 1529) hydrogen bonds : angle 5.70873 ( 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 : 0.833 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: 0.1474 time to fit residues: 136.9368 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 : 0.805 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.155191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.128260 restraints weight = 26270.332| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.47 r_work: 0.3027 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 23901 Z= 0.221 Angle : 0.640 9.473 32385 Z= 0.336 Chirality : 0.045 0.272 3873 Planarity : 0.006 0.063 4062 Dihedral : 9.485 176.480 3335 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.11 % Allowed : 8.62 % Favored : 89.28 % 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: 1.43 (0.15), residues: 3048 helix: 1.66 (0.12), residues: 1695 sheet: 0.48 (0.22), residues: 459 loop : -0.04 (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 0.008 0.001 TRP A 187 HIS 0.003 0.001 HIS A 991 Details of bonding type rmsd covalent geometry : bond 0.00530 (23901) covalent geometry : angle 0.63961 (32385) hydrogen bonds : bond 0.05767 ( 1529) hydrogen bonds : angle 4.55211 ( 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 572 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 518 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 241 SER cc_start: 0.8677 (p) cc_final: 0.8386 (p) REVERT: A 483 LEU cc_start: 0.8554 (tp) cc_final: 0.8304 (tp) REVERT: A 550 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7552 (t80) REVERT: A 642 ASP cc_start: 0.7883 (m-30) cc_final: 0.7623 (m-30) REVERT: A 726 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7722 (tttt) REVERT: A 910 ARG cc_start: 0.9015 (ttt180) cc_final: 0.8729 (tpp80) REVERT: A 931 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.7932 (tmmt) REVERT: A 932 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8246 (m-40) REVERT: A 948 MET cc_start: 0.7593 (ttm) cc_final: 0.6975 (ttp) REVERT: B 110 LYS cc_start: 0.7832 (mttp) cc_final: 0.7115 (mmtp) REVERT: B 252 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7716 (mtmt) REVERT: B 385 LEU cc_start: 0.8506 (mt) cc_final: 0.8274 (mt) REVERT: B 398 MET cc_start: 0.8328 (mtt) cc_final: 0.8111 (mtt) REVERT: B 538 MET cc_start: 0.7375 (mmt) cc_final: 0.6698 (mmm) REVERT: B 627 LYS cc_start: 0.6874 (mttt) cc_final: 0.6569 (mttt) REVERT: B 691 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: B 695 MET cc_start: 0.8541 (mmp) cc_final: 0.8306 (mmp) REVERT: B 706 MET cc_start: 0.8354 (mtt) cc_final: 0.8053 (mtp) REVERT: B 748 MET cc_start: 0.9018 (mtt) cc_final: 0.8757 (mtp) REVERT: B 931 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.5874 (pttm) REVERT: B 959 LYS cc_start: 0.7434 (ttpt) cc_final: 0.6938 (tptp) REVERT: B 1011 PHE cc_start: 0.8014 (m-80) cc_final: 0.7699 (m-80) REVERT: C 69 LEU cc_start: 0.7616 (tp) cc_final: 0.7412 (tp) REVERT: C 402 ILE cc_start: 0.8726 (mm) cc_final: 0.8496 (tp) REVERT: C 408 ASP cc_start: 0.7550 (m-30) cc_final: 0.7219 (m-30) REVERT: C 681 ASN cc_start: 0.7694 (t0) cc_final: 0.7456 (t0) outliers start: 54 outliers final: 36 residues processed: 550 average time/residue: 0.1552 time to fit residues: 136.8527 Evaluate side-chains 533 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 492 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 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 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 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: 6.9990 chunk 36 optimal weight: 0.7980 chunk 188 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 chunk 280 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 201 optimal weight: 10.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 799 GLN B 228 GLN B 594 ASN B 691 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.152250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.124683 restraints weight = 26299.429| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.47 r_work: 0.2971 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 23901 Z= 0.235 Angle : 0.640 9.987 32385 Z= 0.336 Chirality : 0.045 0.246 3873 Planarity : 0.006 0.065 4062 Dihedral : 8.676 177.033 3316 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.73 % Allowed : 11.58 % Favored : 85.69 % 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: 1.15 (0.15), residues: 3048 helix: 1.49 (0.12), residues: 1696 sheet: 0.11 (0.21), residues: 490 loop : -0.13 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 185 TYR 0.018 0.002 TYR B 49 PHE 0.020 0.002 PHE A 569 TRP 0.010 0.001 TRP A 610 HIS 0.002 0.001 HIS B 991 Details of bonding type rmsd covalent geometry : bond 0.00567 (23901) covalent geometry : angle 0.64028 (32385) hydrogen bonds : bond 0.05705 ( 1529) hydrogen bonds : angle 4.53707 ( 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 572 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 502 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.6507 (t80) REVERT: A 241 SER cc_start: 0.8746 (p) cc_final: 0.8480 (p) REVERT: A 435 MET cc_start: 0.7548 (mmm) cc_final: 0.7218 (mmm) REVERT: A 483 LEU cc_start: 0.8538 (tp) cc_final: 0.8244 (tp) REVERT: A 527 MET cc_start: 0.8206 (mmm) cc_final: 0.7691 (tpp) REVERT: A 550 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7620 (t80) REVERT: A 593 ASN cc_start: 0.7958 (m-40) cc_final: 0.7532 (m-40) REVERT: A 638 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8282 (ttpp) REVERT: A 642 ASP cc_start: 0.7931 (m-30) cc_final: 0.7602 (m-30) REVERT: A 726 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7923 (tttt) REVERT: A 931 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7962 (tmmt) REVERT: A 932 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8298 (m-40) REVERT: B 110 LYS cc_start: 0.7849 (mttp) cc_final: 0.7128 (mmtp) REVERT: B 252 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7716 (mtmt) REVERT: B 538 MET cc_start: 0.7400 (mmt) cc_final: 0.6635 (mmm) REVERT: B 627 LYS cc_start: 0.7344 (mttt) cc_final: 0.7127 (mmtp) REVERT: B 639 MET cc_start: 0.8087 (mtp) cc_final: 0.7633 (mtp) REVERT: B 691 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: B 801 ASN cc_start: 0.7983 (OUTLIER) cc_final: 0.7773 (p0) REVERT: B 931 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.6221 (pttp) REVERT: B 959 LYS cc_start: 0.7627 (ttpt) cc_final: 0.7125 (tptp) REVERT: B 1011 PHE cc_start: 0.8100 (m-80) cc_final: 0.7816 (m-80) REVERT: C 69 LEU cc_start: 0.7627 (tp) cc_final: 0.7408 (tp) REVERT: C 334 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7841 (mtpt) REVERT: C 366 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6464 (mm) REVERT: C 408 ASP cc_start: 0.7650 (m-30) cc_final: 0.7320 (m-30) REVERT: C 681 ASN cc_start: 0.7864 (t0) cc_final: 0.7580 (t0) REVERT: C 809 ARG cc_start: 0.8943 (ttm-80) cc_final: 0.8546 (ttt-90) REVERT: C 965 ILE cc_start: 0.7114 (OUTLIER) cc_final: 0.6580 (mp) REVERT: C 1002 ILE cc_start: 0.8088 (mm) cc_final: 0.7757 (mm) outliers start: 70 outliers final: 44 residues processed: 545 average time/residue: 0.1542 time to fit residues: 136.1205 Evaluate side-chains 544 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 491 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 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 357 LEU 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 B residue 21 ILE Chi-restraints excluded: chain B residue 293 LEU 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 691 GLN Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 870 LEU 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 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 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 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 Chi-restraints excluded: chain C residue 980 VAL Chi-restraints excluded: chain C residue 1005 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 277 optimal weight: 5.9990 chunk 222 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 266 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 594 ASN C 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.149856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.119881 restraints weight = 26604.774| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.56 r_work: 0.2988 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 23901 Z= 0.171 Angle : 0.584 11.908 32385 Z= 0.304 Chirality : 0.042 0.224 3873 Planarity : 0.005 0.063 4062 Dihedral : 8.317 176.699 3316 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.81 % Allowed : 13.45 % Favored : 83.74 % 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: 1.27 (0.15), residues: 3048 helix: 1.62 (0.12), residues: 1701 sheet: 0.12 (0.21), residues: 485 loop : -0.14 (0.22), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 515 TYR 0.019 0.001 TYR C 157 PHE 0.016 0.001 PHE A 569 TRP 0.013 0.001 TRP C 556 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00407 (23901) covalent geometry : angle 0.58363 (32385) hydrogen bonds : bond 0.04993 ( 1529) hydrogen bonds : angle 4.38549 ( 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 575 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 503 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6392 (t80) REVERT: A 167 LYS cc_start: 0.8665 (mtmm) cc_final: 0.8383 (mttt) REVERT: A 241 SER cc_start: 0.8810 (p) cc_final: 0.8565 (p) REVERT: A 435 MET cc_start: 0.7517 (mmm) cc_final: 0.7163 (mmm) REVERT: A 483 LEU cc_start: 0.8464 (tp) cc_final: 0.8222 (tp) REVERT: A 527 MET cc_start: 0.8132 (mmm) cc_final: 0.7656 (tpp) REVERT: A 538 MET cc_start: 0.8421 (mmm) cc_final: 0.7938 (mmm) REVERT: A 550 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7654 (t80) REVERT: A 593 ASN cc_start: 0.7907 (m-40) cc_final: 0.7421 (m-40) REVERT: A 638 LYS cc_start: 0.8662 (ttpp) cc_final: 0.8199 (ttpp) REVERT: A 642 ASP cc_start: 0.7943 (m-30) cc_final: 0.7553 (m-30) REVERT: A 726 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7845 (tttt) REVERT: A 910 ARG cc_start: 0.9002 (ttt180) cc_final: 0.8639 (tpp80) REVERT: A 931 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7883 (tmmt) REVERT: A 932 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8214 (m-40) REVERT: B 110 LYS cc_start: 0.7862 (mttp) cc_final: 0.7623 (mttt) REVERT: B 252 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7685 (mtmt) REVERT: B 538 MET cc_start: 0.7343 (mmt) cc_final: 0.6513 (mmm) REVERT: B 627 LYS cc_start: 0.7324 (mttt) cc_final: 0.7108 (mmtp) REVERT: B 639 MET cc_start: 0.8030 (mtp) cc_final: 0.7539 (mtp) REVERT: B 758 ARG cc_start: 0.8072 (ttt90) cc_final: 0.7828 (ttt180) REVERT: B 931 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.6258 (pttp) REVERT: B 959 LYS cc_start: 0.7556 (ttpt) cc_final: 0.7014 (tptp) REVERT: B 1011 PHE cc_start: 0.8067 (m-80) cc_final: 0.7776 (m-80) REVERT: C 69 LEU cc_start: 0.7611 (tp) cc_final: 0.7377 (tp) REVERT: C 110 LYS cc_start: 0.7606 (mmtm) cc_final: 0.7054 (mmtm) REVERT: C 334 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7797 (mtpt) REVERT: C 402 ILE cc_start: 0.8744 (mm) cc_final: 0.8528 (tp) REVERT: C 408 ASP cc_start: 0.7597 (m-30) cc_final: 0.7316 (m-30) REVERT: C 681 ASN cc_start: 0.7873 (t0) cc_final: 0.7585 (t0) REVERT: C 809 ARG cc_start: 0.8902 (ttm-80) cc_final: 0.8549 (ttt-90) REVERT: C 893 MET cc_start: 0.6955 (mmm) cc_final: 0.6717 (mmp) REVERT: C 931 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7589 (ttpt) REVERT: C 965 ILE cc_start: 0.6973 (OUTLIER) cc_final: 0.6430 (mp) outliers start: 72 outliers final: 50 residues processed: 548 average time/residue: 0.1578 time to fit residues: 138.6393 Evaluate side-chains 543 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 486 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 293 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 605 THR 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 878 VAL Chi-restraints excluded: chain A residue 888 ILE 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 B residue 21 ILE Chi-restraints excluded: chain B residue 44 ASN Chi-restraints excluded: chain B residue 293 LEU 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 719 SER Chi-restraints excluded: chain B residue 732 VAL 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 890 LEU 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 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 442 ILE Chi-restraints excluded: chain C residue 536 VAL 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 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 Chi-restraints excluded: chain C residue 1005 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 1.9990 chunk 294 optimal weight: 8.9990 chunk 230 optimal weight: 3.9990 chunk 298 optimal weight: 6.9990 chunk 235 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 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 = 0.3490 r_free = 0.3490 target = 0.150005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.120872 restraints weight = 26416.350| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.49 r_work: 0.2998 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23901 Z= 0.165 Angle : 0.576 10.809 32385 Z= 0.299 Chirality : 0.042 0.207 3873 Planarity : 0.005 0.061 4062 Dihedral : 7.962 171.887 3316 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.31 % Allowed : 14.66 % Favored : 82.03 % 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: 1.33 (0.15), residues: 3048 helix: 1.68 (0.12), residues: 1702 sheet: 0.11 (0.21), residues: 485 loop : -0.15 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 515 TYR 0.016 0.001 TYR B 49 PHE 0.016 0.001 PHE B 824 TRP 0.007 0.001 TRP A 610 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00393 (23901) covalent geometry : angle 0.57598 (32385) hydrogen bonds : bond 0.04804 ( 1529) hydrogen bonds : angle 4.30616 ( 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 580 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 495 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7727 (mt) cc_final: 0.7320 (mt) REVERT: A 22 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6224 (t80) REVERT: A 167 LYS cc_start: 0.8619 (mtmm) cc_final: 0.8331 (mttt) REVERT: A 241 SER cc_start: 0.8804 (p) cc_final: 0.8551 (p) REVERT: A 435 MET cc_start: 0.7545 (mmm) cc_final: 0.7187 (mmm) REVERT: A 456 MET cc_start: 0.8925 (ptt) cc_final: 0.8631 (ptm) REVERT: A 483 LEU cc_start: 0.8505 (tp) cc_final: 0.8274 (tp) REVERT: A 527 MET cc_start: 0.8145 (mmm) cc_final: 0.7671 (tpp) REVERT: A 550 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7642 (t80) REVERT: A 593 ASN cc_start: 0.8026 (m-40) cc_final: 0.7615 (m-40) REVERT: A 726 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7863 (tttt) REVERT: A 910 ARG cc_start: 0.8999 (ttt180) cc_final: 0.8624 (tpp80) REVERT: A 931 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7933 (tmmt) REVERT: A 932 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8172 (m-40) REVERT: B 110 LYS cc_start: 0.7848 (mttp) cc_final: 0.7435 (mttp) REVERT: B 252 LYS cc_start: 0.7870 (mtmm) cc_final: 0.7630 (mtmt) REVERT: B 538 MET cc_start: 0.7342 (mmt) cc_final: 0.6447 (mmm) REVERT: B 627 LYS cc_start: 0.7351 (mttt) cc_final: 0.7126 (mmtp) REVERT: B 639 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7565 (mtp) REVERT: B 665 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: B 931 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.6230 (pttp) REVERT: B 959 LYS cc_start: 0.7530 (ttpt) cc_final: 0.6983 (tptp) REVERT: B 1011 PHE cc_start: 0.8065 (m-80) cc_final: 0.7761 (m-80) REVERT: C 69 LEU cc_start: 0.7537 (tp) cc_final: 0.7301 (tp) REVERT: C 110 LYS cc_start: 0.7533 (mmtm) cc_final: 0.6938 (mmtm) REVERT: C 334 LYS cc_start: 0.8119 (ttmm) cc_final: 0.7792 (mtpt) REVERT: C 366 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6533 (mm) REVERT: C 408 ASP cc_start: 0.7567 (m-30) cc_final: 0.7280 (m-30) REVERT: C 681 ASN cc_start: 0.7824 (t0) cc_final: 0.7522 (t0) REVERT: C 849 GLU cc_start: 0.8634 (mt-10) cc_final: 0.7100 (tt0) REVERT: C 931 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7386 (ttpt) REVERT: C 965 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6517 (mp) outliers start: 85 outliers final: 64 residues processed: 549 average time/residue: 0.1542 time to fit residues: 136.0178 Evaluate side-chains 553 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 479 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 267 ASN Chi-restraints excluded: chain A residue 293 LEU 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 394 THR 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 828 SER 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 960 LEU Chi-restraints excluded: chain A residue 997 VAL Chi-restraints excluded: chain A residue 1014 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 358 PHE Chi-restraints excluded: chain B residue 448 VAL 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 719 SER Chi-restraints excluded: chain B residue 732 VAL 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 890 LEU Chi-restraints excluded: chain B residue 931 LYS Chi-restraints excluded: chain B residue 950 LEU Chi-restraints excluded: chain C residue 17 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 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 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 879 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 980 VAL Chi-restraints excluded: chain C residue 986 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 214 optimal weight: 6.9990 chunk 277 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 271 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 168 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 GLN ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 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 = 0.3479 r_free = 0.3479 target = 0.149014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.119969 restraints weight = 26548.911| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.52 r_work: 0.2969 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 23901 Z= 0.190 Angle : 0.596 12.805 32385 Z= 0.309 Chirality : 0.043 0.198 3873 Planarity : 0.005 0.061 4062 Dihedral : 7.686 171.575 3316 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.51 % Allowed : 15.32 % Favored : 81.17 % 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: 1.24 (0.15), residues: 3048 helix: 1.65 (0.12), residues: 1700 sheet: -0.04 (0.21), residues: 487 loop : -0.21 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 515 TYR 0.016 0.001 TYR B 49 PHE 0.018 0.001 PHE A 569 TRP 0.008 0.001 TRP A 610 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00462 (23901) covalent geometry : angle 0.59618 (32385) hydrogen bonds : bond 0.04998 ( 1529) hydrogen bonds : angle 4.36073 ( 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 587 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 497 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7790 (mt) cc_final: 0.7363 (mt) REVERT: A 22 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6270 (t80) REVERT: A 167 LYS cc_start: 0.8621 (mtmm) cc_final: 0.8333 (mttt) REVERT: A 241 SER cc_start: 0.8824 (p) cc_final: 0.8581 (p) REVERT: A 456 MET cc_start: 0.8931 (ptt) cc_final: 0.8609 (ptm) REVERT: A 483 LEU cc_start: 0.8511 (tp) cc_final: 0.8249 (tp) REVERT: A 527 MET cc_start: 0.8141 (mmm) cc_final: 0.7700 (tpp) REVERT: A 538 MET cc_start: 0.8486 (mmm) cc_final: 0.7955 (mmm) REVERT: A 550 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7784 (t80) REVERT: A 593 ASN cc_start: 0.8030 (m-40) cc_final: 0.7604 (m-40) REVERT: A 638 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8264 (ttpp) REVERT: A 642 ASP cc_start: 0.7996 (m-30) cc_final: 0.7598 (m-30) REVERT: A 684 MET cc_start: 0.8251 (mmm) cc_final: 0.7891 (mmm) REVERT: A 726 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7992 (tttt) REVERT: A 931 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7933 (tmmt) REVERT: A 932 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8190 (m-40) REVERT: B 110 LYS cc_start: 0.7877 (mttp) cc_final: 0.7451 (mttp) REVERT: B 252 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7659 (mtmt) REVERT: B 538 MET cc_start: 0.7379 (mmt) cc_final: 0.6461 (mmm) REVERT: B 627 LYS cc_start: 0.7448 (mttt) cc_final: 0.7233 (mmtp) REVERT: B 639 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7653 (mtp) REVERT: B 665 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: B 691 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: B 931 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.6274 (pttm) REVERT: B 959 LYS cc_start: 0.7569 (ttpt) cc_final: 0.7015 (tptp) REVERT: B 1011 PHE cc_start: 0.8078 (m-80) cc_final: 0.7763 (m-80) REVERT: C 69 LEU cc_start: 0.7572 (tp) cc_final: 0.7338 (tp) REVERT: C 110 LYS cc_start: 0.7545 (mmtm) cc_final: 0.6950 (mmtm) REVERT: C 334 LYS cc_start: 0.8145 (ttmm) cc_final: 0.7806 (mtpt) REVERT: C 366 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6559 (mm) REVERT: C 681 ASN cc_start: 0.7851 (t0) cc_final: 0.7561 (t0) REVERT: C 693 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7342 (mt-10) REVERT: C 794 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: C 849 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8053 (mt-10) REVERT: C 931 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7525 (ttpt) REVERT: C 965 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6523 (mp) outliers start: 90 outliers final: 67 residues processed: 556 average time/residue: 0.1597 time to fit residues: 142.3795 Evaluate side-chains 566 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 487 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 267 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 394 THR 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 828 SER 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 448 VAL 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 732 VAL 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 890 LEU 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 17 ILE Chi-restraints excluded: chain C residue 65 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 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 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 965 ILE Chi-restraints excluded: chain C residue 980 VAL 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: 7.9990 chunk 304 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 187 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 302 optimal weight: 6.9990 chunk 292 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3486 r_free = 0.3486 target = 0.149457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.119830 restraints weight = 26674.315| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.45 r_work: 0.2984 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23901 Z= 0.165 Angle : 0.580 12.160 32385 Z= 0.300 Chirality : 0.042 0.221 3873 Planarity : 0.005 0.061 4062 Dihedral : 7.522 174.580 3314 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.59 % Allowed : 16.02 % Favored : 80.39 % 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: 1.32 (0.15), residues: 3048 helix: 1.74 (0.12), residues: 1689 sheet: -0.13 (0.21), residues: 515 loop : -0.10 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 515 TYR 0.027 0.001 TYR A 157 PHE 0.017 0.001 PHE B 998 TRP 0.007 0.001 TRP C 800 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00396 (23901) covalent geometry : angle 0.58035 (32385) hydrogen bonds : bond 0.04761 ( 1529) hydrogen bonds : angle 4.30885 ( 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 594 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 502 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7728 (mt) cc_final: 0.7328 (mt) REVERT: A 22 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6203 (t80) REVERT: A 167 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8363 (mttt) REVERT: A 241 SER cc_start: 0.8834 (p) cc_final: 0.8594 (p) REVERT: A 435 MET cc_start: 0.7478 (mmm) cc_final: 0.7212 (mmm) REVERT: A 456 MET cc_start: 0.8914 (ptt) cc_final: 0.8596 (ptm) REVERT: A 483 LEU cc_start: 0.8477 (tp) cc_final: 0.8218 (tp) REVERT: A 527 MET cc_start: 0.8131 (mmm) cc_final: 0.7739 (tpp) REVERT: A 538 MET cc_start: 0.8502 (mmm) cc_final: 0.7985 (mmm) REVERT: A 550 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7783 (t80) REVERT: A 593 ASN cc_start: 0.8040 (m-40) cc_final: 0.7601 (m-40) REVERT: A 638 LYS cc_start: 0.8735 (ttpp) cc_final: 0.8291 (ttpp) REVERT: A 642 ASP cc_start: 0.7992 (m-30) cc_final: 0.7583 (m-30) REVERT: A 684 MET cc_start: 0.8268 (mmm) cc_final: 0.7901 (mmm) REVERT: A 726 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7914 (tttt) REVERT: A 931 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.7937 (tmmt) REVERT: A 932 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8205 (m-40) REVERT: B 110 LYS cc_start: 0.7930 (mttp) cc_final: 0.7516 (mttp) REVERT: B 166 LEU cc_start: 0.8102 (mt) cc_final: 0.7870 (mt) REVERT: B 252 LYS cc_start: 0.7872 (mtmm) cc_final: 0.7643 (mtmt) REVERT: B 538 MET cc_start: 0.7345 (mmt) cc_final: 0.6434 (mmm) REVERT: B 627 LYS cc_start: 0.7482 (mttt) cc_final: 0.7276 (mmtp) REVERT: B 639 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7562 (mtp) REVERT: B 665 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: B 691 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7729 (tt0) REVERT: B 931 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.6358 (pttp) REVERT: B 959 LYS cc_start: 0.7579 (ttpt) cc_final: 0.7018 (tptp) REVERT: B 1007 LEU cc_start: 0.8283 (tp) cc_final: 0.8015 (tp) REVERT: B 1011 PHE cc_start: 0.8064 (m-80) cc_final: 0.7735 (m-80) REVERT: C 69 LEU cc_start: 0.7583 (tp) cc_final: 0.7349 (tp) REVERT: C 110 LYS cc_start: 0.7546 (mmtm) cc_final: 0.6956 (mmtm) REVERT: C 334 LYS cc_start: 0.8128 (ttmm) cc_final: 0.7768 (mtpt) REVERT: C 366 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6572 (mm) REVERT: C 408 ASP cc_start: 0.7538 (m-30) cc_final: 0.7220 (m-30) REVERT: C 681 ASN cc_start: 0.7875 (t0) cc_final: 0.7606 (t0) REVERT: C 794 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: C 849 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8009 (mt-10) REVERT: C 931 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7531 (ttpt) REVERT: C 965 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6560 (mp) outliers start: 92 outliers final: 68 residues processed: 561 average time/residue: 0.1542 time to fit residues: 139.5848 Evaluate side-chains 569 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 489 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 243 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 394 THR 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 794 GLU Chi-restraints excluded: chain A residue 828 SER 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 448 VAL 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 732 VAL 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 65 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 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 371 VAL Chi-restraints excluded: chain C residue 442 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 879 LEU 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 980 VAL 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: 4.9990 chunk 87 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 chunk 154 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 282 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.149567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.119920 restraints weight = 26687.746| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.45 r_work: 0.2987 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 23901 Z= 0.160 Angle : 0.576 13.350 32385 Z= 0.297 Chirality : 0.042 0.204 3873 Planarity : 0.005 0.061 4062 Dihedral : 7.317 178.931 3312 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.24 % Allowed : 16.80 % Favored : 79.96 % 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: 1.37 (0.15), residues: 3048 helix: 1.76 (0.12), residues: 1692 sheet: -0.12 (0.21), residues: 525 loop : -0.03 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 515 TYR 0.021 0.001 TYR A 157 PHE 0.031 0.001 PHE B 866 TRP 0.007 0.001 TRP A 610 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00383 (23901) covalent geometry : angle 0.57630 (32385) hydrogen bonds : bond 0.04660 ( 1529) hydrogen bonds : angle 4.27434 ( 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 577 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 494 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7687 (mt) cc_final: 0.7281 (mt) REVERT: A 22 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6163 (t80) REVERT: A 167 LYS cc_start: 0.8611 (mtmm) cc_final: 0.8346 (mttt) REVERT: A 241 SER cc_start: 0.8827 (p) cc_final: 0.8572 (p) REVERT: A 435 MET cc_start: 0.7489 (mmm) cc_final: 0.7218 (mmm) REVERT: A 456 MET cc_start: 0.8956 (ptt) cc_final: 0.8669 (ptm) REVERT: A 483 LEU cc_start: 0.8468 (tp) cc_final: 0.8241 (tp) REVERT: A 527 MET cc_start: 0.8129 (mmm) cc_final: 0.7732 (tpp) REVERT: A 550 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7760 (t80) REVERT: A 593 ASN cc_start: 0.8029 (m-40) cc_final: 0.7614 (m-40) REVERT: A 684 MET cc_start: 0.8255 (mmm) cc_final: 0.7887 (mmm) REVERT: A 726 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7913 (tttt) REVERT: A 931 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7944 (tmmt) REVERT: A 932 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8131 (m-40) REVERT: B 89 GLU cc_start: 0.8410 (tp30) cc_final: 0.8174 (tp30) REVERT: B 110 LYS cc_start: 0.7896 (mttp) cc_final: 0.7569 (mttp) REVERT: B 252 LYS cc_start: 0.7863 (mtmm) cc_final: 0.7631 (mtmt) REVERT: B 538 MET cc_start: 0.7279 (mmt) cc_final: 0.6375 (mmm) REVERT: B 639 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.7577 (mtp) REVERT: B 665 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7637 (mt-10) REVERT: B 674 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8431 (tp) REVERT: B 959 LYS cc_start: 0.7553 (ttpt) cc_final: 0.6992 (tptp) REVERT: B 1011 PHE cc_start: 0.8047 (m-80) cc_final: 0.7733 (m-80) REVERT: C 69 LEU cc_start: 0.7635 (tp) cc_final: 0.7403 (tp) REVERT: C 110 LYS cc_start: 0.7538 (mmtm) cc_final: 0.6943 (mmtm) REVERT: C 314 LYS cc_start: 0.8396 (ttmt) cc_final: 0.8067 (mtmt) REVERT: C 334 LYS cc_start: 0.8032 (ttmm) cc_final: 0.7703 (mtpt) REVERT: C 366 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6567 (mm) REVERT: C 681 ASN cc_start: 0.7865 (t0) cc_final: 0.7622 (t0) REVERT: C 794 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7413 (mp0) REVERT: C 849 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8358 (mt-10) REVERT: C 931 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.7651 (ttpt) REVERT: C 965 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6542 (mp) outliers start: 83 outliers final: 68 residues processed: 549 average time/residue: 0.1516 time to fit residues: 135.2947 Evaluate side-chains 566 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 487 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 70 SER 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 259 VAL Chi-restraints excluded: chain A residue 293 LEU 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 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 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 321 MET Chi-restraints excluded: chain B residue 358 PHE Chi-restraints excluded: chain B residue 448 VAL 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 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 950 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain C residue 65 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 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 371 VAL Chi-restraints excluded: chain C residue 442 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 931 LYS Chi-restraints excluded: chain C residue 939 PHE Chi-restraints excluded: chain C residue 965 ILE Chi-restraints excluded: chain C residue 980 VAL 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: 0.9980 chunk 302 optimal weight: 5.9990 chunk 298 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 240 optimal weight: 0.0470 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN C 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.151484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.122241 restraints weight = 26708.525| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.54 r_work: 0.3015 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23901 Z= 0.127 Angle : 0.554 13.637 32385 Z= 0.285 Chirality : 0.041 0.211 3873 Planarity : 0.005 0.062 4062 Dihedral : 7.010 179.182 3307 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.53 % Allowed : 17.93 % Favored : 79.53 % 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: 1.53 (0.15), residues: 3048 helix: 1.87 (0.13), residues: 1697 sheet: -0.01 (0.21), residues: 523 loop : 0.07 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 515 TYR 0.017 0.001 TYR C 157 PHE 0.027 0.001 PHE B 866 TRP 0.007 0.001 TRP C 800 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00291 (23901) covalent geometry : angle 0.55442 (32385) hydrogen bonds : bond 0.04247 ( 1529) hydrogen bonds : angle 4.17768 ( 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 571 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 506 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7599 (mt) cc_final: 0.7206 (mt) REVERT: A 22 PHE cc_start: 0.7097 (OUTLIER) cc_final: 0.6075 (t80) REVERT: A 167 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8276 (mttt) REVERT: A 241 SER cc_start: 0.8776 (p) cc_final: 0.8531 (p) REVERT: A 435 MET cc_start: 0.7454 (mmm) cc_final: 0.7183 (mmm) REVERT: A 456 MET cc_start: 0.8928 (ptt) cc_final: 0.8647 (ptm) REVERT: A 527 MET cc_start: 0.8096 (mmm) cc_final: 0.7742 (tpp) REVERT: A 550 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7713 (t80) REVERT: A 593 ASN cc_start: 0.7926 (m-40) cc_final: 0.7467 (m-40) REVERT: A 642 ASP cc_start: 0.7972 (m-30) cc_final: 0.7657 (m-30) REVERT: A 684 MET cc_start: 0.8220 (mmm) cc_final: 0.7837 (mmm) REVERT: A 726 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7910 (tttt) REVERT: A 931 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7635 (pptt) REVERT: B 89 GLU cc_start: 0.8404 (tp30) cc_final: 0.8167 (tp30) REVERT: B 110 LYS cc_start: 0.7866 (mttp) cc_final: 0.7527 (mttp) REVERT: B 252 LYS cc_start: 0.7835 (mtmm) cc_final: 0.7598 (mtmt) REVERT: B 538 MET cc_start: 0.7223 (mmt) cc_final: 0.6293 (mmm) REVERT: B 639 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7540 (mtp) REVERT: B 665 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7598 (mt-10) REVERT: B 706 MET cc_start: 0.8308 (mtt) cc_final: 0.8102 (mtp) REVERT: B 748 MET cc_start: 0.8938 (mtp) cc_final: 0.8604 (mtm) REVERT: B 959 LYS cc_start: 0.7511 (ttpt) cc_final: 0.6951 (tptp) REVERT: B 1011 PHE cc_start: 0.8016 (m-80) cc_final: 0.7688 (m-80) REVERT: C 69 LEU cc_start: 0.7631 (tp) cc_final: 0.7386 (tp) REVERT: C 110 LYS cc_start: 0.7558 (mmtm) cc_final: 0.6946 (mmtm) REVERT: C 314 LYS cc_start: 0.8377 (ttmt) cc_final: 0.8046 (mtmt) REVERT: C 334 LYS cc_start: 0.7991 (ttmm) cc_final: 0.7668 (mtpt) REVERT: C 366 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6531 (mm) REVERT: C 408 ASP cc_start: 0.7461 (m-30) cc_final: 0.7196 (m-30) REVERT: C 681 ASN cc_start: 0.7859 (t0) cc_final: 0.7627 (t0) REVERT: C 794 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: C 849 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8332 (mt-10) REVERT: C 965 ILE cc_start: 0.7037 (OUTLIER) cc_final: 0.6555 (mp) outliers start: 65 outliers final: 52 residues processed: 553 average time/residue: 0.1525 time to fit residues: 136.4263 Evaluate side-chains 551 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 491 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 243 LEU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 293 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 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 531 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 950 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 65 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 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 674 LEU Chi-restraints excluded: chain C residue 758 ARG 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 939 PHE Chi-restraints excluded: chain C residue 965 ILE 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: 9.9990 chunk 185 optimal weight: 4.9990 chunk 287 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3497 r_free = 0.3497 target = 0.150475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.121344 restraints weight = 26789.363| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.54 r_work: 0.3009 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 23901 Z= 0.155 Angle : 0.576 13.994 32385 Z= 0.296 Chirality : 0.042 0.213 3873 Planarity : 0.005 0.061 4062 Dihedral : 6.939 178.873 3307 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.65 % Allowed : 17.93 % Favored : 79.42 % 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: 1.49 (0.15), residues: 3048 helix: 1.82 (0.12), residues: 1697 sheet: -0.02 (0.21), residues: 524 loop : 0.06 (0.23), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 515 TYR 0.017 0.001 TYR C 157 PHE 0.027 0.001 PHE C 939 TRP 0.007 0.001 TRP C 800 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00374 (23901) covalent geometry : angle 0.57621 (32385) hydrogen bonds : bond 0.04464 ( 1529) hydrogen bonds : angle 4.20707 ( 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 557 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 489 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.7640 (mt) cc_final: 0.7309 (mt) REVERT: A 22 PHE cc_start: 0.7148 (OUTLIER) cc_final: 0.6118 (t80) REVERT: A 167 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8287 (mttt) REVERT: A 241 SER cc_start: 0.8777 (p) cc_final: 0.8534 (p) REVERT: A 435 MET cc_start: 0.7482 (mmm) cc_final: 0.7204 (mmm) REVERT: A 456 MET cc_start: 0.8951 (ptt) cc_final: 0.8648 (ptm) REVERT: A 527 MET cc_start: 0.8072 (mmm) cc_final: 0.7720 (tpp) REVERT: A 550 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7604 (t80) REVERT: A 593 ASN cc_start: 0.7950 (m-40) cc_final: 0.7488 (m-40) REVERT: A 642 ASP cc_start: 0.8005 (m-30) cc_final: 0.7688 (m-30) REVERT: A 684 MET cc_start: 0.8250 (mmm) cc_final: 0.7881 (mmm) REVERT: A 726 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7955 (tttt) REVERT: A 931 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7690 (pptt) REVERT: B 89 GLU cc_start: 0.8415 (tp30) cc_final: 0.8170 (tp30) REVERT: B 110 LYS cc_start: 0.7891 (mttp) cc_final: 0.7559 (mttp) REVERT: B 252 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7613 (mtmt) REVERT: B 639 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7593 (mtp) REVERT: B 665 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7643 (mt-10) REVERT: B 674 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8418 (tp) REVERT: B 691 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: B 748 MET cc_start: 0.8975 (mtp) cc_final: 0.8588 (mtm) REVERT: B 959 LYS cc_start: 0.7570 (ttpt) cc_final: 0.7044 (tptp) REVERT: B 1011 PHE cc_start: 0.8051 (m-80) cc_final: 0.7755 (m-80) REVERT: C 69 LEU cc_start: 0.7632 (tp) cc_final: 0.7383 (tp) REVERT: C 110 LYS cc_start: 0.7607 (mmtm) cc_final: 0.6950 (mmtm) REVERT: C 314 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8107 (mtmt) REVERT: C 334 LYS cc_start: 0.8004 (ttmm) cc_final: 0.7675 (mtpt) REVERT: C 366 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6575 (mm) REVERT: C 408 ASP cc_start: 0.7467 (m-30) cc_final: 0.7204 (m-30) REVERT: C 639 MET cc_start: 0.8659 (mmm) cc_final: 0.8282 (tpp) REVERT: C 681 ASN cc_start: 0.7887 (t0) cc_final: 0.7669 (t0) REVERT: C 794 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: C 849 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8002 (mt-10) REVERT: C 931 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7525 (ttpt) REVERT: C 965 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6578 (mp) outliers start: 68 outliers final: 55 residues processed: 538 average time/residue: 0.1527 time to fit residues: 133.3371 Evaluate side-chains 552 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 486 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 70 SER 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 259 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 359 LEU 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 358 PHE Chi-restraints excluded: chain B residue 531 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 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 950 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 65 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 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: 3.9990 chunk 148 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 282 optimal weight: 0.9990 chunk 171 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 229 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 691 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.150396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.121293 restraints weight = 26684.565| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.52 r_work: 0.3001 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 23901 Z= 0.155 Angle : 0.575 14.020 32385 Z= 0.295 Chirality : 0.042 0.206 3873 Planarity : 0.005 0.061 4062 Dihedral : 6.849 177.684 3307 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.53 % Allowed : 18.21 % Favored : 79.26 % 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: 1.47 (0.15), residues: 3048 helix: 1.80 (0.12), residues: 1699 sheet: -0.02 (0.21), residues: 524 loop : 0.08 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 515 TYR 0.026 0.001 TYR A 157 PHE 0.027 0.001 PHE C 939 TRP 0.007 0.001 TRP C 800 HIS 0.003 0.001 HIS B 360 Details of bonding type rmsd covalent geometry : bond 0.00372 (23901) covalent geometry : angle 0.57503 (32385) hydrogen bonds : bond 0.04478 ( 1529) hydrogen bonds : angle 4.21031 ( 4653) =============================================================================== Job complete usr+sys time: 6580.12 seconds wall clock time: 113 minutes 27.76 seconds (6807.76 seconds total)