Starting phenix.real_space_refine on Mon Aug 25 13:04:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dkn_46963/08_2025/9dkn_46963.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dkn_46963/08_2025/9dkn_46963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dkn_46963/08_2025/9dkn_46963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dkn_46963/08_2025/9dkn_46963.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dkn_46963/08_2025/9dkn_46963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dkn_46963/08_2025/9dkn_46963.map" } resolution = 3.5 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.057 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: 4 Type Number sf(0) Gaussians S 172 5.16 5 C 18412 2.51 5 N 4632 2.21 5 O 5160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 167 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28376 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7094 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 7094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7094 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 7094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7094 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 7094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 899, 7094 Classifications: {'peptide': 899} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 35, 'TRANS': 863} Chain breaks: 5 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'ARG:plan': 4, 'ASN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Time building chain proxies: 5.68, per 1000 atoms: 0.20 Number of scatterers: 28376 At special positions: 0 Unit cell: (161.872, 162.944, 127.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 172 16.00 O 5160 8.00 N 4632 7.00 C 18412 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: 1.77 Conformation dependent library (CDL) restraints added in 900.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6784 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 20 sheets defined 55.7% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 16 through 44 removed outlier: 3.894A pdb=" N SER A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 removed outlier: 4.102A pdb=" N ALA A 84 " --> pdb=" O TRP A 80 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP A 86 " --> pdb=" O THR A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 123 Processing helix chain 'A' and resid 139 through 159 removed outlier: 4.160A pdb=" N LEU A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 168 Processing helix chain 'A' and resid 169 through 189 Proline residue: A 180 - end of helix removed outlier: 3.882A pdb=" N PHE A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 218 through 249 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 262 through 275 Processing helix chain 'A' and resid 286 through 317 Proline residue: A 309 - end of helix Processing helix chain 'A' and resid 341 through 353 removed outlier: 3.718A pdb=" N PHE A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 396 through 403 Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 454 through 461 removed outlier: 4.129A pdb=" N LEU A 458 " --> pdb=" O ASN A 454 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU A 459 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A 461 " --> pdb=" O TYR A 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 454 through 461' Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.522A pdb=" N LEU A 480 " --> pdb=" O ALA A 476 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE A 483 " --> pdb=" O LYS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 500 removed outlier: 3.626A pdb=" N LEU A 495 " --> pdb=" O GLY A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 523 Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'A' and resid 539 through 550 Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 721 through 725 Processing helix chain 'A' and resid 728 through 735 Processing helix chain 'A' and resid 756 through 761 Processing helix chain 'A' and resid 762 through 765 removed outlier: 3.539A pdb=" N ALA A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 762 through 765' Processing helix chain 'A' and resid 769 through 773 Processing helix chain 'A' and resid 781 through 793 removed outlier: 3.762A pdb=" N ARG A 787 " --> pdb=" O ASP A 783 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR A 791 " --> pdb=" O ARG A 787 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 814 removed outlier: 3.636A pdb=" N LEU A 811 " --> pdb=" O ASN A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 removed outlier: 3.666A pdb=" N CYS A 819 " --> pdb=" O ILE A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 851 Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 894 through 896 No H-bonds generated for 'chain 'A' and resid 894 through 896' Processing helix chain 'A' and resid 897 through 902 removed outlier: 4.030A pdb=" N LEU A 901 " --> pdb=" O ASN A 897 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP A 902 " --> pdb=" O VAL A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 897 through 902' Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 928 through 940 removed outlier: 4.024A pdb=" N SER A 932 " --> pdb=" O SER A 928 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 953 removed outlier: 3.843A pdb=" N GLY A 953 " --> pdb=" O THR A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 965 Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 997 through 1002 removed outlier: 3.644A pdb=" N GLY A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1018 Processing helix chain 'B' and resid 16 through 44 removed outlier: 3.894A pdb=" N SER B 22 " --> pdb=" O SER B 18 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 94 removed outlier: 4.102A pdb=" N ALA B 84 " --> pdb=" O TRP B 80 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 123 Processing helix chain 'B' and resid 139 through 159 removed outlier: 4.160A pdb=" N LEU B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 168 Processing helix chain 'B' and resid 169 through 189 Proline residue: B 180 - end of helix removed outlier: 3.882A pdb=" N PHE B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 218 through 249 Processing helix chain 'B' and resid 250 through 254 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 286 through 317 Proline residue: B 309 - end of helix Processing helix chain 'B' and resid 341 through 353 removed outlier: 3.718A pdb=" N PHE B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 383 Processing helix chain 'B' and resid 396 through 403 Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 454 through 461 removed outlier: 4.129A pdb=" N LEU B 458 " --> pdb=" O ASN B 454 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 459 " --> pdb=" O LYS B 455 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 461 " --> pdb=" O TYR B 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 461' Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.521A pdb=" N LEU B 480 " --> pdb=" O ALA B 476 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 483 " --> pdb=" O LYS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.626A pdb=" N LEU B 495 " --> pdb=" O GLY B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 523 Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'B' and resid 539 through 550 Processing helix chain 'B' and resid 592 through 597 Processing helix chain 'B' and resid 597 through 602 Processing helix chain 'B' and resid 721 through 725 Processing helix chain 'B' and resid 728 through 735 Processing helix chain 'B' and resid 756 through 761 Processing helix chain 'B' and resid 762 through 765 removed outlier: 3.540A pdb=" N ALA B 765 " --> pdb=" O PRO B 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 762 through 765' Processing helix chain 'B' and resid 769 through 773 Processing helix chain 'B' and resid 781 through 793 removed outlier: 3.762A pdb=" N ARG B 787 " --> pdb=" O ASP B 783 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYS B 790 " --> pdb=" O HIS B 786 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N THR B 791 " --> pdb=" O ARG B 787 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 814 removed outlier: 3.637A pdb=" N LEU B 811 " --> pdb=" O ASN B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 819 removed outlier: 3.667A pdb=" N CYS B 819 " --> pdb=" O ILE B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 851 Processing helix chain 'B' and resid 882 through 886 Processing helix chain 'B' and resid 894 through 896 No H-bonds generated for 'chain 'B' and resid 894 through 896' Processing helix chain 'B' and resid 897 through 902 removed outlier: 4.035A pdb=" N LEU B 901 " --> pdb=" O ASN B 897 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASP B 902 " --> pdb=" O VAL B 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 897 through 902' Processing helix chain 'B' and resid 912 through 915 Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 928 through 940 removed outlier: 4.024A pdb=" N SER B 932 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 953 removed outlier: 3.843A pdb=" N GLY B 953 " --> pdb=" O THR B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 965 Processing helix chain 'B' and resid 975 through 980 Processing helix chain 'B' and resid 997 through 1002 removed outlier: 3.643A pdb=" N GLY B1001 " --> pdb=" O LEU B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1018 Processing helix chain 'C' and resid 16 through 44 removed outlier: 3.894A pdb=" N SER C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER C 23 " --> pdb=" O PHE C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 94 removed outlier: 4.103A pdb=" N ALA C 84 " --> pdb=" O TRP C 80 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 123 Processing helix chain 'C' and resid 139 through 159 removed outlier: 4.160A pdb=" N LEU C 143 " --> pdb=" O GLN C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 169 through 189 Proline residue: C 180 - end of helix removed outlier: 3.882A pdb=" N PHE C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 218 through 249 Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 262 through 275 Processing helix chain 'C' and resid 286 through 317 Proline residue: C 309 - end of helix Processing helix chain 'C' and resid 341 through 353 removed outlier: 3.718A pdb=" N PHE C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 383 Processing helix chain 'C' and resid 396 through 403 Processing helix chain 'C' and resid 421 through 440 Processing helix chain 'C' and resid 454 through 461 removed outlier: 4.128A pdb=" N LEU C 458 " --> pdb=" O ASN C 454 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 459 " --> pdb=" O LYS C 455 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE C 461 " --> pdb=" O TYR C 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 454 through 461' Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.522A pdb=" N LEU C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 483 " --> pdb=" O LYS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.625A pdb=" N LEU C 495 " --> pdb=" O GLY C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'C' and resid 539 through 550 Processing helix chain 'C' and resid 592 through 597 Processing helix chain 'C' and resid 597 through 602 Processing helix chain 'C' and resid 721 through 725 Processing helix chain 'C' and resid 728 through 735 Processing helix chain 'C' and resid 756 through 761 Processing helix chain 'C' and resid 762 through 765 removed outlier: 3.539A pdb=" N ALA C 765 " --> pdb=" O PRO C 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 762 through 765' Processing helix chain 'C' and resid 769 through 773 Processing helix chain 'C' and resid 781 through 793 removed outlier: 3.762A pdb=" N ARG C 787 " --> pdb=" O ASP C 783 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N THR C 791 " --> pdb=" O ARG C 787 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 792 " --> pdb=" O GLU C 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 814 removed outlier: 3.636A pdb=" N LEU C 811 " --> pdb=" O ASN C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 819 removed outlier: 3.667A pdb=" N CYS C 819 " --> pdb=" O ILE C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 851 Processing helix chain 'C' and resid 882 through 886 Processing helix chain 'C' and resid 894 through 901 removed outlier: 3.623A pdb=" N GLN C 899 " --> pdb=" O SER C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 915 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 928 through 940 removed outlier: 4.023A pdb=" N SER C 932 " --> pdb=" O SER C 928 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 953 removed outlier: 3.843A pdb=" N GLY C 953 " --> pdb=" O THR C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 965 Processing helix chain 'C' and resid 975 through 980 Processing helix chain 'C' and resid 997 through 1002 removed outlier: 3.643A pdb=" N GLY C1001 " --> pdb=" O LEU C 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1018 Processing helix chain 'D' and resid 16 through 44 removed outlier: 3.895A pdb=" N SER D 22 " --> pdb=" O SER D 18 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER D 23 " --> pdb=" O PHE D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 94 removed outlier: 4.103A pdb=" N ALA D 84 " --> pdb=" O TRP D 80 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 123 Processing helix chain 'D' and resid 139 through 159 removed outlier: 4.159A pdb=" N LEU D 143 " --> pdb=" O GLN D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 168 Processing helix chain 'D' and resid 169 through 189 Proline residue: D 180 - end of helix removed outlier: 3.882A pdb=" N PHE D 183 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 204 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 218 through 249 Processing helix chain 'D' and resid 250 through 254 Processing helix chain 'D' and resid 262 through 275 Processing helix chain 'D' and resid 286 through 317 Proline residue: D 309 - end of helix Processing helix chain 'D' and resid 341 through 353 removed outlier: 3.718A pdb=" N PHE D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP D 351 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 383 Processing helix chain 'D' and resid 396 through 403 Processing helix chain 'D' and resid 421 through 440 Processing helix chain 'D' and resid 454 through 461 removed outlier: 4.128A pdb=" N LEU D 458 " --> pdb=" O ASN D 454 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU D 459 " --> pdb=" O LYS D 455 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE D 461 " --> pdb=" O TYR D 457 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 454 through 461' Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.523A pdb=" N LEU D 480 " --> pdb=" O ALA D 476 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 483 " --> pdb=" O LYS D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 500 removed outlier: 3.625A pdb=" N LEU D 495 " --> pdb=" O GLY D 491 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 523 Processing helix chain 'D' and resid 532 through 536 Processing helix chain 'D' and resid 539 through 550 Processing helix chain 'D' and resid 592 through 597 Processing helix chain 'D' and resid 597 through 602 Processing helix chain 'D' and resid 721 through 725 Processing helix chain 'D' and resid 728 through 735 Processing helix chain 'D' and resid 756 through 761 Processing helix chain 'D' and resid 762 through 765 removed outlier: 3.539A pdb=" N ALA D 765 " --> pdb=" O PRO D 762 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 762 through 765' Processing helix chain 'D' and resid 769 through 773 Processing helix chain 'D' and resid 781 through 793 removed outlier: 3.763A pdb=" N ARG D 787 " --> pdb=" O ASP D 783 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS D 790 " --> pdb=" O HIS D 786 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N THR D 791 " --> pdb=" O ARG D 787 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D 792 " --> pdb=" O GLU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 814 removed outlier: 3.636A pdb=" N LEU D 811 " --> pdb=" O ASN D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 819 removed outlier: 3.667A pdb=" N CYS D 819 " --> pdb=" O ILE D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 851 Processing helix chain 'D' and resid 882 through 886 Processing helix chain 'D' and resid 894 through 896 No H-bonds generated for 'chain 'D' and resid 894 through 896' Processing helix chain 'D' and resid 897 through 902 removed outlier: 3.955A pdb=" N LEU D 901 " --> pdb=" O ASN D 897 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP D 902 " --> pdb=" O VAL D 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 897 through 902' Processing helix chain 'D' and resid 912 through 915 Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 928 through 940 removed outlier: 4.024A pdb=" N SER D 932 " --> pdb=" O SER D 928 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 953 removed outlier: 3.842A pdb=" N GLY D 953 " --> pdb=" O THR D 949 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 965 Processing helix chain 'D' and resid 975 through 980 Processing helix chain 'D' and resid 997 through 1002 removed outlier: 3.643A pdb=" N GLY D1001 " --> pdb=" O LEU D 997 " (cutoff:3.500A) Processing helix chain 'D' and resid 1005 through 1018 Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 391 removed outlier: 4.491A pdb=" N GLY A 338 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N HIS A 333 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N LEU A 412 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 335 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU A 414 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N CYS A 337 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 445 " --> pdb=" O ASP A 471 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL A 473 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL A 447 " --> pdb=" O VAL A 473 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 525 through 530 removed outlier: 4.370A pdb=" N GLN A 585 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 557 " --> pdb=" O PHE A 587 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE A 589 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU A 555 " --> pdb=" O ILE A 589 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 708 through 709 Processing sheet with id=AA4, first strand: chain 'A' and resid 798 through 802 removed outlier: 3.508A pdb=" N GLY A 780 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 741 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL A 779 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL A 743 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N SER A 826 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 986 through 991 removed outlier: 3.827A pdb=" N GLY A1023 " --> pdb=" O TYR A1060 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU A1062 " --> pdb=" O CYS A1021 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N CYS A1021 " --> pdb=" O LEU A1062 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 387 through 391 removed outlier: 4.491A pdb=" N GLY B 338 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N HIS B 333 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N LEU B 412 " --> pdb=" O HIS B 333 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 335 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU B 414 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS B 337 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 445 " --> pdb=" O ASP B 471 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL B 473 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL B 447 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 525 through 530 removed outlier: 4.371A pdb=" N GLN B 585 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 557 " --> pdb=" O PHE B 587 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE B 589 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU B 555 " --> pdb=" O ILE B 589 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 708 through 709 Processing sheet with id=AA9, first strand: chain 'B' and resid 798 through 802 removed outlier: 3.507A pdb=" N GLY B 780 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 741 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL B 779 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL B 743 " --> pdb=" O VAL B 779 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER B 826 " --> pdb=" O GLU B 891 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 986 through 991 removed outlier: 3.827A pdb=" N GLY B1023 " --> pdb=" O TYR B1060 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU B1062 " --> pdb=" O CYS B1021 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N CYS B1021 " --> pdb=" O LEU B1062 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 387 through 391 removed outlier: 4.490A pdb=" N GLY C 338 " --> pdb=" O LEU C 367 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N HIS C 333 " --> pdb=" O ALA C 410 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N LEU C 412 " --> pdb=" O HIS C 333 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL C 335 " --> pdb=" O LEU C 412 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU C 414 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS C 337 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL C 445 " --> pdb=" O ASP C 471 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL C 473 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL C 447 " --> pdb=" O VAL C 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 525 through 530 removed outlier: 4.371A pdb=" N GLN C 585 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA C 557 " --> pdb=" O PHE C 587 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ILE C 589 " --> pdb=" O LEU C 555 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU C 555 " --> pdb=" O ILE C 589 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 708 through 709 Processing sheet with id=AB5, first strand: chain 'C' and resid 798 through 802 removed outlier: 3.506A pdb=" N GLY C 780 " --> pdb=" O LEU C 801 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL C 741 " --> pdb=" O ILE C 777 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL C 779 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL C 743 " --> pdb=" O VAL C 779 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N SER C 826 " --> pdb=" O GLU C 891 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 986 through 991 removed outlier: 3.828A pdb=" N GLY C1023 " --> pdb=" O TYR C1060 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU C1062 " --> pdb=" O CYS C1021 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N CYS C1021 " --> pdb=" O LEU C1062 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 387 through 391 removed outlier: 4.490A pdb=" N GLY D 338 " --> pdb=" O LEU D 367 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N HIS D 333 " --> pdb=" O ALA D 410 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N LEU D 412 " --> pdb=" O HIS D 333 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL D 335 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU D 414 " --> pdb=" O VAL D 335 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N CYS D 337 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL D 445 " --> pdb=" O ASP D 471 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL D 473 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL D 447 " --> pdb=" O VAL D 473 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 525 through 530 removed outlier: 4.371A pdb=" N GLN D 585 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA D 557 " --> pdb=" O PHE D 587 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE D 589 " --> pdb=" O LEU D 555 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU D 555 " --> pdb=" O ILE D 589 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 708 through 709 Processing sheet with id=AC1, first strand: chain 'D' and resid 798 through 802 removed outlier: 3.508A pdb=" N GLY D 780 " --> pdb=" O LEU D 801 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL D 741 " --> pdb=" O ILE D 777 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL D 779 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL D 743 " --> pdb=" O VAL D 779 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N SER D 826 " --> pdb=" O GLU D 891 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 986 through 991 removed outlier: 3.827A pdb=" N GLY D1023 " --> pdb=" O TYR D1060 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU D1062 " --> pdb=" O CYS D1021 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N CYS D1021 " --> pdb=" O LEU D1062 " (cutoff:3.500A) 1408 hydrogen bonds defined for protein. 3924 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: 5.29 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5176 1.32 - 1.44: 7528 1.44 - 1.57: 16092 1.57 - 1.69: 4 1.69 - 1.82: 260 Bond restraints: 29060 Sorted by residual: bond pdb=" CA PRO D1047 " pdb=" C PRO D1047 " ideal model delta sigma weight residual 1.514 1.537 -0.022 5.50e-03 3.31e+04 1.64e+01 bond pdb=" CA PRO A1047 " pdb=" C PRO A1047 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.56e+01 bond pdb=" CA PRO B1047 " pdb=" C PRO B1047 " ideal model delta sigma weight residual 1.514 1.536 -0.021 5.50e-03 3.31e+04 1.50e+01 bond pdb=" CA PRO C1047 " pdb=" C PRO C1047 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.46e+01 bond pdb=" CA ASP D 250 " pdb=" C ASP D 250 " ideal model delta sigma weight residual 1.519 1.552 -0.033 9.50e-03 1.11e+04 1.19e+01 ... (remaining 29055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 28325 1.75 - 3.49: 9189 3.49 - 5.24: 1756 5.24 - 6.99: 210 6.99 - 8.74: 24 Bond angle restraints: 39504 Sorted by residual: angle pdb=" N ASP C 829 " pdb=" CA ASP C 829 " pdb=" C ASP C 829 " ideal model delta sigma weight residual 110.53 101.79 8.74 1.32e+00 5.74e-01 4.38e+01 angle pdb=" N ASP A 829 " pdb=" CA ASP A 829 " pdb=" C ASP A 829 " ideal model delta sigma weight residual 110.53 101.82 8.71 1.32e+00 5.74e-01 4.36e+01 angle pdb=" N ASP D 829 " pdb=" CA ASP D 829 " pdb=" C ASP D 829 " ideal model delta sigma weight residual 110.53 101.84 8.69 1.32e+00 5.74e-01 4.33e+01 angle pdb=" N ASP B 829 " pdb=" CA ASP B 829 " pdb=" C ASP B 829 " ideal model delta sigma weight residual 110.53 101.84 8.69 1.32e+00 5.74e-01 4.33e+01 angle pdb=" O ILE A 308 " pdb=" C ILE A 308 " pdb=" N PRO A 309 " ideal model delta sigma weight residual 120.42 124.43 -4.01 6.40e-01 2.44e+00 3.92e+01 ... (remaining 39499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.73: 15459 15.73 - 31.46: 1222 31.46 - 47.20: 289 47.20 - 62.93: 70 62.93 - 78.66: 20 Dihedral angle restraints: 17060 sinusoidal: 6568 harmonic: 10492 Sorted by residual: dihedral pdb=" CA SER C 248 " pdb=" C SER C 248 " pdb=" N GLY C 249 " pdb=" CA GLY C 249 " ideal model delta harmonic sigma weight residual -180.00 -152.89 -27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA SER A 248 " pdb=" C SER A 248 " pdb=" N GLY A 249 " pdb=" CA GLY A 249 " ideal model delta harmonic sigma weight residual -180.00 -152.89 -27.11 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA SER B 248 " pdb=" C SER B 248 " pdb=" N GLY B 249 " pdb=" CA GLY B 249 " ideal model delta harmonic sigma weight residual -180.00 -152.90 -27.10 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 17057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2824 0.081 - 0.162: 1326 0.162 - 0.243: 266 0.243 - 0.323: 58 0.323 - 0.404: 22 Chirality restraints: 4496 Sorted by residual: chirality pdb=" CA ASP D 409 " pdb=" N ASP D 409 " pdb=" C ASP D 409 " pdb=" CB ASP D 409 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA ASP B 409 " pdb=" N ASP B 409 " pdb=" C ASP B 409 " pdb=" CB ASP B 409 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" CA ASP A 409 " pdb=" N ASP A 409 " pdb=" C ASP A 409 " pdb=" CB ASP A 409 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.95e+00 ... (remaining 4493 not shown) Planarity restraints: 5000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 133 " 0.145 2.00e-02 2.50e+03 7.52e-02 1.42e+02 pdb=" CG TRP B 133 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP B 133 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TRP B 133 " -0.056 2.00e-02 2.50e+03 pdb=" NE1 TRP B 133 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP B 133 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 133 " -0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 133 " 0.106 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 133 " -0.048 2.00e-02 2.50e+03 pdb=" CH2 TRP B 133 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 133 " 0.145 2.00e-02 2.50e+03 7.52e-02 1.41e+02 pdb=" CG TRP C 133 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP C 133 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 TRP C 133 " -0.056 2.00e-02 2.50e+03 pdb=" NE1 TRP C 133 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 TRP C 133 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 133 " -0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 133 " 0.105 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 133 " -0.048 2.00e-02 2.50e+03 pdb=" CH2 TRP C 133 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 133 " 0.145 2.00e-02 2.50e+03 7.51e-02 1.41e+02 pdb=" CG TRP A 133 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 133 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP A 133 " -0.056 2.00e-02 2.50e+03 pdb=" NE1 TRP A 133 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TRP A 133 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 133 " -0.087 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 133 " 0.105 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 133 " -0.048 2.00e-02 2.50e+03 pdb=" CH2 TRP A 133 " 0.070 2.00e-02 2.50e+03 ... (remaining 4997 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 11194 2.90 - 3.40: 30309 3.40 - 3.90: 47155 3.90 - 4.40: 53305 4.40 - 4.90: 87814 Nonbonded interactions: 229777 Sorted by model distance: nonbonded pdb=" O ASP B 709 " pdb=" N GLY B 712 " model vdw 2.399 3.120 nonbonded pdb=" O ASP B 709 " pdb=" C SER B 710 " model vdw 2.432 3.270 nonbonded pdb=" O ASP B 709 " pdb=" N THR B 711 " model vdw 2.447 3.120 nonbonded pdb=" N ASP B 829 " pdb=" O ASP B 829 " model vdw 2.457 2.496 nonbonded pdb=" N ASP C 829 " pdb=" O ASP C 829 " model vdw 2.457 2.496 ... (remaining 229772 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.370 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.012 0.062 29060 Z= 0.717 Angle : 1.722 8.737 39504 Z= 1.152 Chirality : 0.094 0.404 4496 Planarity : 0.013 0.130 5000 Dihedral : 12.859 78.660 10276 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.38 % Favored : 94.53 % Rotamer: Outliers : 0.82 % Allowed : 5.88 % Favored : 93.30 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.81 (0.13), residues: 3548 helix: -1.60 (0.10), residues: 1732 sheet: 0.06 (0.24), residues: 392 loop : -0.78 (0.17), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 598 TYR 0.078 0.016 TYR B 389 PHE 0.081 0.011 PHE D 300 TRP 0.145 0.025 TRP B 133 HIS 0.016 0.003 HIS B 607 Details of bonding type rmsd covalent geometry : bond 0.01185 (29060) covalent geometry : angle 1.72177 (39504) hydrogen bonds : bond 0.17542 ( 1408) hydrogen bonds : angle 7.75465 ( 3924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 365 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 889 ILE cc_start: 0.9107 (mm) cc_final: 0.8823 (mm) REVERT: C 915 MET cc_start: 0.8323 (mmm) cc_final: 0.8070 (tpp) REVERT: D 151 ILE cc_start: 0.8906 (mt) cc_final: 0.8699 (tp) REVERT: D 420 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7643 (tp40) outliers start: 25 outliers final: 5 residues processed: 386 average time/residue: 0.1672 time to fit residues: 102.3199 Evaluate side-chains 201 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 195 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain B residue 906 ASP Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain C residue 709 ASP Chi-restraints excluded: chain D residue 420 GLN Chi-restraints excluded: chain D residue 709 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.0370 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 8.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS A 429 ASN A 460 ASN A 727 GLN A 739 ASN A1016 HIS A1046 ASN B 333 HIS B 429 ASN B 460 ASN B 727 GLN B 739 ASN B1016 HIS B1046 ASN C 333 HIS C 429 ASN C 460 ASN C 727 GLN C 739 ASN C1016 HIS D 333 HIS D 429 ASN D 438 ASN D 460 ASN D 727 GLN D 739 ASN D1016 HIS D1046 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.072462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.049076 restraints weight = 114677.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.051002 restraints weight = 56711.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.052262 restraints weight = 38392.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.053048 restraints weight = 30521.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053523 restraints weight = 26613.420| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29060 Z= 0.163 Angle : 0.702 11.015 39504 Z= 0.364 Chirality : 0.045 0.179 4496 Planarity : 0.004 0.041 5000 Dihedral : 5.968 81.386 3869 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.86 % Allowed : 9.12 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.23 (0.14), residues: 3548 helix: 0.00 (0.12), residues: 1752 sheet: 0.10 (0.23), residues: 448 loop : -0.20 (0.18), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 100 TYR 0.017 0.002 TYR C 152 PHE 0.029 0.002 PHE A 154 TRP 0.019 0.002 TRP A 87 HIS 0.003 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00346 (29060) covalent geometry : angle 0.70210 (39504) hydrogen bonds : bond 0.05760 ( 1408) hydrogen bonds : angle 5.36473 ( 3924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 224 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.9562 (m-10) cc_final: 0.9316 (m-10) REVERT: A 350 LYS cc_start: 0.9206 (mtmm) cc_final: 0.8708 (pttp) REVERT: A 841 GLU cc_start: 0.8985 (mp0) cc_final: 0.8769 (mp0) REVERT: B 317 LYS cc_start: 0.8250 (pptt) cc_final: 0.8038 (tmmt) REVERT: B 350 LYS cc_start: 0.9202 (mtmm) cc_final: 0.8735 (pttp) REVERT: B 451 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8202 (mp10) REVERT: B 713 MET cc_start: 0.9178 (mmm) cc_final: 0.8943 (tpp) REVERT: B 841 GLU cc_start: 0.8971 (mp0) cc_final: 0.8733 (mp0) REVERT: B 915 MET cc_start: 0.9061 (mpp) cc_final: 0.8728 (mpp) REVERT: C 304 PHE cc_start: 0.8519 (t80) cc_final: 0.8245 (t80) REVERT: C 350 LYS cc_start: 0.9037 (mtmm) cc_final: 0.8763 (mtmt) REVERT: D 154 PHE cc_start: 0.9576 (m-10) cc_final: 0.9338 (m-10) REVERT: D 222 ILE cc_start: 0.8907 (mm) cc_final: 0.8701 (mt) REVERT: D 274 MET cc_start: 0.8889 (ttp) cc_final: 0.8677 (ttm) REVERT: D 304 PHE cc_start: 0.8364 (t80) cc_final: 0.8163 (t80) REVERT: D 524 MET cc_start: 0.9116 (mmt) cc_final: 0.8734 (mmt) REVERT: D 841 GLU cc_start: 0.9069 (mp0) cc_final: 0.8704 (mp0) outliers start: 57 outliers final: 26 residues processed: 259 average time/residue: 0.1566 time to fit residues: 67.4239 Evaluate side-chains 215 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 906 ASP Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain D residue 133 TRP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 241 PHE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 709 ASP Chi-restraints excluded: chain D residue 832 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 74 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 201 optimal weight: 9.9990 chunk 293 optimal weight: 9.9990 chunk 254 optimal weight: 8.9990 chunk 313 optimal weight: 20.0000 chunk 117 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 178 optimal weight: 30.0000 chunk 134 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 HIS A 615 GLN B 368 HIS B 615 GLN C 368 HIS C 615 GLN D 368 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.070894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.047545 restraints weight = 116277.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.049355 restraints weight = 58022.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.050563 restraints weight = 39553.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.051305 restraints weight = 31541.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.051812 restraints weight = 27580.868| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29060 Z= 0.241 Angle : 0.656 8.278 39504 Z= 0.336 Chirality : 0.044 0.155 4496 Planarity : 0.004 0.062 5000 Dihedral : 5.127 32.909 3864 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.29 % Allowed : 10.13 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.27 (0.14), residues: 3548 helix: 0.55 (0.12), residues: 1752 sheet: 0.20 (0.23), residues: 440 loop : -0.13 (0.19), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 199 TYR 0.016 0.002 TYR D1042 PHE 0.022 0.002 PHE B 149 TRP 0.017 0.001 TRP A 87 HIS 0.007 0.001 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00548 (29060) covalent geometry : angle 0.65595 (39504) hydrogen bonds : bond 0.04835 ( 1408) hydrogen bonds : angle 5.06216 ( 3924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 200 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.9091 (m-80) cc_final: 0.8727 (m-80) REVERT: A 350 LYS cc_start: 0.9153 (mtmm) cc_final: 0.8868 (mtmt) REVERT: A 713 MET cc_start: 0.9062 (mmm) cc_final: 0.8799 (mmm) REVERT: A 841 GLU cc_start: 0.8952 (mp0) cc_final: 0.8627 (pm20) REVERT: B 350 LYS cc_start: 0.9212 (mtmm) cc_final: 0.8790 (pttp) REVERT: B 451 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8184 (mp10) REVERT: B 496 MET cc_start: 0.8911 (mmm) cc_final: 0.8679 (mmm) REVERT: B 524 MET cc_start: 0.8761 (mmt) cc_final: 0.8520 (mmt) REVERT: B 821 MET cc_start: 0.8894 (tpp) cc_final: 0.8489 (tpp) REVERT: B 891 GLU cc_start: 0.7289 (tm-30) cc_final: 0.7064 (tm-30) REVERT: C 201 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8798 (mp) REVERT: C 304 PHE cc_start: 0.8534 (t80) cc_final: 0.8293 (t80) REVERT: C 350 LYS cc_start: 0.9024 (mtmm) cc_final: 0.8746 (mtmt) REVERT: C 519 MET cc_start: 0.9445 (tpp) cc_final: 0.8945 (mmm) REVERT: C 526 MET cc_start: 0.8181 (tpp) cc_final: 0.7857 (tpp) REVERT: C 841 GLU cc_start: 0.8936 (mp0) cc_final: 0.8680 (mp0) REVERT: C 915 MET cc_start: 0.9609 (tpp) cc_final: 0.9165 (mpp) REVERT: D 350 LYS cc_start: 0.9265 (mtmm) cc_final: 0.8829 (pttp) REVERT: D 519 MET cc_start: 0.9308 (tpp) cc_final: 0.8926 (mmm) REVERT: D 524 MET cc_start: 0.8998 (mmt) cc_final: 0.8567 (mmt) REVERT: D 841 GLU cc_start: 0.9053 (mp0) cc_final: 0.8758 (mp0) outliers start: 70 outliers final: 35 residues processed: 256 average time/residue: 0.1569 time to fit residues: 66.8728 Evaluate side-chains 213 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 906 ASP Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 709 ASP Chi-restraints excluded: chain D residue 832 MET Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 933 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 183 optimal weight: 10.0000 chunk 325 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 337 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 26 optimal weight: 0.0770 chunk 209 optimal weight: 0.6980 chunk 304 optimal weight: 1.9990 chunk 306 optimal weight: 7.9990 overall best weight: 2.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN D 582 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.071934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.048551 restraints weight = 114920.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.050430 restraints weight = 57008.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.051665 restraints weight = 38630.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.052494 restraints weight = 30721.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.052916 restraints weight = 26623.924| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29060 Z= 0.147 Angle : 0.595 8.714 39504 Z= 0.298 Chirality : 0.042 0.307 4496 Planarity : 0.003 0.033 5000 Dihedral : 4.801 32.030 3864 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.96 % Allowed : 11.41 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.61 (0.14), residues: 3548 helix: 0.86 (0.12), residues: 1752 sheet: 0.40 (0.24), residues: 424 loop : -0.02 (0.19), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 199 TYR 0.013 0.001 TYR B 914 PHE 0.046 0.001 PHE A 145 TRP 0.014 0.001 TRP C 87 HIS 0.002 0.001 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00327 (29060) covalent geometry : angle 0.59530 (39504) hydrogen bonds : bond 0.04304 ( 1408) hydrogen bonds : angle 4.81152 ( 3924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 199 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8645 (pttp) REVERT: A 713 MET cc_start: 0.9070 (mmm) cc_final: 0.8730 (mmm) REVERT: A 841 GLU cc_start: 0.8881 (mp0) cc_final: 0.8577 (pm20) REVERT: B 173 PHE cc_start: 0.9149 (OUTLIER) cc_final: 0.8894 (m-80) REVERT: B 350 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8719 (pttp) REVERT: B 451 GLN cc_start: 0.8671 (OUTLIER) cc_final: 0.8117 (mp10) REVERT: B 496 MET cc_start: 0.8843 (mmm) cc_final: 0.8472 (mmm) REVERT: B 519 MET cc_start: 0.9431 (tpp) cc_final: 0.8738 (mmm) REVERT: B 524 MET cc_start: 0.8796 (mmt) cc_final: 0.8583 (mmt) REVERT: B 821 MET cc_start: 0.8889 (tpp) cc_final: 0.8382 (tpp) REVERT: B 891 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7214 (tm-30) REVERT: C 173 PHE cc_start: 0.9193 (OUTLIER) cc_final: 0.8893 (m-80) REVERT: C 526 MET cc_start: 0.8042 (tpp) cc_final: 0.7781 (tpp) REVERT: C 713 MET cc_start: 0.8897 (tpp) cc_final: 0.8350 (mmm) REVERT: C 915 MET cc_start: 0.9605 (tpp) cc_final: 0.9115 (mpp) REVERT: D 350 LYS cc_start: 0.9193 (mtmm) cc_final: 0.8751 (pttp) REVERT: D 524 MET cc_start: 0.9022 (mmt) cc_final: 0.8590 (mmt) REVERT: D 841 GLU cc_start: 0.9019 (mp0) cc_final: 0.8740 (mp0) outliers start: 60 outliers final: 36 residues processed: 248 average time/residue: 0.1607 time to fit residues: 65.8238 Evaluate side-chains 217 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 709 ASP Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 906 ASP Chi-restraints excluded: chain B residue 908 ASP Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 241 PHE Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 933 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 273 optimal weight: 0.3980 chunk 89 optimal weight: 30.0000 chunk 160 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 251 optimal weight: 9.9990 chunk 283 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 275 optimal weight: 30.0000 chunk 247 optimal weight: 7.9990 chunk 322 optimal weight: 0.5980 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 ASN B 15 GLN C 582 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.071381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.047971 restraints weight = 114808.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.049845 restraints weight = 57550.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.051066 restraints weight = 38964.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.051841 restraints weight = 30917.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.052346 restraints weight = 26908.327| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29060 Z= 0.186 Angle : 0.615 12.315 39504 Z= 0.304 Chirality : 0.043 0.289 4496 Planarity : 0.003 0.039 5000 Dihedral : 4.635 30.927 3862 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.09 % Allowed : 12.09 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.65 (0.14), residues: 3548 helix: 0.98 (0.12), residues: 1752 sheet: 0.47 (0.23), residues: 432 loop : -0.15 (0.19), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 468 TYR 0.023 0.001 TYR B 914 PHE 0.038 0.001 PHE A 145 TRP 0.012 0.001 TRP A 87 HIS 0.004 0.001 HIS A 243 Details of bonding type rmsd covalent geometry : bond 0.00423 (29060) covalent geometry : angle 0.61503 (39504) hydrogen bonds : bond 0.04194 ( 1408) hydrogen bonds : angle 4.81359 ( 3924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 189 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.9170 (mtmm) cc_final: 0.8675 (pttp) REVERT: A 841 GLU cc_start: 0.8867 (mp0) cc_final: 0.8570 (pm20) REVERT: B 173 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8919 (m-80) REVERT: B 350 LYS cc_start: 0.9188 (mtmm) cc_final: 0.8777 (pttp) REVERT: B 451 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: B 496 MET cc_start: 0.8822 (mmm) cc_final: 0.8378 (mmm) REVERT: B 891 GLU cc_start: 0.7652 (tm-30) cc_final: 0.7277 (tm-30) REVERT: C 932 SER cc_start: 0.9694 (m) cc_final: 0.9360 (p) REVERT: D 350 LYS cc_start: 0.9234 (mtmm) cc_final: 0.8791 (pttp) REVERT: D 524 MET cc_start: 0.9021 (mmt) cc_final: 0.8596 (mmt) REVERT: D 841 GLU cc_start: 0.8958 (mp0) cc_final: 0.8719 (mp0) outliers start: 64 outliers final: 43 residues processed: 240 average time/residue: 0.1541 time to fit residues: 61.1790 Evaluate side-chains 219 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 756 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 761 MET Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 241 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 933 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 335 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 225 optimal weight: 10.0000 chunk 257 optimal weight: 0.8980 chunk 250 optimal weight: 8.9990 chunk 293 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 177 optimal weight: 0.0060 chunk 173 optimal weight: 3.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN D 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.072557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.049372 restraints weight = 114122.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.051294 restraints weight = 56293.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.052564 restraints weight = 37831.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.053373 restraints weight = 29852.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.053866 restraints weight = 25854.581| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29060 Z= 0.115 Angle : 0.586 11.580 39504 Z= 0.286 Chirality : 0.042 0.303 4496 Planarity : 0.003 0.040 5000 Dihedral : 4.325 21.884 3856 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.83 % Allowed : 12.71 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.79 (0.15), residues: 3548 helix: 1.07 (0.13), residues: 1760 sheet: 0.46 (0.24), residues: 424 loop : -0.03 (0.19), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 100 TYR 0.022 0.001 TYR C 212 PHE 0.022 0.001 PHE A 154 TRP 0.012 0.001 TRP C 87 HIS 0.002 0.000 HIS C 440 Details of bonding type rmsd covalent geometry : bond 0.00249 (29060) covalent geometry : angle 0.58612 (39504) hydrogen bonds : bond 0.03830 ( 1408) hydrogen bonds : angle 4.61095 ( 3924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LYS cc_start: 0.9175 (mtmm) cc_final: 0.8647 (pttp) REVERT: A 519 MET cc_start: 0.9400 (mmm) cc_final: 0.9168 (mmm) REVERT: A 713 MET cc_start: 0.8841 (mmp) cc_final: 0.8571 (mmm) REVERT: A 841 GLU cc_start: 0.8873 (mp0) cc_final: 0.8569 (pm20) REVERT: A 891 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7245 (tm-30) REVERT: B 173 PHE cc_start: 0.9156 (OUTLIER) cc_final: 0.8888 (m-80) REVERT: B 350 LYS cc_start: 0.9204 (mtmm) cc_final: 0.8789 (pttp) REVERT: B 451 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: B 496 MET cc_start: 0.8757 (mmm) cc_final: 0.8338 (mmm) REVERT: B 713 MET cc_start: 0.9216 (mmm) cc_final: 0.8992 (mmm) REVERT: B 821 MET cc_start: 0.8987 (tpp) cc_final: 0.8531 (tpp) REVERT: B 891 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7368 (tm-30) REVERT: C 431 MET cc_start: 0.9336 (tpp) cc_final: 0.8794 (tpp) REVERT: C 713 MET cc_start: 0.8915 (tpp) cc_final: 0.8214 (tpp) REVERT: C 821 MET cc_start: 0.8810 (tpp) cc_final: 0.8558 (tpp) REVERT: C 932 SER cc_start: 0.9633 (m) cc_final: 0.9336 (p) REVERT: D 350 LYS cc_start: 0.9223 (mtmm) cc_final: 0.8770 (pttp) REVERT: D 519 MET cc_start: 0.9453 (mmm) cc_final: 0.9015 (mmm) REVERT: D 524 MET cc_start: 0.8903 (mmt) cc_final: 0.8546 (mmt) REVERT: D 713 MET cc_start: 0.8747 (tpp) cc_final: 0.7919 (mmm) REVERT: D 841 GLU cc_start: 0.8934 (mp0) cc_final: 0.8718 (mp0) outliers start: 56 outliers final: 42 residues processed: 243 average time/residue: 0.1539 time to fit residues: 61.7572 Evaluate side-chains 218 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 241 PHE Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain B residue 906 ASP Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 761 MET Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 241 PHE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 933 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 229 optimal weight: 8.9990 chunk 113 optimal weight: 7.9990 chunk 196 optimal weight: 3.9990 chunk 155 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 189 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 chunk 147 optimal weight: 0.0010 chunk 59 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS C 15 GLN C 243 HIS ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.071305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.048002 restraints weight = 114836.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.049840 restraints weight = 57326.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051068 restraints weight = 38776.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.051805 restraints weight = 30854.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.052324 restraints weight = 26983.713| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29060 Z= 0.191 Angle : 0.623 16.281 39504 Z= 0.303 Chirality : 0.043 0.267 4496 Planarity : 0.003 0.033 5000 Dihedral : 4.324 22.072 3856 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.83 % Allowed : 13.10 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.70 (0.14), residues: 3548 helix: 1.07 (0.12), residues: 1760 sheet: 0.51 (0.23), residues: 432 loop : -0.23 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 468 TYR 0.021 0.001 TYR C 212 PHE 0.056 0.001 PHE A 145 TRP 0.011 0.001 TRP B 87 HIS 0.003 0.001 HIS D 243 Details of bonding type rmsd covalent geometry : bond 0.00438 (29060) covalent geometry : angle 0.62299 (39504) hydrogen bonds : bond 0.04007 ( 1408) hydrogen bonds : angle 4.72174 ( 3924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.9054 (m-80) cc_final: 0.8748 (m-80) REVERT: A 154 PHE cc_start: 0.9526 (m-80) cc_final: 0.9174 (m-80) REVERT: A 350 LYS cc_start: 0.9179 (mtmm) cc_final: 0.8609 (pttp) REVERT: A 841 GLU cc_start: 0.8883 (mp0) cc_final: 0.8577 (pm20) REVERT: A 891 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7455 (tm-30) REVERT: B 173 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8868 (m-80) REVERT: B 350 LYS cc_start: 0.9231 (mtmm) cc_final: 0.8960 (pttm) REVERT: B 451 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: B 496 MET cc_start: 0.8716 (mmm) cc_final: 0.8422 (mmt) REVERT: B 821 MET cc_start: 0.8982 (tpp) cc_final: 0.8497 (tpp) REVERT: B 891 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7340 (tm-30) REVERT: C 176 TYR cc_start: 0.7706 (m-10) cc_final: 0.7211 (m-80) REVERT: C 431 MET cc_start: 0.9417 (tpp) cc_final: 0.8871 (tpp) REVERT: C 821 MET cc_start: 0.8782 (tpp) cc_final: 0.8520 (tpp) REVERT: C 891 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7660 (tm-30) REVERT: C 932 SER cc_start: 0.9724 (m) cc_final: 0.9429 (p) REVERT: D 176 TYR cc_start: 0.7634 (m-10) cc_final: 0.7223 (m-80) REVERT: D 350 LYS cc_start: 0.9239 (mtmm) cc_final: 0.8765 (pttp) REVERT: D 502 MET cc_start: 0.8618 (tpp) cc_final: 0.8210 (tpp) REVERT: D 519 MET cc_start: 0.9454 (mmm) cc_final: 0.8855 (mmm) REVERT: D 524 MET cc_start: 0.8960 (mmt) cc_final: 0.8558 (mmt) REVERT: D 841 GLU cc_start: 0.8952 (mp0) cc_final: 0.8727 (mp0) REVERT: D 915 MET cc_start: 0.9293 (mmm) cc_final: 0.9090 (mpp) outliers start: 56 outliers final: 43 residues processed: 229 average time/residue: 0.1579 time to fit residues: 60.0882 Evaluate side-chains 226 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 181 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 273 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 173 PHE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 761 MET Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 933 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 91 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 257 optimal weight: 0.0470 chunk 289 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 194 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 315 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 overall best weight: 1.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B1046 ASN ** C1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.073076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.050252 restraints weight = 115798.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.052161 restraints weight = 56396.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.053398 restraints weight = 37711.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.054182 restraints weight = 29712.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054646 restraints weight = 25745.822| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29060 Z= 0.120 Angle : 0.606 13.538 39504 Z= 0.289 Chirality : 0.042 0.272 4496 Planarity : 0.003 0.032 5000 Dihedral : 4.191 21.016 3856 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.63 % Allowed : 13.79 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.83 (0.15), residues: 3548 helix: 1.16 (0.13), residues: 1764 sheet: 0.55 (0.24), residues: 416 loop : -0.13 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 468 TYR 0.019 0.001 TYR C 212 PHE 0.021 0.001 PHE B 154 TRP 0.012 0.001 TRP B 87 HIS 0.002 0.000 HIS B 260 Details of bonding type rmsd covalent geometry : bond 0.00265 (29060) covalent geometry : angle 0.60593 (39504) hydrogen bonds : bond 0.03744 ( 1408) hydrogen bonds : angle 4.58866 ( 3924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 194 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.9549 (m-80) cc_final: 0.9164 (m-80) REVERT: A 350 LYS cc_start: 0.9180 (mtmm) cc_final: 0.8572 (pttp) REVERT: A 519 MET cc_start: 0.9388 (mmm) cc_final: 0.9173 (mmm) REVERT: A 841 GLU cc_start: 0.8863 (mp0) cc_final: 0.8550 (pm20) REVERT: A 891 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7435 (tm-30) REVERT: B 350 LYS cc_start: 0.9232 (mtmm) cc_final: 0.8954 (pttm) REVERT: B 451 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8220 (mp10) REVERT: B 496 MET cc_start: 0.8714 (mmm) cc_final: 0.8428 (mmt) REVERT: B 713 MET cc_start: 0.9181 (mmm) cc_final: 0.8834 (tpp) REVERT: B 821 MET cc_start: 0.8964 (tpp) cc_final: 0.8515 (tpp) REVERT: B 891 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7424 (tm-30) REVERT: C 176 TYR cc_start: 0.7656 (m-10) cc_final: 0.7161 (m-80) REVERT: C 298 MET cc_start: 0.9322 (mmm) cc_final: 0.9115 (mmm) REVERT: C 431 MET cc_start: 0.9344 (tpp) cc_final: 0.8846 (tpp) REVERT: C 713 MET cc_start: 0.8865 (tpp) cc_final: 0.8196 (tpp) REVERT: C 821 MET cc_start: 0.8767 (tpp) cc_final: 0.8546 (tpp) REVERT: C 891 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7627 (tm-30) REVERT: C 932 SER cc_start: 0.9606 (m) cc_final: 0.9386 (p) REVERT: D 176 TYR cc_start: 0.7575 (m-10) cc_final: 0.7153 (m-80) REVERT: D 350 LYS cc_start: 0.9233 (mtmm) cc_final: 0.8765 (pttp) REVERT: D 519 MET cc_start: 0.9451 (mmm) cc_final: 0.8935 (mmm) REVERT: D 524 MET cc_start: 0.8882 (mmt) cc_final: 0.8526 (mmt) REVERT: D 713 MET cc_start: 0.8750 (tpp) cc_final: 0.7939 (mmm) REVERT: D 841 GLU cc_start: 0.8910 (mp0) cc_final: 0.8707 (mp0) REVERT: D 915 MET cc_start: 0.9353 (mmm) cc_final: 0.9099 (mpp) outliers start: 50 outliers final: 42 residues processed: 232 average time/residue: 0.1595 time to fit residues: 61.2137 Evaluate side-chains 232 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 847 LEU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 832 MET Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 761 MET Chi-restraints excluded: chain C residue 832 MET Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 367 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 847 LEU Chi-restraints excluded: chain D residue 933 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 66 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 chunk 275 optimal weight: 50.0000 chunk 250 optimal weight: 0.7980 chunk 302 optimal weight: 1.9990 chunk 262 optimal weight: 4.9990 chunk 251 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1046 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.073406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.050609 restraints weight = 115676.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.052518 restraints weight = 56734.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.053735 restraints weight = 38113.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.054562 restraints weight = 30190.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.055034 restraints weight = 26099.350| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29060 Z= 0.115 Angle : 0.608 14.366 39504 Z= 0.290 Chirality : 0.042 0.268 4496 Planarity : 0.003 0.038 5000 Dihedral : 4.082 24.028 3856 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.50 % Allowed : 13.76 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.90 (0.15), residues: 3548 helix: 1.22 (0.13), residues: 1756 sheet: 0.34 (0.24), residues: 456 loop : -0.00 (0.19), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 199 TYR 0.016 0.001 TYR C 212 PHE 0.046 0.001 PHE B 154 TRP 0.012 0.001 TRP B 87 HIS 0.001 0.000 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.00254 (29060) covalent geometry : angle 0.60844 (39504) hydrogen bonds : bond 0.03638 ( 1408) hydrogen bonds : angle 4.53053 ( 3924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.9575 (m-80) cc_final: 0.9199 (m-80) REVERT: A 304 PHE cc_start: 0.8400 (t80) cc_final: 0.8137 (t80) REVERT: A 350 LYS cc_start: 0.9188 (mtmm) cc_final: 0.8575 (pttp) REVERT: A 519 MET cc_start: 0.9387 (mmm) cc_final: 0.9175 (mmm) REVERT: A 841 GLU cc_start: 0.8804 (mp0) cc_final: 0.8539 (pm20) REVERT: A 891 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7460 (tm-30) REVERT: B 154 PHE cc_start: 0.9534 (m-80) cc_final: 0.9271 (m-80) REVERT: B 304 PHE cc_start: 0.8322 (t80) cc_final: 0.8026 (t80) REVERT: B 350 LYS cc_start: 0.9218 (mtmm) cc_final: 0.8940 (pttm) REVERT: B 496 MET cc_start: 0.8719 (mmm) cc_final: 0.8415 (mmt) REVERT: B 524 MET cc_start: 0.7657 (mtm) cc_final: 0.7370 (mtp) REVERT: B 713 MET cc_start: 0.9168 (mmm) cc_final: 0.8818 (tpp) REVERT: B 821 MET cc_start: 0.8980 (tpp) cc_final: 0.8545 (tpp) REVERT: B 891 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7447 (tm-30) REVERT: C 154 PHE cc_start: 0.9531 (m-80) cc_final: 0.9282 (m-80) REVERT: C 173 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8834 (t80) REVERT: C 176 TYR cc_start: 0.7588 (m-10) cc_final: 0.7241 (m-80) REVERT: C 298 MET cc_start: 0.9314 (mmm) cc_final: 0.9104 (mmm) REVERT: C 431 MET cc_start: 0.9319 (tpp) cc_final: 0.8777 (tpp) REVERT: C 713 MET cc_start: 0.8942 (tpp) cc_final: 0.8250 (tpp) REVERT: C 891 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7627 (tm-30) REVERT: D 154 PHE cc_start: 0.9502 (m-80) cc_final: 0.9254 (m-80) REVERT: D 176 TYR cc_start: 0.7574 (m-10) cc_final: 0.7190 (m-80) REVERT: D 350 LYS cc_start: 0.9217 (mtmm) cc_final: 0.8751 (pttp) REVERT: D 519 MET cc_start: 0.9450 (mmm) cc_final: 0.8950 (mmm) REVERT: D 524 MET cc_start: 0.8839 (mmt) cc_final: 0.8577 (mmt) REVERT: D 713 MET cc_start: 0.8732 (tpp) cc_final: 0.7920 (mmm) REVERT: D 821 MET cc_start: 0.8872 (tpp) cc_final: 0.8482 (tpp) REVERT: D 915 MET cc_start: 0.9356 (mmm) cc_final: 0.9058 (mpp) REVERT: D 932 SER cc_start: 0.9619 (m) cc_final: 0.9341 (p) outliers start: 46 outliers final: 34 residues processed: 233 average time/residue: 0.1519 time to fit residues: 58.9582 Evaluate side-chains 228 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 133 TRP Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 761 MET Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 847 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 103 optimal weight: 6.9990 chunk 305 optimal weight: 0.9990 chunk 158 optimal weight: 0.0470 chunk 84 optimal weight: 1.9990 chunk 170 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 254 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 overall best weight: 1.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 940 ASN D 940 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.073659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.050960 restraints weight = 114979.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.052869 restraints weight = 56506.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054123 restraints weight = 37748.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.054905 restraints weight = 29765.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.055368 restraints weight = 25807.236| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29060 Z= 0.112 Angle : 0.622 18.689 39504 Z= 0.293 Chirality : 0.042 0.262 4496 Planarity : 0.003 0.032 5000 Dihedral : 4.024 30.440 3856 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.21 % Allowed : 14.28 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 0.97 (0.15), residues: 3548 helix: 1.26 (0.13), residues: 1760 sheet: 0.47 (0.24), residues: 448 loop : 0.02 (0.19), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 468 TYR 0.015 0.001 TYR C 212 PHE 0.027 0.001 PHE B 149 TRP 0.012 0.001 TRP A 87 HIS 0.001 0.000 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.00245 (29060) covalent geometry : angle 0.62155 (39504) hydrogen bonds : bond 0.03563 ( 1408) hydrogen bonds : angle 4.48721 ( 3924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7096 Ramachandran restraints generated. 3548 Oldfield, 0 Emsley, 3548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.9564 (m-80) cc_final: 0.9182 (m-80) REVERT: A 304 PHE cc_start: 0.8382 (t80) cc_final: 0.8095 (t80) REVERT: A 350 LYS cc_start: 0.9180 (mtmm) cc_final: 0.8564 (pttp) REVERT: A 519 MET cc_start: 0.9370 (mmm) cc_final: 0.9169 (mmm) REVERT: A 841 GLU cc_start: 0.8797 (mp0) cc_final: 0.8547 (pm20) REVERT: B 154 PHE cc_start: 0.9510 (m-80) cc_final: 0.9227 (m-80) REVERT: B 350 LYS cc_start: 0.9229 (mtmm) cc_final: 0.8955 (pttm) REVERT: B 451 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8252 (mp10) REVERT: B 496 MET cc_start: 0.8729 (mmm) cc_final: 0.8440 (mmt) REVERT: B 519 MET cc_start: 0.9443 (mmm) cc_final: 0.8642 (mmm) REVERT: B 713 MET cc_start: 0.9142 (mmm) cc_final: 0.8805 (tpp) REVERT: B 821 MET cc_start: 0.8942 (tpp) cc_final: 0.8535 (tpp) REVERT: B 891 GLU cc_start: 0.7922 (tm-30) cc_final: 0.7455 (tm-30) REVERT: C 154 PHE cc_start: 0.9515 (m-80) cc_final: 0.9253 (m-80) REVERT: C 173 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.8839 (t80) REVERT: C 176 TYR cc_start: 0.7550 (m-10) cc_final: 0.7202 (m-80) REVERT: C 298 MET cc_start: 0.9317 (mmm) cc_final: 0.9094 (mmm) REVERT: C 304 PHE cc_start: 0.8305 (t80) cc_final: 0.7974 (t80) REVERT: C 519 MET cc_start: 0.9247 (tpp) cc_final: 0.8995 (tpp) REVERT: C 713 MET cc_start: 0.8933 (tpp) cc_final: 0.8254 (tpp) REVERT: C 821 MET cc_start: 0.8526 (tpp) cc_final: 0.8212 (tpp) REVERT: C 891 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7619 (tm-30) REVERT: D 154 PHE cc_start: 0.9484 (m-80) cc_final: 0.9171 (m-80) REVERT: D 176 TYR cc_start: 0.7551 (m-10) cc_final: 0.7189 (m-80) REVERT: D 350 LYS cc_start: 0.9226 (mtmm) cc_final: 0.8749 (pttp) REVERT: D 519 MET cc_start: 0.9458 (mmm) cc_final: 0.8961 (mmm) REVERT: D 524 MET cc_start: 0.8727 (mmt) cc_final: 0.8486 (mmt) REVERT: D 713 MET cc_start: 0.8734 (tpp) cc_final: 0.7909 (mmm) REVERT: D 821 MET cc_start: 0.8881 (tpp) cc_final: 0.8482 (tpp) REVERT: D 915 MET cc_start: 0.9381 (mmm) cc_final: 0.9061 (mpp) outliers start: 37 outliers final: 32 residues processed: 230 average time/residue: 0.1511 time to fit residues: 57.4541 Evaluate side-chains 231 residues out of total 3132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 947 ILE Chi-restraints excluded: chain B residue 274 MET Chi-restraints excluded: chain B residue 301 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 451 GLN Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain C residue 173 PHE Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 364 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 761 MET Chi-restraints excluded: chain C residue 847 LEU Chi-restraints excluded: chain C residue 934 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 301 ILE Chi-restraints excluded: chain D residue 364 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 473 VAL Chi-restraints excluded: chain D residue 577 LYS Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 847 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 356 random chunks: chunk 77 optimal weight: 0.0370 chunk 354 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 138 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 319 optimal weight: 1.9990 chunk 288 optimal weight: 6.9990 chunk 345 optimal weight: 0.9980 chunk 295 optimal weight: 0.0970 chunk 247 optimal weight: 0.0370 chunk 131 optimal weight: 8.9990 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 940 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.074542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.051919 restraints weight = 115170.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.053896 restraints weight = 56487.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.055177 restraints weight = 37613.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.055983 restraints weight = 29513.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.056443 restraints weight = 25415.441| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29060 Z= 0.104 Angle : 0.615 13.927 39504 Z= 0.290 Chirality : 0.041 0.273 4496 Planarity : 0.003 0.032 5000 Dihedral : 3.925 30.656 3856 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.01 % Allowed : 14.64 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 aren not related in a simple way. whole: 1.17 (0.15), residues: 3548 helix: 1.43 (0.13), residues: 1724 sheet: 0.55 (0.24), residues: 440 loop : 0.17 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 199 TYR 0.013 0.001 TYR C 212 PHE 0.042 0.001 PHE A 145 TRP 0.012 0.001 TRP A 87 HIS 0.002 0.000 HIS A 453 Details of bonding type rmsd covalent geometry : bond 0.00213 (29060) covalent geometry : angle 0.61529 (39504) hydrogen bonds : bond 0.03413 ( 1408) hydrogen bonds : angle 4.42455 ( 3924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4198.24 seconds wall clock time: 73 minutes 23.79 seconds (4403.79 seconds total)