Starting phenix.real_space_refine on Sat Jul 4 22:11:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kgd_22866/07_2026/7kgd_22866.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kgd_22866/07_2026/7kgd_22866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kgd_22866/07_2026/7kgd_22866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kgd_22866/07_2026/7kgd_22866.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kgd_22866/07_2026/7kgd_22866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kgd_22866/07_2026/7kgd_22866.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kgd_22866/07_2026/7kgd_22866.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kgd_22866/07_2026/7kgd_22866.cif" } resolution = 3.64 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= 0.124 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 6 5.49 5 S 135 5.16 5 C 15285 2.51 5 N 3798 2.21 5 O 4356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23580 Number of models: 1 Model: "" Number of chains: 2 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: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'PTY': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 25 Restraints were copied for chains: B, C Time building chain proxies: 8.38, per 1000 atoms: 0.36 Number of scatterers: 23580 At special positions: 0 Unit cell: (116.64, 120.96, 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 6 15.00 O 4356 8.00 N 3798 7.00 C 15285 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 846.5 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: 111 helices and 24 sheets defined 61.7% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.692A pdb=" N ILE A 6 " --> pdb=" O SER A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 30 removed outlier: 3.505A 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 70 removed outlier: 3.686A pdb=" N ILE A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 115 removed outlier: 3.639A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.028A 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: 3.654A 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 removed outlier: 3.633A pdb=" N VAL A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 262 through 265 No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 298 through 317 removed outlier: 3.964A pdb=" N LEU A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN A 316 " --> pdb=" O GLU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 359 removed outlier: 4.297A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 387 removed outlier: 3.824A pdb=" N THR A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Proline residue: A 368 - end of helix Proline residue: A 373 - end of helix Processing helix chain 'A' and resid 391 through 406 removed outlier: 4.429A pdb=" N GLY A 403 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ILE A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 424 removed outlier: 4.045A pdb=" N VAL A 412 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 458 removed outlier: 5.245A pdb=" N SER A 440 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Proline residue: A 441 - end of helix removed outlier: 3.772A pdb=" N PHE A 453 " --> pdb=" O LEU A 449 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) Proline residue: A 455 - end of helix removed outlier: 3.747A pdb=" N PHE A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 496 removed outlier: 3.587A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 477 " --> pdb=" O THR A 473 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 509 through 533 Processing helix chain 'A' and resid 534 through 556 Processing helix chain 'A' and resid 580 through 598 removed outlier: 3.512A pdb=" N THR A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 597 " --> pdb=" O ASN A 593 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN A 598 " --> pdb=" O ASN A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 648 Processing helix chain 'A' and resid 683 through 701 removed outlier: 4.050A pdb=" N ALA A 699 " --> pdb=" O MET A 695 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 730 removed outlier: 3.530A pdb=" N LEU A 730 " --> pdb=" O LYS A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 746 removed outlier: 4.487A pdb=" N MET A 745 " --> pdb=" O ILE A 741 " (cutoff:3.500A) removed outlier: 4.019A 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 779 removed outlier: 3.710A pdb=" N ILE A 777 " --> pdb=" O GLN A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 795 No H-bonds generated for 'chain 'A' and resid 792 through 795' Processing helix chain 'A' and resid 827 through 841 removed outlier: 3.654A pdb=" N LYS A 841 " --> pdb=" O GLN A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 863 removed outlier: 3.543A pdb=" N GLN A 863 " --> pdb=" O GLN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 884 removed outlier: 4.281A pdb=" N SER A 871 " --> pdb=" O LEU A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 894 removed outlier: 3.842A pdb=" N SER A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 892 " --> pdb=" O ILE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 911 removed outlier: 3.515A pdb=" N GLY A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 947 removed outlier: 3.845A pdb=" N LEU A 935 " --> pdb=" O LYS A 931 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE A 936 " --> pdb=" O ASN A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 976 removed outlier: 4.938A pdb=" N ARG A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Proline residue: A 964 - end of helix removed outlier: 3.524A pdb=" N PHE A 972 " --> pdb=" O THR A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 986 through 1027 removed outlier: 3.783A pdb=" N GLN A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 993 " --> pdb=" O THR A 989 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY A 996 " --> pdb=" O ALA A 992 " (cutoff:3.500A) removed outlier: 5.109A 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 8 removed outlier: 3.692A pdb=" N ILE B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 30 removed outlier: 3.505A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Proline residue: B 28 - end of helix Processing helix chain 'B' and resid 53 through 70 removed outlier: 3.687A pdb=" N ILE B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL B 62 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR B 63 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 70 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.639A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) 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: 3.655A pdb=" N GLU B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.634A pdb=" N VAL B 203 " --> pdb=" O SER B 199 " (cutoff:3.500A) 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 317 removed outlier: 3.964A pdb=" N LEU B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 359 removed outlier: 4.297A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 354 " --> pdb=" O LEU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 387 removed outlier: 3.823A pdb=" N THR B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) Proline residue: B 368 - end of helix Proline residue: B 373 - end of helix Processing helix chain 'B' and resid 391 through 406 removed outlier: 4.428A pdb=" N GLY B 403 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 424 removed outlier: 4.044A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 458 removed outlier: 5.245A pdb=" N SER B 440 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Proline residue: B 441 - end of helix removed outlier: 3.773A pdb=" N PHE B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 454 " --> pdb=" O ALA B 450 " (cutoff:3.500A) Proline residue: B 455 - end of helix removed outlier: 3.747A pdb=" N PHE B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 496 removed outlier: 3.586A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 477 " --> pdb=" O THR B 473 " (cutoff:3.500A) removed outlier: 4.379A 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 533 Processing helix chain 'B' and resid 534 through 556 Processing helix chain 'B' and resid 580 through 598 removed outlier: 3.512A pdb=" N THR B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 597 " --> pdb=" O ASN B 593 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN B 598 " --> pdb=" O ASN B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 648 Processing helix chain 'B' and resid 683 through 701 removed outlier: 4.049A pdb=" N ALA B 699 " --> pdb=" O MET B 695 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS B 700 " --> pdb=" O ALA B 696 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN B 701 " --> pdb=" O MET B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 730 removed outlier: 3.530A pdb=" N LEU B 730 " --> pdb=" O LYS B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 746 removed outlier: 4.488A pdb=" N MET B 745 " --> pdb=" O ILE B 741 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY B 746 " --> pdb=" O SER B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 771 Processing helix chain 'B' and resid 773 through 779 removed outlier: 3.710A pdb=" N ILE B 777 " --> pdb=" O GLN B 773 " (cutoff:3.500A) 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 841 removed outlier: 3.655A pdb=" N LYS B 841 " --> pdb=" O GLN B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 863 removed outlier: 3.544A pdb=" N GLN B 863 " --> pdb=" O GLN B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 884 removed outlier: 4.282A pdb=" N SER B 871 " --> pdb=" O LEU B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 894 removed outlier: 3.842A pdb=" N SER B 891 " --> pdb=" O ALA B 887 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL B 892 " --> pdb=" O ILE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 911 removed outlier: 3.515A pdb=" N GLY B 899 " --> pdb=" O VAL B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 947 removed outlier: 3.845A pdb=" N LEU B 935 " --> pdb=" O LYS B 931 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE B 936 " --> pdb=" O ASN B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 976 removed outlier: 4.938A pdb=" N ARG B 963 " --> pdb=" O LYS B 959 " (cutoff:3.500A) Proline residue: B 964 - end of helix removed outlier: 3.525A pdb=" N PHE B 972 " --> pdb=" O THR B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 986 through 1027 removed outlier: 3.783A pdb=" N GLN B 990 " --> pdb=" O SER B 986 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU B 993 " --> pdb=" O THR B 989 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY B 996 " --> pdb=" O ALA B 992 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N PHE B1010 " --> pdb=" O ILE B1006 " (cutoff:3.500A) Proline residue: B1013 - end of helix Processing helix chain 'C' and resid 2 through 8 removed outlier: 3.692A pdb=" N ILE C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 30 removed outlier: 3.505A 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 70 removed outlier: 3.687A pdb=" N ILE C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL C 62 " --> pdb=" O ASN C 58 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.639A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL C 114 " --> pdb=" O LYS C 110 " (cutoff:3.500A) 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 removed outlier: 3.654A pdb=" N GLU C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 196 Processing helix chain 'C' and resid 199 through 211 removed outlier: 3.633A pdb=" N VAL C 203 " --> pdb=" O SER C 199 " (cutoff:3.500A) 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 317 removed outlier: 3.964A pdb=" N LEU C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 359 removed outlier: 4.297A pdb=" N VAL C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N MET C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 387 removed outlier: 3.824A pdb=" N THR C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) Proline residue: C 368 - end of helix Proline residue: C 373 - end of helix Processing helix chain 'C' and resid 391 through 406 removed outlier: 4.428A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 424 removed outlier: 4.044A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 458 removed outlier: 5.244A pdb=" N SER C 440 " --> pdb=" O LYS C 436 " (cutoff:3.500A) Proline residue: C 441 - end of helix removed outlier: 3.772A pdb=" N PHE C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) Proline residue: C 455 - end of helix removed outlier: 3.747A pdb=" N PHE C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 496 removed outlier: 3.587A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 477 " --> pdb=" O THR C 473 " (cutoff:3.500A) removed outlier: 4.378A 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 533 Processing helix chain 'C' and resid 534 through 556 Processing helix chain 'C' and resid 580 through 598 removed outlier: 3.512A pdb=" N THR C 584 " --> pdb=" O THR C 580 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP C 597 " --> pdb=" O ASN C 593 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN C 598 " --> pdb=" O ASN C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 648 Processing helix chain 'C' and resid 683 through 701 removed outlier: 4.051A pdb=" N ALA C 699 " --> pdb=" O MET C 695 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS C 700 " --> pdb=" O ALA C 696 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN C 701 " --> pdb=" O MET C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 730 removed outlier: 3.530A pdb=" N LEU C 730 " --> pdb=" O LYS C 726 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 746 removed outlier: 4.487A pdb=" N MET C 745 " --> pdb=" O ILE C 741 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY C 746 " --> pdb=" O SER C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 771 Processing helix chain 'C' and resid 773 through 779 removed outlier: 3.710A pdb=" N ILE C 777 " --> pdb=" O GLN C 773 " (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: 3.654A pdb=" N LYS C 841 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 863 removed outlier: 3.544A pdb=" N GLN C 863 " --> pdb=" O GLN C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 884 removed outlier: 4.281A pdb=" N SER C 871 " --> pdb=" O LEU C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 894 removed outlier: 3.843A pdb=" N SER C 891 " --> pdb=" O ALA C 887 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL C 892 " --> pdb=" O ILE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 911 removed outlier: 3.514A pdb=" N GLY C 899 " --> pdb=" O VAL C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 947 removed outlier: 3.845A pdb=" N LEU C 935 " --> pdb=" O LYS C 931 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE C 936 " --> pdb=" O ASN C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 976 removed outlier: 4.938A pdb=" N ARG C 963 " --> pdb=" O LYS C 959 " (cutoff:3.500A) Proline residue: C 964 - end of helix removed outlier: 3.525A pdb=" N PHE C 972 " --> pdb=" O THR C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 986 through 1027 removed outlier: 3.783A pdb=" N GLN C 990 " --> pdb=" O SER C 986 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU C 993 " --> pdb=" O THR C 989 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY C 996 " --> pdb=" O ALA C 992 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N PHE C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Proline residue: C1013 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 130 removed outlier: 3.899A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N SER A 817 " --> pdb=" O ASN A 709 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASN A 709 " --> pdb=" O SER A 817 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ALA A 819 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL A 707 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE A 821 " --> pdb=" O TYR A 705 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 130 removed outlier: 3.899A pdb=" N ASN A 808 " --> pdb=" O SER A 815 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER A 673 " --> pdb=" O THR A 851 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.634A pdb=" N LYS A 174 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 292 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 removed outlier: 4.634A pdb=" N LYS A 174 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 292 " --> pdb=" O LYS A 174 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A 286 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE A 279 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER A 603 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 572 " --> pdb=" O MET A 656 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU A 654 " --> pdb=" O GLN A 574 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.282A pdb=" N LYS A 182 " --> pdb=" O MET A 759 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLN A 761 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 765 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 751 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL A 764 " --> pdb=" O TYR A 749 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TYR A 749 " --> pdb=" O VAL A 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 217 through 218 removed outlier: 7.997A pdb=" N LEU C 720 " --> pdb=" O PRO A 233 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N SER A 235 " --> pdb=" O LEU C 720 " (cutoff:3.500A) removed outlier: 8.146A 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 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 130 removed outlier: 3.900A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N SER B 817 " --> pdb=" O ASN B 709 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASN B 709 " --> pdb=" O SER B 817 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA B 819 " --> pdb=" O VAL B 707 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL B 707 " --> pdb=" O ALA B 819 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE B 821 " --> pdb=" O TYR B 705 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 127 through 130 removed outlier: 3.900A pdb=" N ASN B 808 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER B 673 " --> pdb=" O THR B 851 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.633A pdb=" N LYS B 174 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 292 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 172 through 177 removed outlier: 4.633A pdb=" N LYS B 174 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 292 " --> pdb=" O LYS B 174 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA B 286 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE B 279 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER B 603 " --> pdb=" O THR B 625 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 572 " --> pdb=" O MET B 656 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU B 654 " --> pdb=" O GLN B 574 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 266 through 272 removed outlier: 8.282A pdb=" N LYS B 182 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLN B 761 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN B 765 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN B 751 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 764 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 5.535A 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 Processing sheet with id=AB8, first strand: chain 'B' and resid 781 through 782 Processing sheet with id=AB9, first strand: chain 'C' and resid 127 through 130 removed outlier: 3.899A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N SER C 817 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ASN C 709 " --> pdb=" O SER C 817 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALA C 819 " --> pdb=" O VAL C 707 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL C 707 " --> pdb=" O ALA C 819 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE C 821 " --> pdb=" O TYR C 705 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 127 through 130 removed outlier: 3.899A pdb=" N ASN C 808 " --> pdb=" O SER C 815 " (cutoff:3.500A) removed outlier: 4.405A 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: 4.633A pdb=" N LYS C 174 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN C 292 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.633A pdb=" N LYS C 174 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN C 292 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA C 286 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C 603 " --> pdb=" O THR C 625 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER C 572 " --> pdb=" O MET C 656 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU C 654 " --> pdb=" O GLN C 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.282A pdb=" N LYS C 182 " --> pdb=" O MET C 759 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLN C 761 " --> pdb=" O LYS C 182 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN C 765 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN C 751 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL C 764 " --> pdb=" O TYR C 749 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TYR C 749 " --> pdb=" O VAL C 764 " (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 1569 hydrogen bonds defined for protein. 4617 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: 5.10 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 3855 1.28 - 1.41: 5298 1.41 - 1.54: 14539 1.54 - 1.68: 44 1.68 - 1.81: 264 Bond restraints: 24000 Sorted by residual: bond pdb=" C PHE A 11 " pdb=" O PHE A 11 " ideal model delta sigma weight residual 1.236 1.146 0.091 1.15e-02 7.56e+03 6.22e+01 bond pdb=" C PHE B 11 " pdb=" O PHE B 11 " ideal model delta sigma weight residual 1.236 1.146 0.091 1.15e-02 7.56e+03 6.20e+01 bond pdb=" C PHE C 11 " pdb=" O PHE C 11 " ideal model delta sigma weight residual 1.236 1.146 0.090 1.15e-02 7.56e+03 6.16e+01 bond pdb=" CG PRO B 368 " pdb=" CD PRO B 368 " ideal model delta sigma weight residual 1.503 1.292 0.211 3.40e-02 8.65e+02 3.86e+01 bond pdb=" CG PRO A 368 " pdb=" CD PRO A 368 " ideal model delta sigma weight residual 1.503 1.293 0.210 3.40e-02 8.65e+02 3.83e+01 ... (remaining 23995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 31981 3.59 - 7.19: 434 7.19 - 10.78: 66 10.78 - 14.38: 12 14.38 - 17.97: 6 Bond angle restraints: 32499 Sorted by residual: angle pdb=" CA PHE C 11 " pdb=" C PHE C 11 " pdb=" O PHE C 11 " ideal model delta sigma weight residual 120.82 108.89 11.93 1.05e+00 9.07e-01 1.29e+02 angle pdb=" CA PHE B 11 " pdb=" C PHE B 11 " pdb=" O PHE B 11 " ideal model delta sigma weight residual 120.82 108.96 11.86 1.05e+00 9.07e-01 1.28e+02 angle pdb=" CA PHE A 11 " pdb=" C PHE A 11 " pdb=" O PHE A 11 " ideal model delta sigma weight residual 120.82 109.01 11.81 1.05e+00 9.07e-01 1.27e+02 angle pdb=" CA PRO B 368 " pdb=" N PRO B 368 " pdb=" CD PRO B 368 " ideal model delta sigma weight residual 112.00 99.14 12.86 1.40e+00 5.10e-01 8.44e+01 angle pdb=" CA PRO C 368 " pdb=" N PRO C 368 " pdb=" CD PRO C 368 " ideal model delta sigma weight residual 112.00 99.16 12.84 1.40e+00 5.10e-01 8.41e+01 ... (remaining 32494 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.44: 14181 33.44 - 66.89: 336 66.89 - 100.33: 30 100.33 - 133.78: 0 133.78 - 167.22: 3 Dihedral angle restraints: 14550 sinusoidal: 5733 harmonic: 8817 Sorted by residual: dihedral pdb=" N1 PTY C1102 " pdb=" C2 PTY C1102 " pdb=" C3 PTY C1102 " pdb=" O11 PTY C1102 " ideal model delta sinusoidal sigma weight residual 65.33 -127.45 -167.22 1 3.00e+01 1.11e-03 2.11e+01 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 -127.51 -167.16 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N1 PTY A1102 " pdb=" C2 PTY A1102 " pdb=" C3 PTY A1102 " pdb=" O11 PTY A1102 " ideal model delta sinusoidal sigma weight residual 65.33 -127.52 -167.15 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 14547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.344: 3867 0.344 - 0.689: 6 0.689 - 1.033: 0 1.033 - 1.377: 0 1.377 - 1.722: 3 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CG LEU B 158 " pdb=" CB LEU B 158 " pdb=" CD1 LEU B 158 " pdb=" CD2 LEU B 158 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.41e+01 chirality pdb=" CG LEU A 158 " pdb=" CB LEU A 158 " pdb=" CD1 LEU A 158 " pdb=" CD2 LEU A 158 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.72 2.00e-01 2.50e+01 7.36e+01 chirality pdb=" CG LEU C 158 " pdb=" CB LEU C 158 " pdb=" CD1 LEU C 158 " pdb=" CD2 LEU C 158 " both_signs ideal model delta sigma weight residual False -2.59 -0.87 -1.71 2.00e-01 2.50e+01 7.35e+01 ... (remaining 3873 not shown) Planarity restraints: 4068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 883 " 0.021 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C TYR B 883 " -0.075 2.00e-02 2.50e+03 pdb=" O TYR B 883 " 0.028 2.00e-02 2.50e+03 pdb=" N GLU B 884 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 883 " 0.020 2.00e-02 2.50e+03 4.33e-02 1.88e+01 pdb=" C TYR A 883 " -0.075 2.00e-02 2.50e+03 pdb=" O TYR A 883 " 0.028 2.00e-02 2.50e+03 pdb=" N GLU A 884 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 883 " -0.020 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C TYR C 883 " 0.075 2.00e-02 2.50e+03 pdb=" O TYR C 883 " -0.028 2.00e-02 2.50e+03 pdb=" N GLU C 884 " -0.026 2.00e-02 2.50e+03 ... (remaining 4065 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 174 2.58 - 3.16: 20860 3.16 - 3.74: 36641 3.74 - 4.32: 49894 4.32 - 4.90: 84101 Nonbonded interactions: 191670 Sorted by model distance: nonbonded pdb=" OD2 ASP C 565 " pdb=" OG SER C 635 " model vdw 1.997 3.040 nonbonded pdb=" OD2 ASP B 565 " pdb=" OG SER B 635 " model vdw 1.997 3.040 nonbonded pdb=" OD2 ASP A 565 " pdb=" OG SER A 635 " model vdw 1.997 3.040 nonbonded pdb=" O LEU C 219 " pdb=" OG1 THR C 231 " model vdw 2.007 3.040 nonbonded pdb=" O LEU A 219 " pdb=" OG1 THR A 231 " model vdw 2.007 3.040 ... (remaining 191665 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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 group one per residue 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 23.440 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 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 : 0.006 0.211 24000 Z= 0.358 Angle : 1.013 17.974 32499 Z= 0.637 Chirality : 0.071 1.722 3876 Planarity : 0.006 0.091 4068 Dihedral : 14.678 167.221 8844 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.44 % Allowed : 2.03 % Favored : 96.53 % Cbeta Deviations : 0.42 % 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: 0.77 (0.16), residues: 3048 helix: 1.20 (0.13), residues: 1680 sheet: -0.47 (0.23), residues: 474 loop : -0.01 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 418 TYR 0.061 0.003 TYR C 883 PHE 0.021 0.002 PHE C 612 TRP 0.026 0.002 TRP B 708 HIS 0.004 0.001 HIS C 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.36 (24000) covalent geometry : angle 1.01291 / 0.64 (32499) hydrogen bonds : bond 0.15870 / 10.41 ( 1500) hydrogen bonds : angle 6.84401 / 4.97 ( 4617) *********************** 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 705 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 668 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8065 (tptp) cc_final: 0.7800 (ttpt) REVERT: A 273 GLN cc_start: 0.7397 (tt0) cc_final: 0.7155 (tt0) REVERT: A 292 GLN cc_start: 0.6234 (OUTLIER) cc_final: 0.6006 (pp30) REVERT: A 377 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7239 (mt) REVERT: A 433 LYS cc_start: 0.6380 (ttpp) cc_final: 0.6164 (ttpp) REVERT: A 456 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7259 (mtm) REVERT: A 458 PHE cc_start: 0.7143 (m-10) cc_final: 0.6645 (m-80) REVERT: A 677 GLN cc_start: 0.7356 (pt0) cc_final: 0.6881 (mt0) REVERT: A 706 MET cc_start: 0.6589 (ptp) cc_final: 0.6056 (ptt) REVERT: A 710 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7879 (tt0) REVERT: A 716 ASP cc_start: 0.7042 (p0) cc_final: 0.6493 (p0) REVERT: A 720 LEU cc_start: 0.5322 (mt) cc_final: 0.4846 (mp) REVERT: A 772 MET cc_start: 0.6162 (mmt) cc_final: 0.5791 (mmt) REVERT: A 781 LYS cc_start: 0.7203 (mppt) cc_final: 0.6939 (mmtt) REVERT: A 783 MET cc_start: 0.4083 (tmm) cc_final: 0.3279 (tmm) REVERT: B 189 ASP cc_start: 0.7825 (m-30) cc_final: 0.7413 (m-30) REVERT: B 208 ARG cc_start: 0.6441 (mmm-85) cc_final: 0.5361 (mtm-85) REVERT: B 292 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6442 (pp30) REVERT: B 356 TYR cc_start: 0.7752 (t80) cc_final: 0.7427 (t80) REVERT: B 377 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.6593 (mt) REVERT: B 456 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7248 (mtm) REVERT: B 639 MET cc_start: 0.7285 (mmm) cc_final: 0.6940 (ttt) REVERT: B 677 GLN cc_start: 0.7633 (pt0) cc_final: 0.7403 (mt0) REVERT: B 697 MET cc_start: 0.7324 (mtp) cc_final: 0.6944 (mtp) REVERT: B 716 ASP cc_start: 0.7043 (p0) cc_final: 0.6691 (p0) REVERT: B 720 LEU cc_start: 0.5662 (mt) cc_final: 0.4971 (mp) REVERT: B 748 MET cc_start: 0.7304 (mtm) cc_final: 0.7090 (mtm) REVERT: B 772 MET cc_start: 0.6105 (mmt) cc_final: 0.4733 (mmt) REVERT: B 781 LYS cc_start: 0.6938 (mppt) cc_final: 0.6428 (mmtt) REVERT: B 783 MET cc_start: 0.4191 (tmm) cc_final: 0.3519 (tmm) REVERT: C 112 LYS cc_start: 0.8123 (tptp) cc_final: 0.7833 (ttpt) REVERT: C 208 ARG cc_start: 0.6255 (mmm-85) cc_final: 0.5594 (ttm110) REVERT: C 229 LEU cc_start: 0.7372 (tp) cc_final: 0.7034 (pt) REVERT: C 267 ASN cc_start: 0.7848 (OUTLIER) cc_final: 0.7573 (p0) REVERT: C 273 GLN cc_start: 0.7523 (tt0) cc_final: 0.7291 (tt0) REVERT: C 345 LEU cc_start: 0.7659 (mm) cc_final: 0.7408 (mt) REVERT: C 377 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7134 (mt) REVERT: C 433 LYS cc_start: 0.6236 (ttpp) cc_final: 0.5991 (ttpp) REVERT: C 456 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7129 (mtm) REVERT: C 639 MET cc_start: 0.7447 (mmm) cc_final: 0.7089 (ttt) REVERT: C 641 SER cc_start: 0.7100 (m) cc_final: 0.6852 (p) REVERT: C 656 MET cc_start: 0.7395 (mtt) cc_final: 0.7140 (mtt) REVERT: C 677 GLN cc_start: 0.7384 (pt0) cc_final: 0.7003 (mt0) REVERT: C 720 LEU cc_start: 0.5767 (mt) cc_final: 0.5161 (mp) REVERT: C 748 MET cc_start: 0.7444 (mtm) cc_final: 0.6852 (mtp) REVERT: C 776 ASP cc_start: 0.6486 (m-30) cc_final: 0.6238 (m-30) REVERT: C 779 ASN cc_start: 0.6310 (t0) cc_final: 0.5831 (t0) REVERT: C 783 MET cc_start: 0.4198 (tmm) cc_final: 0.2979 (tpp) REVERT: C 835 MET cc_start: 0.7561 (tpt) cc_final: 0.7021 (tpt) outliers start: 37 outliers final: 11 residues processed: 695 average time/residue: 0.1321 time to fit residues: 150.0640 Evaluate side-chains 607 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 587 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 292 GLN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 555 TYR Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 555 TYR Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 267 ASN Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 867 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.0770 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 3.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN A 292 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 120 GLN B 176 GLN B 292 GLN B 360 HIS B 534 HIS ** B 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 GLN C 108 GLN C 120 GLN C 176 GLN ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS C 415 ASN C 534 HIS ** C 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.186069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.153000 restraints weight = 28983.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.157162 restraints weight = 17485.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.159945 restraints weight = 12568.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.161708 restraints weight = 10112.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.162811 restraints weight = 8783.593| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24000 Z= 0.173 Angle : 0.657 13.057 32499 Z= 0.341 Chirality : 0.044 0.220 3876 Planarity : 0.005 0.056 4068 Dihedral : 10.136 177.528 3383 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.57 % Allowed : 12.44 % Favored : 84.99 % 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: 1.01 (0.15), residues: 3048 helix: 1.54 (0.13), residues: 1698 sheet: -0.40 (0.23), residues: 438 loop : -0.28 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 515 TYR 0.025 0.002 TYR B 77 PHE 0.034 0.002 PHE B 22 TRP 0.019 0.002 TRP C 556 HIS 0.006 0.002 HIS B 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 (24000) covalent geometry : angle 0.65695 / 0.34 (32499) hydrogen bonds : bond 0.05049 / 3.44 ( 1500) hydrogen bonds : angle 5.01937 / 3.62 ( 4617) *********************** 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 660 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 594 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.8257 (tptp) cc_final: 0.7848 (ttpt) REVERT: A 273 GLN cc_start: 0.7505 (tt0) cc_final: 0.7244 (tt0) REVERT: A 367 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7910 (mp) REVERT: A 433 LYS cc_start: 0.6501 (ttpp) cc_final: 0.6260 (tttm) REVERT: A 456 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7313 (mtm) REVERT: A 526 LEU cc_start: 0.7538 (pp) cc_final: 0.7327 (tt) REVERT: A 695 MET cc_start: 0.6029 (tmm) cc_final: 0.5106 (mmm) REVERT: A 710 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7933 (mt-10) REVERT: A 720 LEU cc_start: 0.5466 (mt) cc_final: 0.4856 (mp) REVERT: A 755 ASN cc_start: 0.6777 (t0) cc_final: 0.6539 (t0) REVERT: A 783 MET cc_start: 0.3866 (tmm) cc_final: 0.3083 (tmm) REVERT: B 1 MET cc_start: 0.2760 (mtm) cc_final: 0.2541 (mmm) REVERT: B 34 ARG cc_start: 0.7900 (ttt180) cc_final: 0.7642 (ttt180) REVERT: B 35 PHE cc_start: 0.7850 (m-80) cc_final: 0.7531 (m-10) REVERT: B 433 LYS cc_start: 0.6708 (tttm) cc_final: 0.6126 (pttp) REVERT: B 695 MET cc_start: 0.6054 (tmm) cc_final: 0.5269 (mmm) REVERT: B 697 MET cc_start: 0.7126 (mtp) cc_final: 0.6748 (mtp) REVERT: B 710 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7831 (tt0) REVERT: B 779 ASN cc_start: 0.7190 (t0) cc_final: 0.6305 (t0) REVERT: B 781 LYS cc_start: 0.6982 (mppt) cc_final: 0.6490 (mmtt) REVERT: B 783 MET cc_start: 0.3645 (tmm) cc_final: 0.2390 (tpp) REVERT: B 824 PHE cc_start: 0.7060 (t80) cc_final: 0.6773 (t80) REVERT: B 857 GLU cc_start: 0.8250 (tt0) cc_final: 0.8009 (tt0) REVERT: B 1009 ILE cc_start: 0.6820 (pt) cc_final: 0.6497 (pt) REVERT: C 1 MET cc_start: 0.3324 (mtm) cc_final: 0.2979 (mmm) REVERT: C 44 ASN cc_start: 0.7044 (t0) cc_final: 0.6531 (p0) REVERT: C 112 LYS cc_start: 0.8240 (tptp) cc_final: 0.7759 (ttpt) REVERT: C 125 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7791 (mm-40) REVERT: C 127 LEU cc_start: 0.7011 (mp) cc_final: 0.6465 (pt) REVERT: C 208 ARG cc_start: 0.6395 (mmm-85) cc_final: 0.5698 (ttm110) REVERT: C 229 LEU cc_start: 0.7500 (tp) cc_final: 0.7202 (tt) REVERT: C 273 GLN cc_start: 0.7548 (tt0) cc_final: 0.7293 (tt0) REVERT: C 456 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7025 (mtm) REVERT: C 526 LEU cc_start: 0.7604 (pp) cc_final: 0.7257 (tt) REVERT: C 641 SER cc_start: 0.7163 (m) cc_final: 0.6872 (p) REVERT: C 677 GLN cc_start: 0.7813 (pt0) cc_final: 0.7505 (mt0) REVERT: C 695 MET cc_start: 0.6239 (tmm) cc_final: 0.5375 (mmm) REVERT: C 748 MET cc_start: 0.7248 (mtm) cc_final: 0.6783 (mtp) REVERT: C 776 ASP cc_start: 0.6587 (m-30) cc_final: 0.6356 (m-30) REVERT: C 783 MET cc_start: 0.3972 (tmm) cc_final: 0.2793 (tpp) REVERT: C 835 MET cc_start: 0.7611 (tpt) cc_final: 0.7059 (tpt) REVERT: C 948 MET cc_start: 0.5049 (tpp) cc_final: 0.4785 (tpt) outliers start: 66 outliers final: 36 residues processed: 630 average time/residue: 0.1407 time to fit residues: 144.0328 Evaluate side-chains 601 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 562 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 556 TRP Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 556 TRP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 556 TRP Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 890 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 173 optimal weight: 10.0000 chunk 285 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 223 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 204 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 GLN ** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 ASN B 245 GLN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** B 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 GLN C 176 GLN C 211 ASN C 245 GLN C 292 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 GLN ** C 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.181175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.147608 restraints weight = 28980.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.151652 restraints weight = 17670.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.154345 restraints weight = 12817.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.155896 restraints weight = 10377.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.157157 restraints weight = 9097.962| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24000 Z= 0.207 Angle : 0.662 14.113 32499 Z= 0.341 Chirality : 0.045 0.194 3876 Planarity : 0.005 0.058 4068 Dihedral : 9.195 156.215 3359 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.63 % Allowed : 14.89 % Favored : 81.48 % 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: 0.80 (0.15), residues: 3048 helix: 1.32 (0.12), residues: 1704 sheet: -0.43 (0.22), residues: 471 loop : -0.31 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 515 TYR 0.025 0.002 TYR B 77 PHE 0.027 0.002 PHE A 824 TRP 0.019 0.002 TRP C 556 HIS 0.005 0.002 HIS C 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (24000) covalent geometry : angle 0.66243 / 0.34 (32499) hydrogen bonds : bond 0.05187 / 3.53 ( 1500) hydrogen bonds : angle 4.86366 / 3.50 ( 4617) *********************** 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 674 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 581 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.7851 (mp) cc_final: 0.7649 (mt) REVERT: A 112 LYS cc_start: 0.8282 (tptp) cc_final: 0.7900 (ttpt) REVERT: A 273 GLN cc_start: 0.7784 (tt0) cc_final: 0.7468 (tt0) REVERT: A 343 THR cc_start: 0.8097 (m) cc_final: 0.7816 (m) REVERT: A 367 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7895 (mp) REVERT: A 433 LYS cc_start: 0.6638 (ttpp) cc_final: 0.6301 (ttpp) REVERT: A 456 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7250 (mtm) REVERT: A 526 LEU cc_start: 0.7572 (pp) cc_final: 0.7366 (tt) REVERT: A 527 MET cc_start: 0.6480 (ttp) cc_final: 0.6203 (ttt) REVERT: A 720 LEU cc_start: 0.5721 (mt) cc_final: 0.5489 (mt) REVERT: A 779 ASN cc_start: 0.6967 (t0) cc_final: 0.6018 (t0) REVERT: A 781 LYS cc_start: 0.7198 (mppt) cc_final: 0.6659 (mmtt) REVERT: A 783 MET cc_start: 0.3652 (tmm) cc_final: 0.2922 (tmm) REVERT: A 970 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6930 (mp) REVERT: B 35 PHE cc_start: 0.7947 (m-80) cc_final: 0.7720 (m-10) REVERT: B 181 GLU cc_start: 0.5701 (pp20) cc_final: 0.5419 (pp20) REVERT: B 273 GLN cc_start: 0.7745 (tt0) cc_final: 0.7061 (tt0) REVERT: B 356 TYR cc_start: 0.8010 (t80) cc_final: 0.7380 (t80) REVERT: B 367 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7838 (mp) REVERT: B 456 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7436 (mpm) REVERT: B 697 MET cc_start: 0.6960 (mtp) cc_final: 0.6668 (mtp) REVERT: B 706 MET cc_start: 0.6963 (OUTLIER) cc_final: 0.6421 (mtm) REVERT: B 779 ASN cc_start: 0.7252 (t0) cc_final: 0.6579 (t0) REVERT: B 781 LYS cc_start: 0.7025 (mppt) cc_final: 0.6728 (mmtt) REVERT: B 783 MET cc_start: 0.3824 (tmm) cc_final: 0.2475 (tpp) REVERT: B 791 SER cc_start: 0.7504 (t) cc_final: 0.7127 (p) REVERT: B 857 GLU cc_start: 0.8252 (tt0) cc_final: 0.7976 (tt0) REVERT: B 893 MET cc_start: 0.7181 (mpp) cc_final: 0.6697 (mmm) REVERT: B 932 ASN cc_start: 0.8450 (m-40) cc_final: 0.8117 (m-40) REVERT: C 1 MET cc_start: 0.3206 (mtm) cc_final: 0.2927 (mmm) REVERT: C 44 ASN cc_start: 0.7154 (t0) cc_final: 0.6826 (p0) REVERT: C 112 LYS cc_start: 0.8221 (tptp) cc_final: 0.7728 (ttpt) REVERT: C 229 LEU cc_start: 0.7544 (tp) cc_final: 0.7263 (tt) REVERT: C 292 GLN cc_start: 0.5425 (OUTLIER) cc_final: 0.5097 (pp30) REVERT: C 343 THR cc_start: 0.7858 (m) cc_final: 0.7636 (m) REVERT: C 357 LEU cc_start: 0.8513 (tp) cc_final: 0.8269 (tp) REVERT: C 394 THR cc_start: 0.8386 (m) cc_final: 0.8097 (p) REVERT: C 398 MET cc_start: 0.8718 (mtt) cc_final: 0.8437 (mtt) REVERT: C 456 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.6941 (mtm) REVERT: C 527 MET cc_start: 0.6769 (ttt) cc_final: 0.6469 (ttt) REVERT: C 586 ASN cc_start: 0.6585 (m-40) cc_final: 0.6285 (m-40) REVERT: C 641 SER cc_start: 0.7265 (m) cc_final: 0.6917 (p) REVERT: C 695 MET cc_start: 0.6428 (tmm) cc_final: 0.5050 (mmm) REVERT: C 706 MET cc_start: 0.7447 (ptp) cc_final: 0.7172 (mtm) REVERT: C 748 MET cc_start: 0.7299 (mtm) cc_final: 0.6789 (mtp) REVERT: C 776 ASP cc_start: 0.6707 (m-30) cc_final: 0.6255 (m-30) REVERT: C 783 MET cc_start: 0.3940 (tmm) cc_final: 0.3084 (tmm) REVERT: C 835 MET cc_start: 0.7388 (tpt) cc_final: 0.6965 (tpt) outliers start: 93 outliers final: 62 residues processed: 639 average time/residue: 0.1502 time to fit residues: 156.8005 Evaluate side-chains 625 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 555 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 545 ILE Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 617 GLN Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 823 ASN Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 556 TRP Chi-restraints excluded: chain C residue 565 ASP Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 759 MET Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 860 SER Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 970 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 238 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 230 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 269 optimal weight: 0.4980 chunk 231 optimal weight: 9.9990 chunk 198 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 294 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN B 204 ASN B 415 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN B 644 ASN B 701 ASN B 761 GLN C 245 GLN C 292 GLN C 415 ASN C 677 GLN C 701 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.185573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.152993 restraints weight = 29076.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.156999 restraints weight = 17782.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.159640 restraints weight = 12903.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.161381 restraints weight = 10460.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.162466 restraints weight = 9104.525| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24000 Z= 0.127 Angle : 0.583 12.723 32499 Z= 0.300 Chirality : 0.041 0.279 3876 Planarity : 0.004 0.055 4068 Dihedral : 8.293 127.632 3355 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.88 % Allowed : 17.43 % Favored : 79.69 % 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: 1.22 (0.15), residues: 3048 helix: 1.69 (0.13), residues: 1713 sheet: -0.36 (0.22), residues: 471 loop : -0.15 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 208 TYR 0.023 0.001 TYR B 77 PHE 0.021 0.001 PHE C 824 TRP 0.018 0.001 TRP C 556 HIS 0.003 0.001 HIS B 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (24000) covalent geometry : angle 0.58320 / 0.30 (32499) hydrogen bonds : bond 0.04295 / 2.94 ( 1500) hydrogen bonds : angle 4.54775 / 3.26 ( 4617) *********************** 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 655 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 581 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.6561 (m-80) cc_final: 0.6092 (m-80) REVERT: A 125 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7396 (mm-40) REVERT: A 273 GLN cc_start: 0.7618 (tt0) cc_final: 0.7370 (tt0) REVERT: A 433 LYS cc_start: 0.6712 (ttpp) cc_final: 0.6330 (ttpp) REVERT: A 456 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7520 (mpm) REVERT: A 527 MET cc_start: 0.6473 (ttp) cc_final: 0.6192 (ttt) REVERT: A 695 MET cc_start: 0.6155 (OUTLIER) cc_final: 0.5009 (mmm) REVERT: A 720 LEU cc_start: 0.5748 (mt) cc_final: 0.5188 (mp) REVERT: A 748 MET cc_start: 0.7264 (mtm) cc_final: 0.7009 (mtm) REVERT: A 755 ASN cc_start: 0.6864 (t0) cc_final: 0.6638 (t0) REVERT: A 779 ASN cc_start: 0.6947 (t0) cc_final: 0.6243 (t0) REVERT: A 781 LYS cc_start: 0.7232 (mppt) cc_final: 0.6838 (mmtt) REVERT: A 783 MET cc_start: 0.3769 (tmm) cc_final: 0.3028 (tmm) REVERT: A 948 MET cc_start: 0.5184 (tpp) cc_final: 0.4948 (tpt) REVERT: B 34 ARG cc_start: 0.7770 (ttt180) cc_final: 0.7472 (ttt180) REVERT: B 35 PHE cc_start: 0.7896 (m-80) cc_final: 0.7579 (m-10) REVERT: B 44 ASN cc_start: 0.6772 (t0) cc_final: 0.6548 (p0) REVERT: B 181 GLU cc_start: 0.5522 (pp20) cc_final: 0.5261 (pp20) REVERT: B 273 GLN cc_start: 0.7595 (tt0) cc_final: 0.6846 (tt0) REVERT: B 356 TYR cc_start: 0.7930 (t80) cc_final: 0.7325 (t80) REVERT: B 367 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7842 (mp) REVERT: B 433 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6442 (tttm) REVERT: B 628 ASP cc_start: 0.7591 (t0) cc_final: 0.7297 (t0) REVERT: B 675 ARG cc_start: 0.8306 (mmt-90) cc_final: 0.7760 (mpt180) REVERT: B 695 MET cc_start: 0.5966 (OUTLIER) cc_final: 0.5366 (mmm) REVERT: B 697 MET cc_start: 0.7049 (mtp) cc_final: 0.6709 (mtp) REVERT: B 761 GLN cc_start: 0.6495 (mt0) cc_final: 0.6201 (mt0) REVERT: B 779 ASN cc_start: 0.7240 (t0) cc_final: 0.6126 (t0) REVERT: B 781 LYS cc_start: 0.6949 (mppt) cc_final: 0.6555 (mmtt) REVERT: B 783 MET cc_start: 0.3837 (tmm) cc_final: 0.2494 (tpp) REVERT: B 857 GLU cc_start: 0.8311 (tt0) cc_final: 0.7986 (tt0) REVERT: B 893 MET cc_start: 0.7150 (mpp) cc_final: 0.6698 (mmm) REVERT: C 22 PHE cc_start: 0.7122 (m-80) cc_final: 0.6680 (m-80) REVERT: C 44 ASN cc_start: 0.7269 (t0) cc_final: 0.6874 (p0) REVERT: C 229 LEU cc_start: 0.7583 (tp) cc_final: 0.7304 (tt) REVERT: C 292 GLN cc_start: 0.5628 (OUTLIER) cc_final: 0.5426 (pp30) REVERT: C 343 THR cc_start: 0.7783 (m) cc_final: 0.7571 (m) REVERT: C 456 MET cc_start: 0.8028 (mpm) cc_final: 0.6714 (mtm) REVERT: C 483 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5400 (pp) REVERT: C 527 MET cc_start: 0.6714 (ttt) cc_final: 0.6491 (ttt) REVERT: C 586 ASN cc_start: 0.6605 (m-40) cc_final: 0.6273 (m-40) REVERT: C 641 SER cc_start: 0.7097 (m) cc_final: 0.6801 (p) REVERT: C 677 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.6875 (mt0) REVERT: C 695 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.5206 (mmm) REVERT: C 748 MET cc_start: 0.7250 (mtm) cc_final: 0.6809 (mtp) REVERT: C 779 ASN cc_start: 0.6638 (t0) cc_final: 0.6173 (t0) REVERT: C 783 MET cc_start: 0.3909 (tmm) cc_final: 0.3044 (tmm) REVERT: C 835 MET cc_start: 0.7529 (tpt) cc_final: 0.7111 (tpt) REVERT: C 900 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.6961 (mm) REVERT: C 948 MET cc_start: 0.5565 (tpp) cc_final: 0.4948 (tpt) outliers start: 74 outliers final: 41 residues processed: 627 average time/residue: 0.1463 time to fit residues: 148.8394 Evaluate side-chains 597 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 546 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 292 GLN Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 556 TRP Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 900 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 143 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN B 42 GLN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 GLN ** B 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 GLN ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.185271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.152383 restraints weight = 28973.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.156537 restraints weight = 17446.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.159298 restraints weight = 12491.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.160995 restraints weight = 10015.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.162220 restraints weight = 8655.219| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24000 Z= 0.129 Angle : 0.576 12.268 32499 Z= 0.296 Chirality : 0.041 0.192 3876 Planarity : 0.004 0.058 4068 Dihedral : 7.458 86.801 3350 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.00 % Allowed : 17.86 % Favored : 79.14 % 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: 1.31 (0.15), residues: 3048 helix: 1.75 (0.13), residues: 1713 sheet: -0.14 (0.23), residues: 435 loop : -0.21 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 208 TYR 0.026 0.001 TYR C 77 PHE 0.026 0.002 PHE C 824 TRP 0.018 0.001 TRP C 556 HIS 0.002 0.001 HIS B 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (24000) covalent geometry : angle 0.57621 / 0.30 (32499) hydrogen bonds : bond 0.04195 / 2.88 ( 1500) hydrogen bonds : angle 4.45964 / 3.20 ( 4617) *********************** 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 645 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 568 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 22 PHE cc_start: 0.6535 (m-80) cc_final: 0.6062 (m-80) REVERT: A 44 ASN cc_start: 0.6739 (t0) cc_final: 0.6298 (p0) REVERT: A 273 GLN cc_start: 0.7584 (tt0) cc_final: 0.7306 (tt0) REVERT: A 433 LYS cc_start: 0.6700 (ttpp) cc_final: 0.6407 (ttmm) REVERT: A 456 MET cc_start: 0.7932 (mpm) cc_final: 0.7108 (mtm) REVERT: A 527 MET cc_start: 0.6448 (ttp) cc_final: 0.6231 (ttt) REVERT: A 639 MET cc_start: 0.7591 (mmm) cc_final: 0.6935 (tpt) REVERT: A 675 ARG cc_start: 0.8144 (mmt-90) cc_final: 0.7788 (mpt180) REVERT: A 695 MET cc_start: 0.6129 (OUTLIER) cc_final: 0.4846 (mmm) REVERT: A 720 LEU cc_start: 0.5735 (mt) cc_final: 0.5223 (mp) REVERT: A 748 MET cc_start: 0.7212 (mtm) cc_final: 0.6789 (mtp) REVERT: A 779 ASN cc_start: 0.6940 (t0) cc_final: 0.6210 (t0) REVERT: A 781 LYS cc_start: 0.7231 (mppt) cc_final: 0.6827 (mmtt) REVERT: A 783 MET cc_start: 0.3707 (tmm) cc_final: 0.2963 (tmm) REVERT: A 799 GLN cc_start: 0.7544 (pm20) cc_final: 0.7283 (pm20) REVERT: B 35 PHE cc_start: 0.7900 (m-80) cc_final: 0.7510 (m-10) REVERT: B 181 GLU cc_start: 0.5600 (pp20) cc_final: 0.5395 (pp20) REVERT: B 273 GLN cc_start: 0.7571 (tt0) cc_final: 0.6315 (tt0) REVERT: B 356 TYR cc_start: 0.7939 (t80) cc_final: 0.7332 (t80) REVERT: B 367 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7808 (mp) REVERT: B 433 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6465 (tttm) REVERT: B 564 GLU cc_start: 0.6621 (mm-30) cc_final: 0.6248 (mp0) REVERT: B 695 MET cc_start: 0.5969 (OUTLIER) cc_final: 0.5132 (mmm) REVERT: B 697 MET cc_start: 0.7093 (mtp) cc_final: 0.6748 (mtp) REVERT: B 761 GLN cc_start: 0.6532 (mt0) cc_final: 0.5915 (mt0) REVERT: B 779 ASN cc_start: 0.7375 (t0) cc_final: 0.6206 (t0) REVERT: B 781 LYS cc_start: 0.6997 (mppt) cc_final: 0.6596 (mmtt) REVERT: B 783 MET cc_start: 0.3907 (tmm) cc_final: 0.2526 (tpp) REVERT: B 857 GLU cc_start: 0.8252 (tt0) cc_final: 0.7850 (tt0) REVERT: B 893 MET cc_start: 0.7147 (mpp) cc_final: 0.6676 (mmm) REVERT: C 22 PHE cc_start: 0.7112 (m-80) cc_final: 0.6586 (m-80) REVERT: C 44 ASN cc_start: 0.7181 (t0) cc_final: 0.6849 (p0) REVERT: C 273 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: C 390 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8309 (mt) REVERT: C 456 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.6754 (mtm) REVERT: C 483 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5380 (pp) REVERT: C 527 MET cc_start: 0.6689 (ttt) cc_final: 0.6285 (ttt) REVERT: C 564 GLU cc_start: 0.6617 (mm-30) cc_final: 0.6220 (mp0) REVERT: C 586 ASN cc_start: 0.6527 (m-40) cc_final: 0.6163 (m-40) REVERT: C 641 SER cc_start: 0.7121 (m) cc_final: 0.6812 (p) REVERT: C 695 MET cc_start: 0.6115 (OUTLIER) cc_final: 0.5003 (mmm) REVERT: C 748 MET cc_start: 0.7290 (mtm) cc_final: 0.6826 (mtp) REVERT: C 776 ASP cc_start: 0.6699 (m-30) cc_final: 0.6258 (m-30) REVERT: C 779 ASN cc_start: 0.6708 (t0) cc_final: 0.6204 (t0) REVERT: C 783 MET cc_start: 0.3851 (tmm) cc_final: 0.2989 (tmm) REVERT: C 835 MET cc_start: 0.7443 (tpt) cc_final: 0.7085 (tpt) REVERT: C 900 ILE cc_start: 0.7318 (OUTLIER) cc_final: 0.6965 (mm) REVERT: C 962 LEU cc_start: 0.7655 (tt) cc_final: 0.7449 (tt) outliers start: 77 outliers final: 49 residues processed: 618 average time/residue: 0.1478 time to fit residues: 148.4971 Evaluate side-chains 609 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 550 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 939 PHE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 806 GLN Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 900 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 40 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 269 optimal weight: 0.0870 chunk 13 optimal weight: 8.9990 chunk 251 optimal weight: 4.9990 chunk 57 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 104 optimal weight: 0.0020 overall best weight: 1.5970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN A 823 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.185404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.152431 restraints weight = 29032.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.156488 restraints weight = 17588.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.159127 restraints weight = 12710.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.160926 restraints weight = 10291.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.162028 restraints weight = 8917.695| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 24000 Z= 0.131 Angle : 0.590 12.606 32499 Z= 0.300 Chirality : 0.042 0.215 3876 Planarity : 0.004 0.060 4068 Dihedral : 6.894 59.659 3345 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.66 % Allowed : 18.01 % Favored : 78.32 % 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: 1.77 (0.13), residues: 1713 sheet: -0.12 (0.23), residues: 435 loop : -0.22 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 515 TYR 0.024 0.001 TYR A 77 PHE 0.027 0.001 PHE C 824 TRP 0.009 0.001 TRP A 512 HIS 0.002 0.001 HIS B 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (24000) covalent geometry : angle 0.58995 / 0.30 (32499) hydrogen bonds : bond 0.04145 / 2.85 ( 1500) hydrogen bonds : angle 4.42706 / 3.17 ( 4617) *********************** 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 656 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 562 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.6577 (m-80) cc_final: 0.6087 (m-80) REVERT: A 44 ASN cc_start: 0.6714 (t0) cc_final: 0.6261 (p0) REVERT: A 125 GLN cc_start: 0.8109 (mm110) cc_final: 0.7215 (mm-40) REVERT: A 394 THR cc_start: 0.8291 (m) cc_final: 0.8090 (p) REVERT: A 433 LYS cc_start: 0.6739 (ttpp) cc_final: 0.6413 (ttmm) REVERT: A 456 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.6936 (mtm) REVERT: A 527 MET cc_start: 0.6416 (ttp) cc_final: 0.6055 (ttt) REVERT: A 639 MET cc_start: 0.7589 (mmm) cc_final: 0.6948 (tpt) REVERT: A 647 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.5211 (tpt) REVERT: A 675 ARG cc_start: 0.8179 (mmt-90) cc_final: 0.7769 (mpt180) REVERT: A 695 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.4800 (mmm) REVERT: A 720 LEU cc_start: 0.5772 (mt) cc_final: 0.5268 (mp) REVERT: A 748 MET cc_start: 0.7219 (mtm) cc_final: 0.6770 (mtp) REVERT: A 779 ASN cc_start: 0.6910 (t0) cc_final: 0.6200 (t0) REVERT: A 781 LYS cc_start: 0.7252 (mppt) cc_final: 0.6870 (mmtt) REVERT: A 783 MET cc_start: 0.3819 (tmm) cc_final: 0.3014 (tmm) REVERT: A 944 LYS cc_start: 0.7311 (tptm) cc_final: 0.7017 (tppp) REVERT: A 970 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6873 (mp) REVERT: B 229 LEU cc_start: 0.7380 (tp) cc_final: 0.7093 (tt) REVERT: B 273 GLN cc_start: 0.7638 (tt0) cc_final: 0.6911 (tt0) REVERT: B 356 TYR cc_start: 0.8034 (t80) cc_final: 0.7429 (t80) REVERT: B 367 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7801 (mp) REVERT: B 433 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6415 (tttm) REVERT: B 564 GLU cc_start: 0.6605 (mm-30) cc_final: 0.6332 (mp0) REVERT: B 695 MET cc_start: 0.6055 (OUTLIER) cc_final: 0.5128 (mmm) REVERT: B 697 MET cc_start: 0.7096 (mtp) cc_final: 0.6757 (mtp) REVERT: B 772 MET cc_start: 0.5460 (mmt) cc_final: 0.4577 (mmt) REVERT: B 779 ASN cc_start: 0.7419 (t0) cc_final: 0.6214 (t0) REVERT: B 781 LYS cc_start: 0.7013 (mppt) cc_final: 0.6592 (mmtt) REVERT: B 783 MET cc_start: 0.4106 (tmm) cc_final: 0.2653 (tpp) REVERT: B 857 GLU cc_start: 0.8277 (tt0) cc_final: 0.7877 (tt0) REVERT: B 893 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6540 (mmm) REVERT: C 22 PHE cc_start: 0.7111 (m-80) cc_final: 0.6590 (m-80) REVERT: C 44 ASN cc_start: 0.7178 (t0) cc_final: 0.6836 (p0) REVERT: C 273 GLN cc_start: 0.7639 (tt0) cc_final: 0.7165 (tt0) REVERT: C 323 PHE cc_start: 0.6598 (m-80) cc_final: 0.6304 (m-80) REVERT: C 390 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8341 (mt) REVERT: C 456 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.6748 (mtm) REVERT: C 523 LYS cc_start: 0.6097 (mmtt) cc_final: 0.5894 (mmmm) REVERT: C 527 MET cc_start: 0.6657 (ttt) cc_final: 0.6236 (ttt) REVERT: C 564 GLU cc_start: 0.6486 (mm-30) cc_final: 0.6264 (mp0) REVERT: C 586 ASN cc_start: 0.6544 (m-40) cc_final: 0.6192 (m-40) REVERT: C 641 SER cc_start: 0.7167 (m) cc_final: 0.6847 (p) REVERT: C 677 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7456 (mt0) REVERT: C 695 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5068 (mmm) REVERT: C 748 MET cc_start: 0.7312 (mtm) cc_final: 0.6876 (mtp) REVERT: C 776 ASP cc_start: 0.6720 (m-30) cc_final: 0.6475 (m-30) REVERT: C 779 ASN cc_start: 0.6683 (t0) cc_final: 0.6151 (t0) REVERT: C 783 MET cc_start: 0.3872 (tmm) cc_final: 0.3003 (tmm) REVERT: C 835 MET cc_start: 0.7487 (tpt) cc_final: 0.7066 (tpt) REVERT: C 900 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.6922 (mm) outliers start: 94 outliers final: 62 residues processed: 626 average time/residue: 0.1409 time to fit residues: 143.1225 Evaluate side-chains 623 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 548 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 556 TRP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 561 MET Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 806 GLN Chi-restraints excluded: chain C residue 860 SER Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 970 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 69 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 292 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 274 optimal weight: 0.1980 chunk 213 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 ASN A 211 ASN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN B 204 ASN B 415 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 859 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN C 245 GLN C 282 ASN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 717 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.182640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.149385 restraints weight = 28885.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.153345 restraints weight = 17693.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.156025 restraints weight = 12847.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.157707 restraints weight = 10427.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.158825 restraints weight = 9094.880| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24000 Z= 0.173 Angle : 0.635 14.563 32499 Z= 0.322 Chirality : 0.043 0.271 3876 Planarity : 0.004 0.063 4068 Dihedral : 6.912 59.982 3345 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.09 % Allowed : 18.52 % Favored : 77.39 % 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: 1.11 (0.15), residues: 3048 helix: 1.60 (0.13), residues: 1701 sheet: -0.15 (0.23), residues: 435 loop : -0.35 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 515 TYR 0.023 0.002 TYR A 77 PHE 0.028 0.002 PHE C 824 TRP 0.019 0.001 TRP B 512 HIS 0.002 0.001 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (24000) covalent geometry : angle 0.63453 / 0.32 (32499) hydrogen bonds : bond 0.04468 / 3.05 ( 1500) hydrogen bonds : angle 4.51645 / 3.24 ( 4617) *********************** 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 667 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 562 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.6777 (m-80) cc_final: 0.6332 (m-80) REVERT: A 44 ASN cc_start: 0.6805 (t0) cc_final: 0.6309 (p0) REVERT: A 125 GLN cc_start: 0.8186 (mm110) cc_final: 0.7263 (mm-40) REVERT: A 367 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7926 (mp) REVERT: A 433 LYS cc_start: 0.6779 (ttpp) cc_final: 0.6442 (ttpp) REVERT: A 456 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7041 (mtm) REVERT: A 539 MET cc_start: 0.7259 (mmm) cc_final: 0.6956 (mmm) REVERT: A 647 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.5221 (tpt) REVERT: A 675 ARG cc_start: 0.8194 (mmt-90) cc_final: 0.7886 (mpt180) REVERT: A 695 MET cc_start: 0.6067 (OUTLIER) cc_final: 0.5197 (mmm) REVERT: A 779 ASN cc_start: 0.6898 (t0) cc_final: 0.6150 (t0) REVERT: A 781 LYS cc_start: 0.7277 (mppt) cc_final: 0.6843 (mmtt) REVERT: A 783 MET cc_start: 0.3663 (tmm) cc_final: 0.2882 (tmm) REVERT: A 944 LYS cc_start: 0.7296 (tptm) cc_final: 0.7000 (tppp) REVERT: A 970 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.6999 (mp) REVERT: B 93 THR cc_start: 0.7946 (m) cc_final: 0.7530 (p) REVERT: B 229 LEU cc_start: 0.7414 (tp) cc_final: 0.7112 (tt) REVERT: B 273 GLN cc_start: 0.7749 (tt0) cc_final: 0.7009 (tt0) REVERT: B 356 TYR cc_start: 0.8090 (t80) cc_final: 0.7441 (t80) REVERT: B 367 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7839 (mp) REVERT: B 433 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6412 (tttm) REVERT: B 564 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6282 (mp0) REVERT: B 677 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7377 (mt0) REVERT: B 697 MET cc_start: 0.7085 (mtp) cc_final: 0.6743 (mtp) REVERT: B 706 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6665 (mtp) REVERT: B 779 ASN cc_start: 0.7429 (t0) cc_final: 0.6649 (t0) REVERT: B 781 LYS cc_start: 0.7063 (mppt) cc_final: 0.6848 (mmtt) REVERT: B 783 MET cc_start: 0.4117 (tmm) cc_final: 0.2641 (tpp) REVERT: B 857 GLU cc_start: 0.8240 (tt0) cc_final: 0.8010 (tt0) REVERT: B 893 MET cc_start: 0.7049 (OUTLIER) cc_final: 0.6621 (mmm) REVERT: C 44 ASN cc_start: 0.7179 (t0) cc_final: 0.6849 (p0) REVERT: C 95 LYS cc_start: 0.7604 (mtmt) cc_final: 0.6676 (mmtt) REVERT: C 218 ARG cc_start: 0.7028 (mtp85) cc_final: 0.5428 (mpt90) REVERT: C 273 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: C 390 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8340 (mt) REVERT: C 456 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.6826 (mtm) REVERT: C 523 LYS cc_start: 0.6518 (mmtt) cc_final: 0.6318 (mmmm) REVERT: C 527 MET cc_start: 0.6687 (ttt) cc_final: 0.6233 (ttt) REVERT: C 564 GLU cc_start: 0.6565 (mm-30) cc_final: 0.6256 (mp0) REVERT: C 586 ASN cc_start: 0.6578 (m-40) cc_final: 0.6152 (m-40) REVERT: C 641 SER cc_start: 0.7220 (m) cc_final: 0.6891 (p) REVERT: C 695 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.5057 (mmm) REVERT: C 706 MET cc_start: 0.7462 (ptp) cc_final: 0.7244 (mtm) REVERT: C 748 MET cc_start: 0.7336 (mtm) cc_final: 0.6849 (mtp) REVERT: C 779 ASN cc_start: 0.6698 (t0) cc_final: 0.6156 (t0) REVERT: C 783 MET cc_start: 0.3835 (tmm) cc_final: 0.2917 (tmm) REVERT: C 835 MET cc_start: 0.7375 (tpt) cc_final: 0.6913 (tpt) REVERT: C 944 LYS cc_start: 0.7581 (tptp) cc_final: 0.7263 (tppp) outliers start: 105 outliers final: 70 residues processed: 626 average time/residue: 0.1471 time to fit residues: 149.2031 Evaluate side-chains 627 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 543 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 824 PHE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 556 TRP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 759 MET Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 806 GLN Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 846 ILE Chi-restraints excluded: chain C residue 860 SER Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 893 MET Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 970 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 147 optimal weight: 2.9990 chunk 238 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 301 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 268 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 ASN A 761 GLN B 204 ASN B 245 GLN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 292 GLN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.182451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.149057 restraints weight = 28853.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.153018 restraints weight = 17600.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.155655 restraints weight = 12766.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.157207 restraints weight = 10374.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.158459 restraints weight = 9086.933| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24000 Z= 0.168 Angle : 0.642 14.454 32499 Z= 0.328 Chirality : 0.043 0.309 3876 Planarity : 0.004 0.061 4068 Dihedral : 6.931 59.649 3345 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.94 % Allowed : 18.48 % Favored : 77.58 % 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: 1.01 (0.15), residues: 3048 helix: 1.52 (0.13), residues: 1698 sheet: -0.18 (0.22), residues: 429 loop : -0.39 (0.21), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 515 TYR 0.023 0.002 TYR A 77 PHE 0.028 0.002 PHE C 824 TRP 0.011 0.001 TRP A 512 HIS 0.002 0.001 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (24000) covalent geometry : angle 0.64237 / 0.33 (32499) hydrogen bonds : bond 0.04481 / 3.07 ( 1500) hydrogen bonds : angle 4.55244 / 3.26 ( 4617) *********************** 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 650 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 549 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 PHE cc_start: 0.6773 (m-10) cc_final: 0.6377 (m-80) REVERT: A 44 ASN cc_start: 0.6805 (t0) cc_final: 0.6326 (p0) REVERT: A 273 GLN cc_start: 0.7583 (tt0) cc_final: 0.7010 (tt0) REVERT: A 367 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7884 (mp) REVERT: A 433 LYS cc_start: 0.6816 (ttpp) cc_final: 0.6467 (ttpp) REVERT: A 456 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.6952 (mtm) REVERT: A 527 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.6112 (ttp) REVERT: A 539 MET cc_start: 0.7360 (mmm) cc_final: 0.7109 (mmm) REVERT: A 647 MET cc_start: 0.6806 (OUTLIER) cc_final: 0.5184 (tpt) REVERT: A 675 ARG cc_start: 0.8312 (mmt-90) cc_final: 0.8029 (mpt180) REVERT: A 695 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5320 (mmm) REVERT: A 779 ASN cc_start: 0.6898 (t0) cc_final: 0.6216 (t0) REVERT: A 781 LYS cc_start: 0.7287 (mppt) cc_final: 0.6937 (mmtt) REVERT: A 783 MET cc_start: 0.3672 (tmm) cc_final: 0.2893 (tmm) REVERT: A 970 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.6943 (mp) REVERT: B 229 LEU cc_start: 0.7440 (tp) cc_final: 0.7203 (tt) REVERT: B 273 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.6971 (tt0) REVERT: B 356 TYR cc_start: 0.8055 (t80) cc_final: 0.7382 (t80) REVERT: B 367 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7857 (mp) REVERT: B 433 LYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6407 (tttm) REVERT: B 564 GLU cc_start: 0.6643 (mm-30) cc_final: 0.6313 (mp0) REVERT: B 675 ARG cc_start: 0.8246 (mmt-90) cc_final: 0.7778 (mpt180) REVERT: B 677 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7381 (mt0) REVERT: B 695 MET cc_start: 0.6435 (tmm) cc_final: 0.5387 (mmm) REVERT: B 697 MET cc_start: 0.7072 (mtp) cc_final: 0.6686 (mtp) REVERT: B 706 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6385 (mtm) REVERT: B 779 ASN cc_start: 0.7417 (t0) cc_final: 0.6644 (t0) REVERT: B 783 MET cc_start: 0.4123 (tmm) cc_final: 0.3216 (tmm) REVERT: B 857 GLU cc_start: 0.8249 (tt0) cc_final: 0.8007 (tt0) REVERT: B 893 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6611 (mmm) REVERT: C 44 ASN cc_start: 0.7216 (t0) cc_final: 0.6892 (p0) REVERT: C 95 LYS cc_start: 0.7651 (mtmt) cc_final: 0.6735 (mmtt) REVERT: C 218 ARG cc_start: 0.7002 (mtp85) cc_final: 0.5428 (mpt90) REVERT: C 273 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7395 (tt0) REVERT: C 390 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8363 (mt) REVERT: C 456 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.6872 (mtm) REVERT: C 527 MET cc_start: 0.6635 (ttt) cc_final: 0.6179 (ttt) REVERT: C 564 GLU cc_start: 0.6581 (mm-30) cc_final: 0.6329 (mp0) REVERT: C 586 ASN cc_start: 0.6539 (m-40) cc_final: 0.6091 (m-40) REVERT: C 641 SER cc_start: 0.7223 (m) cc_final: 0.6900 (p) REVERT: C 677 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: C 695 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.5329 (mmm) REVERT: C 748 MET cc_start: 0.7375 (mtm) cc_final: 0.6869 (mtp) REVERT: C 779 ASN cc_start: 0.6631 (t0) cc_final: 0.6130 (t0) REVERT: C 783 MET cc_start: 0.3851 (tmm) cc_final: 0.2925 (tmm) REVERT: C 835 MET cc_start: 0.7420 (tpt) cc_final: 0.6859 (tpt) REVERT: C 944 LYS cc_start: 0.7541 (tptp) cc_final: 0.7248 (tppp) REVERT: C 962 LEU cc_start: 0.7778 (tt) cc_final: 0.7572 (tt) outliers start: 101 outliers final: 72 residues processed: 607 average time/residue: 0.1451 time to fit residues: 142.0540 Evaluate side-chains 628 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 539 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 527 MET Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 761 GLN Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 824 PHE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 706 MET Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 759 MET Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 677 GLN Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 806 GLN Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 860 SER Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 893 MET Chi-restraints excluded: chain C residue 907 ILE Chi-restraints excluded: chain C residue 970 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 45 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 285 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 228 optimal weight: 0.0370 chunk 234 optimal weight: 5.9990 chunk 295 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 overall best weight: 1.1660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS A 677 GLN A 761 GLN B 204 ASN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 ASN C 677 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.184671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.151402 restraints weight = 28995.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.155487 restraints weight = 17538.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.158216 restraints weight = 12606.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.159732 restraints weight = 10160.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.160986 restraints weight = 8885.712| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 24000 Z= 0.133 Angle : 0.629 13.347 32499 Z= 0.319 Chirality : 0.042 0.297 3876 Planarity : 0.004 0.060 4068 Dihedral : 6.816 59.285 3345 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.24 % Allowed : 19.34 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.15), residues: 3048 helix: 1.69 (0.13), residues: 1710 sheet: -0.22 (0.22), residues: 435 loop : -0.29 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 515 TYR 0.023 0.001 TYR B 77 PHE 0.037 0.001 PHE A 972 TRP 0.010 0.001 TRP C 708 HIS 0.001 0.000 HIS B 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (24000) covalent geometry : angle 0.62894 / 0.32 (32499) hydrogen bonds : bond 0.04172 / 2.86 ( 1500) hydrogen bonds : angle 4.46018 / 3.19 ( 4617) *********************** 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 649 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 566 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2549 (mmm) cc_final: 0.2292 (mmm) REVERT: A 22 PHE cc_start: 0.6700 (m-10) cc_final: 0.6345 (m-80) REVERT: A 44 ASN cc_start: 0.6782 (t0) cc_final: 0.6343 (p0) REVERT: A 125 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7017 (mm-40) REVERT: A 273 GLN cc_start: 0.7264 (tt0) cc_final: 0.6869 (tt0) REVERT: A 364 TYR cc_start: 0.7999 (m-80) cc_final: 0.7775 (m-80) REVERT: A 367 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8017 (mp) REVERT: A 393 LEU cc_start: 0.7412 (mt) cc_final: 0.6811 (mt) REVERT: A 433 LYS cc_start: 0.6884 (ttpp) cc_final: 0.6537 (ttpp) REVERT: A 456 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.6944 (mtm) REVERT: A 539 MET cc_start: 0.7378 (mmm) cc_final: 0.7139 (mmt) REVERT: A 647 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.5209 (tpt) REVERT: A 675 ARG cc_start: 0.8341 (mmt-90) cc_final: 0.8073 (mpt180) REVERT: A 695 MET cc_start: 0.6301 (OUTLIER) cc_final: 0.4808 (mmm) REVERT: A 779 ASN cc_start: 0.6904 (t0) cc_final: 0.6204 (t0) REVERT: A 781 LYS cc_start: 0.7204 (mppt) cc_final: 0.6821 (mmtt) REVERT: A 783 MET cc_start: 0.3683 (tmm) cc_final: 0.2918 (tmm) REVERT: A 970 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.6880 (mp) REVERT: B 8 ARG cc_start: 0.7432 (mmt90) cc_final: 0.7210 (mmm-85) REVERT: B 22 PHE cc_start: 0.6908 (m-80) cc_final: 0.6606 (m-80) REVERT: B 44 ASN cc_start: 0.6763 (t0) cc_final: 0.6537 (p0) REVERT: B 93 THR cc_start: 0.7964 (m) cc_final: 0.7450 (p) REVERT: B 218 ARG cc_start: 0.6531 (mtp85) cc_final: 0.5481 (mpt90) REVERT: B 229 LEU cc_start: 0.7425 (tp) cc_final: 0.7193 (tt) REVERT: B 273 GLN cc_start: 0.7733 (tt0) cc_final: 0.6886 (tt0) REVERT: B 356 TYR cc_start: 0.7917 (t80) cc_final: 0.7339 (t80) REVERT: B 367 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7810 (mp) REVERT: B 433 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6419 (tttm) REVERT: B 675 ARG cc_start: 0.8257 (mmt-90) cc_final: 0.7774 (mpt180) REVERT: B 677 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: B 695 MET cc_start: 0.6527 (tmm) cc_final: 0.5229 (mmm) REVERT: B 697 MET cc_start: 0.7027 (mtp) cc_final: 0.6688 (mtp) REVERT: B 772 MET cc_start: 0.5720 (mmt) cc_final: 0.4901 (mmt) REVERT: B 779 ASN cc_start: 0.7426 (t0) cc_final: 0.6299 (t0) REVERT: B 783 MET cc_start: 0.4164 (tmm) cc_final: 0.3888 (tmm) REVERT: B 857 GLU cc_start: 0.8229 (tt0) cc_final: 0.7997 (tt0) REVERT: B 893 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6521 (mmm) REVERT: C 44 ASN cc_start: 0.7223 (t0) cc_final: 0.6898 (p0) REVERT: C 95 LYS cc_start: 0.7637 (mtmt) cc_final: 0.6737 (mmtt) REVERT: C 218 ARG cc_start: 0.6873 (mtp85) cc_final: 0.5495 (mpt90) REVERT: C 229 LEU cc_start: 0.7708 (tp) cc_final: 0.7406 (tt) REVERT: C 273 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: C 390 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8375 (mt) REVERT: C 456 MET cc_start: 0.7774 (mpm) cc_final: 0.6813 (mtm) REVERT: C 523 LYS cc_start: 0.6301 (mmmm) cc_final: 0.6084 (mmtt) REVERT: C 527 MET cc_start: 0.6587 (ttt) cc_final: 0.6117 (ttt) REVERT: C 586 ASN cc_start: 0.6688 (m-40) cc_final: 0.6240 (m-40) REVERT: C 641 SER cc_start: 0.7179 (m) cc_final: 0.6871 (p) REVERT: C 695 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.5288 (mmm) REVERT: C 748 MET cc_start: 0.7323 (mtm) cc_final: 0.6836 (mtp) REVERT: C 779 ASN cc_start: 0.6714 (t0) cc_final: 0.6235 (t0) REVERT: C 783 MET cc_start: 0.3914 (tmm) cc_final: 0.2972 (tmm) REVERT: C 835 MET cc_start: 0.7456 (tpt) cc_final: 0.6954 (tpt) REVERT: C 944 LYS cc_start: 0.7427 (tptp) cc_final: 0.7140 (tppp) REVERT: C 962 LEU cc_start: 0.7779 (tt) cc_final: 0.7575 (tt) outliers start: 83 outliers final: 62 residues processed: 616 average time/residue: 0.1573 time to fit residues: 156.0305 Evaluate side-chains 626 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 552 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 761 GLN Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 824 PHE Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 759 MET Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 806 GLN Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 860 SER Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 893 MET Chi-restraints excluded: chain C residue 970 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 305 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 264 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 289 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN A 761 GLN A 863 GLN ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.180776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.147069 restraints weight = 28833.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.151071 restraints weight = 17574.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.153712 restraints weight = 12707.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.155373 restraints weight = 10307.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.156546 restraints weight = 9002.572| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24000 Z= 0.208 Angle : 0.698 15.278 32499 Z= 0.356 Chirality : 0.045 0.291 3876 Planarity : 0.005 0.062 4068 Dihedral : 6.995 59.655 3345 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.43 % Allowed : 19.45 % Favored : 77.12 % 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: 0.83 (0.15), residues: 3048 helix: 1.35 (0.13), residues: 1701 sheet: -0.28 (0.22), residues: 432 loop : -0.41 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 515 TYR 0.028 0.002 TYR B 364 PHE 0.033 0.002 PHE A 972 TRP 0.008 0.001 TRP A 800 HIS 0.003 0.001 HIS C 991 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (24000) covalent geometry : angle 0.69776 / 0.36 (32499) hydrogen bonds : bond 0.04801 / 3.28 ( 1500) hydrogen bonds : angle 4.64530 / 3.33 ( 4617) ********************** 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 627 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 539 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.2775 (mmm) cc_final: 0.2503 (mmm) REVERT: A 22 PHE cc_start: 0.6970 (m-10) cc_final: 0.6590 (m-80) REVERT: A 44 ASN cc_start: 0.6843 (t0) cc_final: 0.6378 (p0) REVERT: A 125 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7104 (mm-40) REVERT: A 273 GLN cc_start: 0.7296 (tt0) cc_final: 0.6938 (tp40) REVERT: A 367 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7926 (mp) REVERT: A 393 LEU cc_start: 0.7589 (mt) cc_final: 0.7021 (mt) REVERT: A 433 LYS cc_start: 0.6726 (ttpp) cc_final: 0.6361 (ttpp) REVERT: A 456 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.6945 (mtm) REVERT: A 539 MET cc_start: 0.7485 (mmm) cc_final: 0.7282 (mmt) REVERT: A 647 MET cc_start: 0.6812 (OUTLIER) cc_final: 0.5263 (tpt) REVERT: A 675 ARG cc_start: 0.8394 (mmt-90) cc_final: 0.8134 (mpt180) REVERT: A 695 MET cc_start: 0.6286 (OUTLIER) cc_final: 0.5496 (mmm) REVERT: A 779 ASN cc_start: 0.6836 (t0) cc_final: 0.6220 (t0) REVERT: A 781 LYS cc_start: 0.7251 (mppt) cc_final: 0.7030 (mmtt) REVERT: A 783 MET cc_start: 0.3704 (tmm) cc_final: 0.2918 (tmm) REVERT: A 970 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7069 (mp) REVERT: B 8 ARG cc_start: 0.7507 (mmt90) cc_final: 0.7292 (mmm-85) REVERT: B 44 ASN cc_start: 0.6862 (t0) cc_final: 0.6628 (p0) REVERT: B 229 LEU cc_start: 0.7564 (tp) cc_final: 0.7330 (tt) REVERT: B 273 GLN cc_start: 0.7863 (tt0) cc_final: 0.7061 (tt0) REVERT: B 356 TYR cc_start: 0.7984 (t80) cc_final: 0.7337 (t80) REVERT: B 367 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7906 (mp) REVERT: B 433 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6441 (tttm) REVERT: B 675 ARG cc_start: 0.8252 (mmt-90) cc_final: 0.7905 (mpt180) REVERT: B 677 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7494 (mt0) REVERT: B 695 MET cc_start: 0.6492 (tmm) cc_final: 0.5466 (mmm) REVERT: B 697 MET cc_start: 0.7122 (mtp) cc_final: 0.6788 (mtp) REVERT: B 767 GLU cc_start: 0.6206 (tp30) cc_final: 0.5761 (tp30) REVERT: B 779 ASN cc_start: 0.7238 (t0) cc_final: 0.6406 (t0) REVERT: B 783 MET cc_start: 0.4048 (tmm) cc_final: 0.3774 (tmm) REVERT: B 872 MET cc_start: 0.7570 (mmm) cc_final: 0.7336 (mtt) REVERT: B 893 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6571 (mmm) REVERT: C 44 ASN cc_start: 0.7272 (t0) cc_final: 0.6930 (p0) REVERT: C 95 LYS cc_start: 0.7689 (mtmt) cc_final: 0.6777 (mmtt) REVERT: C 112 LYS cc_start: 0.8122 (tptp) cc_final: 0.7652 (ttpt) REVERT: C 218 ARG cc_start: 0.7040 (mtp85) cc_final: 0.5472 (mpt90) REVERT: C 273 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: C 390 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8357 (mt) REVERT: C 417 GLU cc_start: 0.7566 (tm-30) cc_final: 0.6588 (tm-30) REVERT: C 456 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.6922 (mtm) REVERT: C 523 LYS cc_start: 0.6344 (mmmm) cc_final: 0.6110 (mmtt) REVERT: C 527 MET cc_start: 0.6658 (ttt) cc_final: 0.6122 (ttt) REVERT: C 586 ASN cc_start: 0.6756 (m-40) cc_final: 0.6310 (m-40) REVERT: C 641 SER cc_start: 0.7249 (m) cc_final: 0.6921 (p) REVERT: C 695 MET cc_start: 0.6507 (OUTLIER) cc_final: 0.5667 (mmm) REVERT: C 748 MET cc_start: 0.7356 (mtm) cc_final: 0.6848 (mtp) REVERT: C 779 ASN cc_start: 0.6671 (t0) cc_final: 0.6159 (t0) REVERT: C 783 MET cc_start: 0.3926 (tmm) cc_final: 0.2971 (tmm) REVERT: C 835 MET cc_start: 0.7480 (tpt) cc_final: 0.6980 (tpt) REVERT: C 944 LYS cc_start: 0.7413 (tptp) cc_final: 0.7149 (tppp) REVERT: C 962 LEU cc_start: 0.7752 (tt) cc_final: 0.7537 (tt) outliers start: 88 outliers final: 69 residues processed: 594 average time/residue: 0.1458 time to fit residues: 139.5883 Evaluate side-chains 612 residues out of total 2565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 530 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 613 SER Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 695 MET Chi-restraints excluded: chain A residue 759 MET Chi-restraints excluded: chain A residue 763 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 824 PHE Chi-restraints excluded: chain A residue 860 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 884 GLU Chi-restraints excluded: chain A residue 893 MET Chi-restraints excluded: chain A residue 970 LEU Chi-restraints excluded: chain B residue 6 ILE Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 433 LYS Chi-restraints excluded: chain B residue 438 ILE Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 483 LEU Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 613 SER Chi-restraints excluded: chain B residue 677 GLN Chi-restraints excluded: chain B residue 717 ASN Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 759 MET Chi-restraints excluded: chain B residue 818 ILE Chi-restraints excluded: chain B residue 860 SER Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 893 MET Chi-restraints excluded: chain B residue 904 ILE Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 970 LEU Chi-restraints excluded: chain C residue 6 ILE Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 273 GLN Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 390 ILE Chi-restraints excluded: chain C residue 394 THR Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 655 THR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 806 GLN Chi-restraints excluded: chain C residue 816 LEU Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 860 SER Chi-restraints excluded: chain C residue 884 GLU Chi-restraints excluded: chain C residue 890 LEU Chi-restraints excluded: chain C residue 893 MET Chi-restraints excluded: chain C residue 970 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 219 optimal weight: 0.2980 chunk 100 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 179 optimal weight: 0.4980 chunk 277 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 127 optimal weight: 50.0000 chunk 201 optimal weight: 10.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.181053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.147404 restraints weight = 28848.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.151356 restraints weight = 17584.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.153994 restraints weight = 12768.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.155735 restraints weight = 10360.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.156780 restraints weight = 8993.796| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.217 24000 Z= 0.226 Angle : 0.812 59.200 32499 Z= 0.441 Chirality : 0.044 0.366 3876 Planarity : 0.005 0.061 4068 Dihedral : 7.000 59.618 3345 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.59 % Allowed : 19.53 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.15), residues: 3048 helix: 1.34 (0.13), residues: 1701 sheet: -0.29 (0.22), residues: 432 loop : -0.41 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 515 TYR 0.024 0.002 TYR B 364 PHE 0.025 0.002 PHE A 972 TRP 0.022 0.001 TRP C 512 HIS 0.002 0.001 HIS B 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.23 (24000) covalent geometry : angle 0.81209 / 0.44 (32499) hydrogen bonds : bond 0.04738 / 3.24 ( 1500) hydrogen bonds : angle 4.64641 / 3.33 ( 4617) =============================================================================== Job complete usr+sys time: 4160.20 seconds wall clock time: 72 minutes 38.37 seconds (4358.37 seconds total)