Starting phenix.real_space_refine on Fri May 23 07:42:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gjj_40091/05_2025/8gjj_40091.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gjj_40091/05_2025/8gjj_40091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gjj_40091/05_2025/8gjj_40091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gjj_40091/05_2025/8gjj_40091.map" model { file = "/net/cci-nas-00/data/ceres_data/8gjj_40091/05_2025/8gjj_40091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gjj_40091/05_2025/8gjj_40091.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 84 5.16 5 C 15521 2.51 5 N 3860 2.21 5 O 4463 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23928 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 7976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7976 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 7982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7982 Classifications: {'peptide': 1032} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Chain: "C" Number of atoms: 7970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 7970 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 990} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 13.77, per 1000 atoms: 0.58 Number of scatterers: 23928 At special positions: 0 Unit cell: (118.77, 121.98, 146.59, 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 84 16.00 O 4463 8.00 N 3860 7.00 C 15521 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: 6.23 Conformation dependent library (CDL) restraints added in 3.3 seconds 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 24 sheets defined 60.4% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.02 Creating SS restraints... Processing helix chain 'B' and resid 1 through 8 removed outlier: 3.743A pdb=" N PHE B 6 " --> pdb=" O PHE B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 54 through 62 Processing helix chain 'B' and resid 62 through 70 Processing helix chain 'B' and resid 99 through 116 removed outlier: 4.300A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 161 Processing helix chain 'B' and resid 161 through 168 removed outlier: 3.579A pdb=" N GLU B 165 " --> pdb=" O ASN B 161 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 200 through 212 Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 263 through 266 No H-bonds generated for 'chain 'B' and resid 263 through 266' Processing helix chain 'B' and resid 299 through 316 Processing helix chain 'B' and resid 330 through 360 removed outlier: 3.975A pdb=" N VAL B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 388 removed outlier: 3.571A pdb=" N THR B 366 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 368 " --> pdb=" O LYS B 364 " (cutoff:3.500A) Proline residue: B 369 - end of helix Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 392 through 424 removed outlier: 4.443A pdb=" N GLY B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP B 409 " --> pdb=" O ILE B 405 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 410 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 459 removed outlier: 5.642A pdb=" N SER B 442 " --> pdb=" O ASN B 438 " (cutoff:3.500A) Proline residue: B 443 - end of helix Proline residue: B 457 - end of helix Processing helix chain 'B' and resid 463 through 498 removed outlier: 4.089A pdb=" N ILE B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 472 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 507 through 534 Processing helix chain 'B' and resid 534 through 556 removed outlier: 4.211A pdb=" N PHE B 538 " --> pdb=" O ARG B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 598 removed outlier: 3.511A pdb=" N THR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN B 597 " --> pdb=" O LYS B 593 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET B 598 " --> pdb=" O ASN B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 649 Processing helix chain 'B' and resid 685 through 703 Processing helix chain 'B' and resid 725 through 732 Processing helix chain 'B' and resid 735 through 747 Processing helix chain 'B' and resid 770 through 773 removed outlier: 3.682A pdb=" N ARG B 773 " --> pdb=" O GLY B 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 770 through 773' Processing helix chain 'B' and resid 777 through 782 removed outlier: 4.183A pdb=" N ASN B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 782 " --> pdb=" O ALA B 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 777 through 782' Processing helix chain 'B' and resid 829 through 845 Processing helix chain 'B' and resid 855 through 863 Processing helix chain 'B' and resid 867 through 887 Processing helix chain 'B' and resid 891 through 898 removed outlier: 4.192A pdb=" N VAL B 895 " --> pdb=" O MET B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 899 through 914 removed outlier: 4.020A pdb=" N VAL B 903 " --> pdb=" O VAL B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 950 Processing helix chain 'B' and resid 953 through 985 removed outlier: 4.541A pdb=" N ARG B 967 " --> pdb=" O LYS B 963 " (cutoff:3.500A) Proline residue: B 968 - end of helix Proline residue: B 982 - end of helix removed outlier: 3.902A pdb=" N PHE B 985 " --> pdb=" O LEU B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 990 through 1011 Processing helix chain 'B' and resid 1011 through 1032 Proline residue: B1017 - end of helix Processing helix chain 'A' and resid 2 through 8 removed outlier: 3.691A pdb=" N PHE A 6 " --> pdb=" O PHE A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 54 through 71 Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 99 through 114 removed outlier: 3.605A pdb=" N ALA A 104 " --> pdb=" O PRO A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.503A pdb=" N LYS A 123 " --> pdb=" O PRO A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 169 removed outlier: 4.459A pdb=" N LEU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ASP A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU A 165 " --> pdb=" O ASN A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 263 through 266 No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 299 through 316 Processing helix chain 'A' and resid 330 through 361 Processing helix chain 'A' and resid 362 through 371 Proline residue: A 369 - end of helix Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.548A pdb=" N VAL A 375 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 removed outlier: 4.662A pdb=" N GLY A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASP A 409 " --> pdb=" O ILE A 405 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ALA A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 455 removed outlier: 5.579A pdb=" N SER A 442 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Proline residue: A 443 - end of helix Processing helix chain 'A' and resid 455 through 461 removed outlier: 3.930A pdb=" N SER A 459 " --> pdb=" O PHE A 455 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 499 removed outlier: 3.826A pdb=" N THR A 475 " --> pdb=" O GLN A 471 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 507 through 534 Processing helix chain 'A' and resid 535 through 556 Processing helix chain 'A' and resid 580 through 598 removed outlier: 3.571A pdb=" N GLN A 597 " --> pdb=" O LYS A 593 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET A 598 " --> pdb=" O ASN A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 649 Processing helix chain 'A' and resid 685 through 702 removed outlier: 3.817A pdb=" N GLN A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 735 through 747 Processing helix chain 'A' and resid 777 through 782 Processing helix chain 'A' and resid 794 through 797 No H-bonds generated for 'chain 'A' and resid 794 through 797' Processing helix chain 'A' and resid 829 through 846 removed outlier: 3.650A pdb=" N GLY A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 864 removed outlier: 3.596A pdb=" N TYR A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 887 Processing helix chain 'A' and resid 889 through 897 removed outlier: 3.936A pdb=" N LEU A 893 " --> pdb=" O TRP A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 913 removed outlier: 3.687A pdb=" N ALA A 902 " --> pdb=" O ALA A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 950 removed outlier: 3.715A pdb=" N GLY A 930 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 939 " --> pdb=" O ASN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 985 removed outlier: 4.849A pdb=" N ARG A 967 " --> pdb=" O LYS A 963 " (cutoff:3.500A) Proline residue: A 968 - end of helix Proline residue: A 982 - end of helix Processing helix chain 'A' and resid 990 through 1011 removed outlier: 4.067A pdb=" N GLY A1000 " --> pdb=" O SER A 996 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1032 Proline residue: A1017 - end of helix Processing helix chain 'C' and resid 2 through 8 removed outlier: 3.725A pdb=" N PHE C 6 " --> pdb=" O PHE C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 31 Processing helix chain 'C' and resid 54 through 62 Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 99 through 115 removed outlier: 3.528A pdb=" N ALA C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 119 through 126 Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 161 through 169 removed outlier: 3.668A pdb=" N GLU C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 169 " --> pdb=" O GLU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 200 through 212 Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 263 through 266 No H-bonds generated for 'chain 'C' and resid 263 through 266' Processing helix chain 'C' and resid 299 through 317 removed outlier: 3.803A pdb=" N ASN C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 360 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 366 through 388 removed outlier: 3.616A pdb=" N MET C 370 " --> pdb=" O THR C 366 " (cutoff:3.500A) Proline residue: C 374 - end of helix Processing helix chain 'C' and resid 392 through 424 removed outlier: 4.016A pdb=" N GLY C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 405 " --> pdb=" O LEU C 401 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP C 424 " --> pdb=" O ILE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 460 removed outlier: 5.078A pdb=" N SER C 442 " --> pdb=" O ASN C 438 " (cutoff:3.500A) Proline residue: C 443 - end of helix Proline residue: C 457 - end of helix removed outlier: 3.579A pdb=" N PHE C 460 " --> pdb=" O ILE C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 499 removed outlier: 3.544A pdb=" N GLY C 466 " --> pdb=" O SER C 462 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 472 " --> pdb=" O ILE C 468 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR C 491 " --> pdb=" O ALA C 487 " (cutoff:3.500A) Proline residue: C 492 - end of helix Processing helix chain 'C' and resid 507 through 534 Processing helix chain 'C' and resid 534 through 556 removed outlier: 3.899A pdb=" N PHE C 538 " --> pdb=" O ARG C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 598 removed outlier: 3.685A pdb=" N THR C 584 " --> pdb=" O SER C 580 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN C 597 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET C 598 " --> pdb=" O ASN C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 649 Processing helix chain 'C' and resid 685 through 703 removed outlier: 3.725A pdb=" N THR C 702 " --> pdb=" O GLU C 698 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG C 703 " --> pdb=" O LEU C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 732 Processing helix chain 'C' and resid 735 through 747 Processing helix chain 'C' and resid 770 through 773 removed outlier: 3.634A pdb=" N ARG C 773 " --> pdb=" O GLY C 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 770 through 773' Processing helix chain 'C' and resid 775 through 781 removed outlier: 4.421A pdb=" N LEU C 779 " --> pdb=" O GLN C 776 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN C 781 " --> pdb=" O ALA C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 845 Processing helix chain 'C' and resid 855 through 887 removed outlier: 4.214A pdb=" N LYS C 864 " --> pdb=" O GLU C 860 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY C 865 " --> pdb=" O VAL C 861 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA C 866 " --> pdb=" O SER C 862 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLY C 867 " --> pdb=" O SER C 863 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA C 868 " --> pdb=" O LYS C 864 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N TYR C 869 " --> pdb=" O GLY C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 899 removed outlier: 4.206A pdb=" N VAL C 895 " --> pdb=" O MET C 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 914 removed outlier: 4.059A pdb=" N VAL C 903 " --> pdb=" O VAL C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 949 Processing helix chain 'C' and resid 953 through 985 removed outlier: 4.383A pdb=" N ARG C 967 " --> pdb=" O LYS C 963 " (cutoff:3.500A) Proline residue: C 968 - end of helix Proline residue: C 982 - end of helix removed outlier: 4.054A pdb=" N PHE C 985 " --> pdb=" O LEU C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1032 removed outlier: 3.612A pdb=" N ARG C 994 " --> pdb=" O GLY C 990 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C1013 " --> pdb=" O SER C1009 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N PHE C1014 " --> pdb=" O THR C1010 " (cutoff:3.500A) Proline residue: C1017 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA2, first strand: chain 'B' and resid 172 through 177 removed outlier: 6.609A pdb=" N VAL B 172 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N GLN B 295 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 174 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA B 286 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B 144 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B 138 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 294 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE B 136 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 328 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 322 through 324 removed outlier: 7.976A pdb=" N ILE B 136 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 294 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU B 138 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER B 144 " --> pdb=" O ALA B 286 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ALA B 286 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 623 " --> pdb=" O LEU B 607 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ALA B 621 " --> pdb=" O GLY B 609 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ASP B 611 " --> pdb=" O GLU B 619 " (cutoff:3.500A) removed outlier: 9.503A pdb=" N GLU B 619 " --> pdb=" O ASP B 611 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 572 " --> pdb=" O TYR B 658 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 267 through 273 removed outlier: 7.705A pdb=" N TYR B 183 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLN B 763 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS B 760 " --> pdb=" O PRO B 756 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE B 762 " --> pdb=" O ASP B 754 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP B 754 " --> pdb=" O PHE B 762 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 764 " --> pdb=" O VAL B 752 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 219 through 220 removed outlier: 3.905A pdb=" N SER B 234 " --> pdb=" O PRO C 718 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 799 " --> pdb=" O ILE C 723 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 251 through 254 removed outlier: 3.610A pdb=" N ARG B 253 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 706 through 711 removed outlier: 3.504A pdb=" N ASN B 708 " --> pdb=" O ASP B 823 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 798 through 804 removed outlier: 4.138A pdb=" N SER A 234 " --> pdb=" O PRO B 718 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 783 through 785 Processing sheet with id=AB1, first strand: chain 'A' and resid 127 through 132 removed outlier: 4.433A pdb=" N THR A 43 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 78 " --> pdb=" O TYR A 93 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS A 810 " --> pdb=" O ALA A 817 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 172 through 177 removed outlier: 3.571A pdb=" N GLU A 138 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU A 294 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 136 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N LEU A 137 " --> pdb=" O ASP A 329 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASP A 329 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A 139 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 267 through 273 removed outlier: 8.061A pdb=" N TYR A 183 " --> pdb=" O ASN A 761 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 763 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN A 753 " --> pdb=" O VAL A 764 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE A 766 " --> pdb=" O TYR A 751 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N TYR A 751 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 251 through 254 Processing sheet with id=AB5, first strand: chain 'A' and resid 279 through 282 removed outlier: 5.911A pdb=" N ALA A 621 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ASP A 611 " --> pdb=" O GLU A 619 " (cutoff:3.500A) removed outlier: 9.670A pdb=" N GLU A 619 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 706 through 711 removed outlier: 4.292A pdb=" N VAL A 709 " --> pdb=" O GLN A 821 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLN A 821 " --> pdb=" O VAL A 709 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR A 711 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 819 " --> pdb=" O THR A 711 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 822 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 798 through 805 removed outlier: 3.754A pdb=" N SER C 234 " --> pdb=" O PRO A 718 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN C 238 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE A 724 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 239 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLN C 214 " --> pdb=" O GLY C 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 783 through 785 Processing sheet with id=AB9, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.590A pdb=" N TYR C 78 " --> pdb=" O TYR C 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.509A pdb=" N ALA C 286 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU C 294 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE C 136 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N LEU C 137 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ASP C 329 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL C 139 " --> pdb=" O PRO C 327 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.169A pdb=" N GLY C 280 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 267 through 273 removed outlier: 7.713A pdb=" N TYR C 183 " --> pdb=" O ASN C 761 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN C 763 " --> pdb=" O TYR C 183 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN C 753 " --> pdb=" O VAL C 764 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ILE C 766 " --> pdb=" O TYR C 751 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR C 751 " --> pdb=" O ILE C 766 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 251 through 254 Processing sheet with id=AC5, first strand: chain 'C' and resid 707 through 711 removed outlier: 4.872A pdb=" N ASN C 708 " --> pdb=" O ASP C 823 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP C 823 " --> pdb=" O ASN C 708 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY C 822 " --> pdb=" O PHE C 674 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU C 675 " --> pdb=" O SER C 854 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 783 through 785 1595 hydrogen bonds defined for protein. 4689 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: 9.79 Time building geometry restraints manager: 7.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7590 1.34 - 1.46: 3642 1.46 - 1.57: 12996 1.57 - 1.69: 0 1.69 - 1.81: 162 Bond restraints: 24390 Sorted by residual: bond pdb=" C VAL B 288 " pdb=" N PRO B 289 " ideal model delta sigma weight residual 1.335 1.318 0.017 8.70e-03 1.32e+04 3.87e+00 bond pdb=" C GLN C 242 " pdb=" N THR C 243 " ideal model delta sigma weight residual 1.327 1.273 0.054 2.86e-02 1.22e+03 3.53e+00 bond pdb=" C LYS A 228 " pdb=" N SER A 229 " ideal model delta sigma weight residual 1.331 1.293 0.038 2.07e-02 2.33e+03 3.46e+00 bond pdb=" C VAL A 288 " pdb=" N PRO A 289 " ideal model delta sigma weight residual 1.334 1.321 0.013 1.11e-02 8.12e+03 1.42e+00 bond pdb=" C PRO B 663 " pdb=" N PRO B 664 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.19e-02 7.06e+03 1.36e+00 ... (remaining 24385 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 32630 1.77 - 3.55: 422 3.55 - 5.32: 69 5.32 - 7.10: 10 7.10 - 8.87: 1 Bond angle restraints: 33132 Sorted by residual: angle pdb=" C LEU A 360 " pdb=" N LYS A 361 " pdb=" CA LYS A 361 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 9.99e+00 angle pdb=" CA VAL A 561 " pdb=" C VAL A 561 " pdb=" N PRO A 562 " ideal model delta sigma weight residual 116.57 119.35 -2.78 9.80e-01 1.04e+00 8.04e+00 angle pdb=" C SER B 459 " pdb=" N PHE B 460 " pdb=" CA PHE B 460 " ideal model delta sigma weight residual 122.61 127.00 -4.39 1.56e+00 4.11e-01 7.91e+00 angle pdb=" C VAL B 465 " pdb=" N GLY B 466 " pdb=" CA GLY B 466 " ideal model delta sigma weight residual 120.14 123.57 -3.43 1.25e+00 6.40e-01 7.53e+00 angle pdb=" C ASN A 255 " pdb=" N GLU A 256 " pdb=" CA GLU A 256 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.86e+00 ... (remaining 33127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 13776 16.79 - 33.59: 716 33.59 - 50.38: 143 50.38 - 67.17: 24 67.17 - 83.97: 2 Dihedral angle restraints: 14661 sinusoidal: 5622 harmonic: 9039 Sorted by residual: dihedral pdb=" CA TYR B 731 " pdb=" C TYR B 731 " pdb=" N TYR B 732 " pdb=" CA TYR B 732 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LYS B 704 " pdb=" C LYS B 704 " pdb=" N GLU B 705 " pdb=" CA GLU B 705 " ideal model delta harmonic sigma weight residual 180.00 159.85 20.15 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA SER A 60 " pdb=" C SER A 60 " pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta harmonic sigma weight residual -180.00 -163.03 -16.97 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 14658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2249 0.028 - 0.057: 1100 0.057 - 0.085: 343 0.085 - 0.114: 206 0.114 - 0.142: 44 Chirality restraints: 3942 Sorted by residual: chirality pdb=" CA ILE B 169 " pdb=" N ILE B 169 " pdb=" C ILE B 169 " pdb=" CB ILE B 169 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA PHE B 460 " pdb=" N PHE B 460 " pdb=" C PHE B 460 " pdb=" CB PHE B 460 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA THR B 64 " pdb=" N THR B 64 " pdb=" C THR B 64 " pdb=" CB THR B 64 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 3939 not shown) Planarity restraints: 4200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 60 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.64e+00 pdb=" C SER A 60 " -0.037 2.00e-02 2.50e+03 pdb=" O SER A 60 " 0.014 2.00e-02 2.50e+03 pdb=" N THR A 61 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 662 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO B 663 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 663 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 663 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 59 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ALA A 59 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA A 59 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 60 " -0.010 2.00e-02 2.50e+03 ... (remaining 4197 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 803 2.71 - 3.26: 25110 3.26 - 3.81: 40472 3.81 - 4.35: 49245 4.35 - 4.90: 87507 Nonbonded interactions: 203137 Sorted by model distance: nonbonded pdb=" NZ LYS C 684 " pdb=" OD2 ASP C 692 " model vdw 2.166 3.120 nonbonded pdb=" OH TYR B 36 " pdb=" OH TYR B 920 " model vdw 2.180 3.040 nonbonded pdb=" O TYR C 858 " pdb=" OG SER C 862 " model vdw 2.185 3.040 nonbonded pdb=" O ILE B 456 " pdb=" OG SER B 459 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR C 43 " pdb=" OG SER C 132 " model vdw 2.188 3.040 ... (remaining 203132 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 502 or (resid 503 and (name N or \ name CA or name C or name O or name CB )) or resid 504 or (resid 505 and (name \ N or name CA or name C or name O or name CB )) or resid 506 through 702 or (resi \ d 703 and (name N or name CA or name C or name O or name CB )) or resid 704 thro \ ugh 1032)) selection = (chain 'B' and (resid 1 through 308 or (resid 309 and (name N or name CA or name \ C or name O or name CB )) or resid 310 through 502 or (resid 503 and (name N or \ name CA or name C or name O or name CB )) or resid 504 or (resid 505 and (name \ N or name CA or name C or name O or name CB )) or resid 506 through 1032)) selection = (chain 'C' and (resid 1 through 702 or (resid 703 and (name N or name CA or name \ C or name O or name CB )) or resid 704 through 1032)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.040 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 54.360 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.090 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 0.005 0.054 24390 Z= 0.229 Angle : 0.573 8.873 33132 Z= 0.327 Chirality : 0.041 0.142 3942 Planarity : 0.004 0.052 4200 Dihedral : 10.866 83.966 8817 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.74 % Allowed : 6.51 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.15), residues: 3090 helix: 2.03 (0.12), residues: 1720 sheet: 0.11 (0.23), residues: 460 loop : -0.25 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 519 HIS 0.004 0.001 HIS C 582 PHE 0.017 0.002 PHE C 740 TYR 0.013 0.002 TYR A 751 ARG 0.003 0.000 ARG A 994 Details of bonding type rmsd hydrogen bonds : bond 0.13528 ( 1586) hydrogen bonds : angle 5.97685 ( 4689) covalent geometry : bond 0.00530 (24390) covalent geometry : angle 0.57280 (33132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 543 time to evaluate : 2.770 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: B 1 MET cc_start: 0.6161 (mtp) cc_final: 0.5432 (ptp) REVERT: B 352 VAL cc_start: 0.8644 (t) cc_final: 0.8321 (m) REVERT: B 408 ASP cc_start: 0.7421 (t0) cc_final: 0.6778 (t0) REVERT: B 534 ARG cc_start: 0.7703 (mmm160) cc_final: 0.7336 (mmm160) REVERT: B 542 PHE cc_start: 0.8420 (t80) cc_final: 0.8212 (t80) REVERT: B 731 TYR cc_start: 0.7912 (t80) cc_final: 0.7488 (t80) REVERT: B 891 MET cc_start: 0.8291 (tpp) cc_final: 0.8074 (tpp) REVERT: B 901 PHE cc_start: 0.7539 (m-80) cc_final: 0.7122 (m-10) REVERT: B 955 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.6938 (t80) REVERT: B 985 PHE cc_start: 0.8535 (m-80) cc_final: 0.8191 (m-80) REVERT: A 40 THR cc_start: 0.9082 (m) cc_final: 0.8814 (p) REVERT: A 598 MET cc_start: 0.8210 (mmm) cc_final: 0.7926 (mtp) REVERT: A 981 LEU cc_start: 0.8992 (tp) cc_final: 0.8683 (tp) REVERT: C 412 ILE cc_start: 0.8810 (mt) cc_final: 0.8512 (mt) REVERT: C 474 LEU cc_start: 0.9191 (mt) cc_final: 0.8700 (mt) outliers start: 72 outliers final: 24 residues processed: 594 average time/residue: 0.3298 time to fit residues: 311.7598 Evaluate side-chains 361 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 336 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 955 PHE Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 738 ASP Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 752 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 242 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 180 optimal weight: 0.7980 chunk 280 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN B 582 HIS B 640 GLN B 648 GLN B 680 ASN A 202 ASN A 255 ASN A 325 GLN A 582 HIS A 594 ASN A 620 ASN A 679 GLN A 765 ASN C 238 GLN C 245 GLN C 293 ASN C 312 GLN C 325 GLN C 469 GLN C 511 GLN C 679 GLN C 691 GLN C 694 ASN C 765 ASN C 917 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.092145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.069632 restraints weight = 53405.671| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.84 r_work: 0.2831 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24390 Z= 0.148 Angle : 0.555 11.482 33132 Z= 0.293 Chirality : 0.043 0.241 3942 Planarity : 0.004 0.049 4200 Dihedral : 5.115 58.205 3335 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.31 % Allowed : 10.77 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.15), residues: 3090 helix: 2.11 (0.12), residues: 1747 sheet: -0.14 (0.23), residues: 446 loop : -0.17 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 519 HIS 0.003 0.001 HIS A 995 PHE 0.021 0.001 PHE B 507 TYR 0.019 0.001 TYR A 886 ARG 0.004 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 1586) hydrogen bonds : angle 4.81681 ( 4689) covalent geometry : bond 0.00328 (24390) covalent geometry : angle 0.55511 (33132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 390 time to evaluate : 2.713 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: B 1 MET cc_start: 0.5401 (mtp) cc_final: 0.4467 (ptp) REVERT: B 185 MET cc_start: 0.9130 (tpp) cc_final: 0.8123 (tpp) REVERT: B 405 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8462 (tp) REVERT: B 408 ASP cc_start: 0.8863 (t0) cc_final: 0.8473 (t0) REVERT: B 415 GLU cc_start: 0.8761 (tp30) cc_final: 0.8469 (mt-10) REVERT: B 534 ARG cc_start: 0.7794 (mmm160) cc_final: 0.7434 (mmm160) REVERT: B 540 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8465 (pp) REVERT: B 891 MET cc_start: 0.8971 (tpp) cc_final: 0.8597 (tpp) REVERT: B 901 PHE cc_start: 0.7411 (m-80) cc_final: 0.7132 (m-10) REVERT: B 934 LYS cc_start: 0.9394 (tttm) cc_final: 0.9096 (tttm) REVERT: B 955 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.7743 (t80) REVERT: B 1011 LEU cc_start: 0.9254 (tp) cc_final: 0.8599 (tp) REVERT: B 1015 PHE cc_start: 0.9352 (m-80) cc_final: 0.8851 (m-80) REVERT: B 1021 TYR cc_start: 0.8366 (t80) cc_final: 0.8018 (t80) REVERT: A 40 THR cc_start: 0.9492 (m) cc_final: 0.9264 (p) REVERT: A 409 ASP cc_start: 0.9134 (m-30) cc_final: 0.8931 (m-30) REVERT: A 460 PHE cc_start: 0.8909 (m-10) cc_final: 0.7916 (t80) REVERT: A 532 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8882 (mm) REVERT: A 676 MET cc_start: 0.9056 (ttm) cc_final: 0.8767 (ttm) REVERT: A 848 GLU cc_start: 0.8402 (mp0) cc_final: 0.8187 (pm20) REVERT: C 106 ASP cc_start: 0.9014 (m-30) cc_final: 0.8653 (m-30) REVERT: C 347 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8415 (pt0) REVERT: C 412 ILE cc_start: 0.9024 (mt) cc_final: 0.8688 (mt) REVERT: C 469 GLN cc_start: 0.9091 (mt0) cc_final: 0.8562 (mm-40) REVERT: C 474 LEU cc_start: 0.9200 (mt) cc_final: 0.8936 (mt) REVERT: C 853 TRP cc_start: 0.6714 (m100) cc_final: 0.6514 (m100) REVERT: C 881 ILE cc_start: 0.9314 (mt) cc_final: 0.9051 (mp) REVERT: C 944 MET cc_start: 0.9147 (mmm) cc_final: 0.8889 (mmm) REVERT: C 1010 THR cc_start: 0.8990 (t) cc_final: 0.8560 (p) outliers start: 87 outliers final: 46 residues processed: 448 average time/residue: 0.3094 time to fit residues: 228.9096 Evaluate side-chains 372 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 322 time to evaluate : 2.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 955 PHE Chi-restraints excluded: chain B residue 1022 LEU Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain C residue 1006 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 228 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 284 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 289 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 120 optimal weight: 0.0020 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 ASN C 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.091120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.068738 restraints weight = 53715.181| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.83 r_work: 0.2817 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24390 Z= 0.172 Angle : 0.542 10.058 33132 Z= 0.281 Chirality : 0.043 0.287 3942 Planarity : 0.004 0.061 4200 Dihedral : 4.931 57.627 3324 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.16 % Allowed : 12.07 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.15), residues: 3090 helix: 2.18 (0.12), residues: 1747 sheet: -0.15 (0.23), residues: 453 loop : -0.14 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1029 HIS 0.002 0.001 HIS C 582 PHE 0.016 0.001 PHE A 901 TYR 0.021 0.001 TYR B 36 ARG 0.004 0.000 ARG B 965 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 1586) hydrogen bonds : angle 4.60822 ( 4689) covalent geometry : bond 0.00393 (24390) covalent geometry : angle 0.54239 (33132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 345 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5337 (mtp) cc_final: 0.4389 (ptp) REVERT: B 185 MET cc_start: 0.9178 (tpp) cc_final: 0.8206 (tpp) REVERT: B 405 ILE cc_start: 0.8761 (tp) cc_final: 0.8515 (tp) REVERT: B 408 ASP cc_start: 0.8846 (t0) cc_final: 0.8496 (t0) REVERT: B 422 HIS cc_start: 0.8613 (m90) cc_final: 0.8119 (m90) REVERT: B 449 LEU cc_start: 0.9251 (mt) cc_final: 0.9033 (mt) REVERT: B 534 ARG cc_start: 0.7860 (mmm160) cc_final: 0.7476 (mmm160) REVERT: B 540 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8337 (pp) REVERT: B 807 ASP cc_start: 0.8807 (t0) cc_final: 0.7920 (t0) REVERT: B 891 MET cc_start: 0.8963 (tpp) cc_final: 0.8742 (tpp) REVERT: B 934 LYS cc_start: 0.9393 (tttm) cc_final: 0.9185 (tttm) REVERT: B 955 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.7851 (t80) REVERT: B 1011 LEU cc_start: 0.9233 (tp) cc_final: 0.8798 (tp) REVERT: B 1015 PHE cc_start: 0.9395 (m-80) cc_final: 0.9086 (m-80) REVERT: B 1021 TYR cc_start: 0.8257 (t80) cc_final: 0.8015 (t80) REVERT: A 40 THR cc_start: 0.9480 (m) cc_final: 0.9235 (p) REVERT: A 99 ASP cc_start: 0.8637 (t0) cc_final: 0.8361 (t70) REVERT: A 313 GLU cc_start: 0.9013 (tp30) cc_final: 0.8652 (tp30) REVERT: A 409 ASP cc_start: 0.9149 (m-30) cc_final: 0.8908 (m-30) REVERT: A 460 PHE cc_start: 0.8940 (m-10) cc_final: 0.7968 (t80) REVERT: A 532 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8914 (mm) REVERT: A 789 ASN cc_start: 0.8842 (t0) cc_final: 0.8622 (t0) REVERT: A 807 ASP cc_start: 0.8713 (t0) cc_final: 0.8373 (t0) REVERT: A 835 ASP cc_start: 0.8729 (m-30) cc_final: 0.8519 (m-30) REVERT: A 847 ASP cc_start: 0.8943 (p0) cc_final: 0.8558 (p0) REVERT: C 34 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8237 (pt0) REVERT: C 106 ASP cc_start: 0.9046 (m-30) cc_final: 0.8830 (m-30) REVERT: C 347 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8432 (pt0) REVERT: C 412 ILE cc_start: 0.9054 (mt) cc_final: 0.8699 (mt) REVERT: C 474 LEU cc_start: 0.9174 (mt) cc_final: 0.8962 (mt) REVERT: C 598 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8651 (mtm) REVERT: C 881 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9073 (mp) REVERT: C 1010 THR cc_start: 0.9054 (t) cc_final: 0.8607 (p) outliers start: 83 outliers final: 47 residues processed: 400 average time/residue: 0.3083 time to fit residues: 206.6304 Evaluate side-chains 359 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 306 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 955 PHE Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 150 ASN Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 598 MET Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 103 optimal weight: 0.6980 chunk 67 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 227 optimal weight: 0.7980 chunk 306 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 308 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 301 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 GLN A 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.069561 restraints weight = 53930.914| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.89 r_work: 0.2831 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 24390 Z= 0.138 Angle : 0.526 9.328 33132 Z= 0.271 Chirality : 0.042 0.275 3942 Planarity : 0.004 0.048 4200 Dihedral : 4.816 57.620 3321 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.05 % Allowed : 12.33 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.15), residues: 3090 helix: 2.24 (0.12), residues: 1742 sheet: -0.15 (0.23), residues: 448 loop : -0.11 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1029 HIS 0.002 0.001 HIS C 582 PHE 0.023 0.001 PHE A 538 TYR 0.022 0.001 TYR C1021 ARG 0.004 0.000 ARG C 653 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 1586) hydrogen bonds : angle 4.50631 ( 4689) covalent geometry : bond 0.00313 (24390) covalent geometry : angle 0.52565 (33132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 338 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5328 (mtp) cc_final: 0.4379 (ptp) REVERT: B 185 MET cc_start: 0.9142 (tpp) cc_final: 0.8150 (tpp) REVERT: B 408 ASP cc_start: 0.8822 (t0) cc_final: 0.8353 (t0) REVERT: B 422 HIS cc_start: 0.8611 (m90) cc_final: 0.8072 (m90) REVERT: B 534 ARG cc_start: 0.7878 (mmm160) cc_final: 0.7475 (mmm160) REVERT: B 540 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8367 (pp) REVERT: B 807 ASP cc_start: 0.8770 (t0) cc_final: 0.7884 (t0) REVERT: B 891 MET cc_start: 0.9074 (tpp) cc_final: 0.8698 (tpp) REVERT: B 955 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.7904 (t80) REVERT: B 959 ILE cc_start: 0.9185 (tp) cc_final: 0.8798 (pt) REVERT: B 995 HIS cc_start: 0.7585 (m170) cc_final: 0.7355 (m-70) REVERT: B 1011 LEU cc_start: 0.9191 (tp) cc_final: 0.8740 (tp) REVERT: B 1015 PHE cc_start: 0.9390 (m-80) cc_final: 0.9149 (m-80) REVERT: B 1021 TYR cc_start: 0.8215 (t80) cc_final: 0.7902 (t80) REVERT: A 40 THR cc_start: 0.9473 (m) cc_final: 0.9208 (p) REVERT: A 64 THR cc_start: 0.9103 (m) cc_final: 0.8892 (p) REVERT: A 99 ASP cc_start: 0.8739 (t0) cc_final: 0.8491 (t0) REVERT: A 185 MET cc_start: 0.9280 (tpp) cc_final: 0.9033 (tpt) REVERT: A 313 GLU cc_start: 0.9007 (tp30) cc_final: 0.8660 (tp30) REVERT: A 340 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8777 (tp30) REVERT: A 409 ASP cc_start: 0.9111 (m-30) cc_final: 0.8823 (m-30) REVERT: A 460 PHE cc_start: 0.8943 (m-10) cc_final: 0.7975 (t80) REVERT: A 532 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8847 (mm) REVERT: A 789 ASN cc_start: 0.8861 (t0) cc_final: 0.8560 (t0) REVERT: A 807 ASP cc_start: 0.8745 (t0) cc_final: 0.8367 (t0) REVERT: A 835 ASP cc_start: 0.8741 (m-30) cc_final: 0.8536 (m-30) REVERT: C 34 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: C 88 MET cc_start: 0.9464 (tmm) cc_final: 0.9178 (tmm) REVERT: C 106 ASP cc_start: 0.9083 (m-30) cc_final: 0.8845 (m-30) REVERT: C 347 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8501 (pt0) REVERT: C 412 ILE cc_start: 0.9031 (mt) cc_final: 0.8665 (mt) REVERT: C 469 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8861 (mm110) REVERT: C 474 LEU cc_start: 0.9171 (mt) cc_final: 0.8911 (mt) REVERT: C 598 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8688 (mtm) REVERT: C 881 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9064 (mp) REVERT: C 919 ILE cc_start: 0.9202 (tp) cc_final: 0.8930 (tp) REVERT: C 1029 TRP cc_start: 0.8338 (t60) cc_final: 0.7849 (t60) outliers start: 80 outliers final: 53 residues processed: 393 average time/residue: 0.3021 time to fit residues: 198.6478 Evaluate side-chains 375 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 315 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 955 PHE Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 514 ASN Chi-restraints excluded: chain C residue 598 MET Chi-restraints excluded: chain C residue 599 LYS Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 0.0040 chunk 9 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 679 GLN C 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.068584 restraints weight = 53855.387| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.84 r_work: 0.2810 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 24390 Z= 0.188 Angle : 0.541 12.474 33132 Z= 0.279 Chirality : 0.042 0.221 3942 Planarity : 0.004 0.047 4200 Dihedral : 4.771 57.462 3316 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.35 % Allowed : 12.94 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.15), residues: 3090 helix: 2.25 (0.12), residues: 1744 sheet: -0.26 (0.23), residues: 454 loop : -0.14 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1029 HIS 0.002 0.001 HIS A 995 PHE 0.020 0.001 PHE A 538 TYR 0.022 0.001 TYR C1021 ARG 0.004 0.000 ARG C 653 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 1586) hydrogen bonds : angle 4.51103 ( 4689) covalent geometry : bond 0.00433 (24390) covalent geometry : angle 0.54084 (33132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 334 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5321 (mtp) cc_final: 0.4203 (ptp) REVERT: B 76 MET cc_start: 0.9333 (ttt) cc_final: 0.9001 (ttt) REVERT: B 185 MET cc_start: 0.9164 (tpp) cc_final: 0.8234 (tpp) REVERT: B 274 GLU cc_start: 0.8722 (tt0) cc_final: 0.8422 (pt0) REVERT: B 389 PHE cc_start: 0.8188 (m-80) cc_final: 0.7893 (m-80) REVERT: B 408 ASP cc_start: 0.8826 (t0) cc_final: 0.8439 (t0) REVERT: B 422 HIS cc_start: 0.8626 (m90) cc_final: 0.8072 (m90) REVERT: B 534 ARG cc_start: 0.7839 (mmm160) cc_final: 0.7415 (mmm160) REVERT: B 537 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8216 (ptp90) REVERT: B 540 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8341 (pp) REVERT: B 807 ASP cc_start: 0.8796 (t0) cc_final: 0.7887 (t0) REVERT: B 891 MET cc_start: 0.9093 (tpp) cc_final: 0.8531 (tpp) REVERT: B 901 PHE cc_start: 0.7498 (m-10) cc_final: 0.6821 (m-80) REVERT: B 934 LYS cc_start: 0.9361 (tttm) cc_final: 0.9080 (tttm) REVERT: B 955 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.7925 (t80) REVERT: B 959 ILE cc_start: 0.9205 (tp) cc_final: 0.8823 (pt) REVERT: B 995 HIS cc_start: 0.7594 (m170) cc_final: 0.7370 (m-70) REVERT: B 1011 LEU cc_start: 0.9092 (tp) cc_final: 0.8288 (tp) REVERT: B 1015 PHE cc_start: 0.9418 (m-80) cc_final: 0.8854 (m-80) REVERT: B 1021 TYR cc_start: 0.8265 (t80) cc_final: 0.7932 (t80) REVERT: A 40 THR cc_start: 0.9459 (m) cc_final: 0.9204 (p) REVERT: A 340 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8797 (tp30) REVERT: A 409 ASP cc_start: 0.9123 (m-30) cc_final: 0.8837 (m-30) REVERT: A 437 MET cc_start: 0.9362 (mmm) cc_final: 0.8743 (mmm) REVERT: A 460 PHE cc_start: 0.8954 (m-10) cc_final: 0.7973 (t80) REVERT: A 532 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8990 (mm) REVERT: A 789 ASN cc_start: 0.8895 (t0) cc_final: 0.8571 (t0) REVERT: A 807 ASP cc_start: 0.8750 (t0) cc_final: 0.8399 (t0) REVERT: A 835 ASP cc_start: 0.8745 (m-30) cc_final: 0.8522 (m-30) REVERT: C 34 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: C 88 MET cc_start: 0.9460 (tmm) cc_final: 0.9160 (tmm) REVERT: C 347 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8485 (pt0) REVERT: C 412 ILE cc_start: 0.8996 (mt) cc_final: 0.8650 (mt) REVERT: C 469 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8684 (mm110) REVERT: C 598 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8709 (mtm) REVERT: C 881 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9100 (mp) REVERT: C 919 ILE cc_start: 0.9165 (tp) cc_final: 0.8881 (tp) REVERT: C 1029 TRP cc_start: 0.8375 (t60) cc_final: 0.7842 (t60) outliers start: 88 outliers final: 57 residues processed: 394 average time/residue: 0.2965 time to fit residues: 195.7467 Evaluate side-chains 380 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 315 time to evaluate : 2.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 955 PHE Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 151 ASP Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 514 ASN Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 596 THR Chi-restraints excluded: chain C residue 598 MET Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 190 optimal weight: 2.9990 chunk 293 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 178 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 307 optimal weight: 0.4980 chunk 251 optimal weight: 0.9990 chunk 240 optimal weight: 0.9990 chunk 276 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.092332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.070082 restraints weight = 53391.413| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.80 r_work: 0.2848 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24390 Z= 0.126 Angle : 0.519 11.111 33132 Z= 0.267 Chirality : 0.042 0.245 3942 Planarity : 0.004 0.043 4200 Dihedral : 4.676 57.280 3316 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.08 % Allowed : 13.59 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.15), residues: 3090 helix: 2.27 (0.12), residues: 1741 sheet: -0.22 (0.23), residues: 449 loop : -0.06 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1029 HIS 0.002 0.001 HIS A 995 PHE 0.017 0.001 PHE A 538 TYR 0.023 0.001 TYR C1021 ARG 0.005 0.000 ARG C 653 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 1586) hydrogen bonds : angle 4.40574 ( 4689) covalent geometry : bond 0.00285 (24390) covalent geometry : angle 0.51858 (33132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 336 time to evaluate : 2.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5175 (mtp) cc_final: 0.4038 (ptp) REVERT: B 185 MET cc_start: 0.9093 (tpp) cc_final: 0.8126 (tpp) REVERT: B 274 GLU cc_start: 0.8649 (tt0) cc_final: 0.8392 (pt0) REVERT: B 408 ASP cc_start: 0.8674 (t0) cc_final: 0.8351 (t0) REVERT: B 534 ARG cc_start: 0.7813 (mmm160) cc_final: 0.7371 (mmm160) REVERT: B 537 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8352 (ptp90) REVERT: B 540 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8277 (pp) REVERT: B 675 GLU cc_start: 0.8544 (mp0) cc_final: 0.8104 (mp0) REVERT: B 807 ASP cc_start: 0.8706 (t0) cc_final: 0.7893 (t0) REVERT: B 891 MET cc_start: 0.9105 (tpp) cc_final: 0.8449 (tpp) REVERT: B 901 PHE cc_start: 0.7388 (m-80) cc_final: 0.6823 (m-80) REVERT: B 947 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7875 (ttm170) REVERT: B 959 ILE cc_start: 0.9225 (tp) cc_final: 0.8809 (pt) REVERT: B 995 HIS cc_start: 0.7604 (m170) cc_final: 0.7357 (m-70) REVERT: B 1011 LEU cc_start: 0.9014 (tp) cc_final: 0.8189 (tp) REVERT: B 1015 PHE cc_start: 0.9416 (m-80) cc_final: 0.8831 (m-80) REVERT: B 1021 TYR cc_start: 0.8243 (t80) cc_final: 0.7956 (t80) REVERT: A 40 THR cc_start: 0.9452 (m) cc_final: 0.9171 (p) REVERT: A 185 MET cc_start: 0.9253 (tpp) cc_final: 0.9005 (tpt) REVERT: A 409 ASP cc_start: 0.9014 (m-30) cc_final: 0.8725 (m-30) REVERT: A 437 MET cc_start: 0.9459 (mmm) cc_final: 0.8712 (mmm) REVERT: A 460 PHE cc_start: 0.8941 (m-10) cc_final: 0.7991 (t80) REVERT: A 532 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8928 (mm) REVERT: A 696 MET cc_start: 0.9297 (tmm) cc_final: 0.8694 (tmm) REVERT: A 789 ASN cc_start: 0.8835 (t0) cc_final: 0.8541 (t0) REVERT: A 835 ASP cc_start: 0.8675 (m-30) cc_final: 0.8442 (m-30) REVERT: A 916 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8204 (p0) REVERT: C 34 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8171 (pt0) REVERT: C 88 MET cc_start: 0.9382 (tmm) cc_final: 0.9163 (tmm) REVERT: C 106 ASP cc_start: 0.8986 (m-30) cc_final: 0.8646 (m-30) REVERT: C 347 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8503 (pt0) REVERT: C 412 ILE cc_start: 0.9046 (mt) cc_final: 0.8690 (mt) REVERT: C 871 PHE cc_start: 0.8958 (m-10) cc_final: 0.8701 (m-10) REVERT: C 881 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9124 (mp) REVERT: C 1021 TYR cc_start: 0.8896 (t80) cc_final: 0.8647 (t80) REVERT: C 1029 TRP cc_start: 0.8427 (t60) cc_final: 0.7989 (t60) outliers start: 81 outliers final: 50 residues processed: 388 average time/residue: 0.3077 time to fit residues: 198.1411 Evaluate side-chains 367 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 310 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 272 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 149 optimal weight: 0.0570 chunk 235 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 22 optimal weight: 0.0670 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 789 ASN C 566 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.092099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.069818 restraints weight = 53926.112| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.81 r_work: 0.2841 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 24390 Z= 0.144 Angle : 0.534 13.764 33132 Z= 0.272 Chirality : 0.042 0.296 3942 Planarity : 0.004 0.040 4200 Dihedral : 4.595 57.042 3314 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.08 % Allowed : 14.27 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.15), residues: 3090 helix: 2.29 (0.12), residues: 1742 sheet: -0.20 (0.23), residues: 448 loop : -0.07 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 853 HIS 0.002 0.001 HIS B 582 PHE 0.016 0.001 PHE A 538 TYR 0.019 0.001 TYR C1021 ARG 0.005 0.000 ARG C 653 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 1586) hydrogen bonds : angle 4.39594 ( 4689) covalent geometry : bond 0.00332 (24390) covalent geometry : angle 0.53393 (33132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 329 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5025 (mtp) cc_final: 0.3932 (ptp) REVERT: B 185 MET cc_start: 0.9108 (tpp) cc_final: 0.8134 (tpp) REVERT: B 274 GLU cc_start: 0.8687 (tt0) cc_final: 0.8412 (pt0) REVERT: B 530 TYR cc_start: 0.8242 (t80) cc_final: 0.7977 (t80) REVERT: B 537 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8064 (ptp90) REVERT: B 540 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8249 (pp) REVERT: B 675 GLU cc_start: 0.8573 (mp0) cc_final: 0.8098 (mp0) REVERT: B 807 ASP cc_start: 0.8759 (t0) cc_final: 0.7910 (t0) REVERT: B 891 MET cc_start: 0.9093 (tpp) cc_final: 0.8439 (tpp) REVERT: B 901 PHE cc_start: 0.7465 (m-80) cc_final: 0.6869 (m-80) REVERT: B 934 LYS cc_start: 0.9359 (tttm) cc_final: 0.9099 (ptmm) REVERT: B 947 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7889 (ttm170) REVERT: B 959 ILE cc_start: 0.9222 (tp) cc_final: 0.8803 (pt) REVERT: B 995 HIS cc_start: 0.7410 (m170) cc_final: 0.7119 (m-70) REVERT: B 1011 LEU cc_start: 0.9005 (tp) cc_final: 0.8162 (tp) REVERT: B 1015 PHE cc_start: 0.9419 (m-80) cc_final: 0.8827 (m-80) REVERT: B 1021 TYR cc_start: 0.8274 (t80) cc_final: 0.7955 (t80) REVERT: A 40 THR cc_start: 0.9452 (m) cc_final: 0.9178 (p) REVERT: A 185 MET cc_start: 0.9263 (tpp) cc_final: 0.9033 (tpt) REVERT: A 409 ASP cc_start: 0.9041 (m-30) cc_final: 0.8741 (m-30) REVERT: A 437 MET cc_start: 0.9462 (mmm) cc_final: 0.8710 (mmm) REVERT: A 460 PHE cc_start: 0.8936 (m-10) cc_final: 0.7985 (t80) REVERT: A 532 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9015 (mm) REVERT: A 537 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7327 (mtm-85) REVERT: A 789 ASN cc_start: 0.8852 (t0) cc_final: 0.8581 (t0) REVERT: A 807 ASP cc_start: 0.8612 (t0) cc_final: 0.8384 (t0) REVERT: A 835 ASP cc_start: 0.8734 (m-30) cc_final: 0.8472 (m-30) REVERT: A 916 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8248 (p0) REVERT: C 34 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8181 (pt0) REVERT: C 88 MET cc_start: 0.9388 (tmm) cc_final: 0.9157 (tmm) REVERT: C 106 ASP cc_start: 0.8962 (m-30) cc_final: 0.8413 (m-30) REVERT: C 347 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8481 (pt0) REVERT: C 412 ILE cc_start: 0.9043 (mt) cc_final: 0.8692 (mt) REVERT: C 871 PHE cc_start: 0.8987 (m-10) cc_final: 0.8700 (m-10) REVERT: C 881 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9112 (mp) REVERT: C 1021 TYR cc_start: 0.8937 (t80) cc_final: 0.8615 (t80) REVERT: C 1029 TRP cc_start: 0.8442 (t60) cc_final: 0.7996 (t60) outliers start: 81 outliers final: 59 residues processed: 382 average time/residue: 0.3015 time to fit residues: 190.4107 Evaluate side-chains 382 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 315 time to evaluate : 2.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 947 ARG Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 537 ARG Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 118 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 122 optimal weight: 0.5980 chunk 291 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 212 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.092560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.070271 restraints weight = 53661.027| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.81 r_work: 0.2851 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 24390 Z= 0.129 Angle : 0.534 13.021 33132 Z= 0.272 Chirality : 0.042 0.250 3942 Planarity : 0.004 0.043 4200 Dihedral : 4.552 56.966 3314 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.05 % Allowed : 14.47 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.15), residues: 3090 helix: 2.31 (0.12), residues: 1743 sheet: -0.21 (0.23), residues: 448 loop : -0.10 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C 853 HIS 0.002 0.001 HIS A 995 PHE 0.033 0.001 PHE B 879 TYR 0.019 0.001 TYR C1021 ARG 0.009 0.000 ARG C 653 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 1586) hydrogen bonds : angle 4.34381 ( 4689) covalent geometry : bond 0.00294 (24390) covalent geometry : angle 0.53382 (33132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 337 time to evaluate : 2.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5214 (mtp) cc_final: 0.4126 (ptp) REVERT: B 185 MET cc_start: 0.9108 (tpp) cc_final: 0.8110 (tpp) REVERT: B 274 GLU cc_start: 0.8704 (tt0) cc_final: 0.8428 (pt0) REVERT: B 530 TYR cc_start: 0.8305 (t80) cc_final: 0.8066 (t80) REVERT: B 537 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8098 (ptp90) REVERT: B 540 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8229 (pp) REVERT: B 675 GLU cc_start: 0.8558 (mp0) cc_final: 0.8065 (mp0) REVERT: B 807 ASP cc_start: 0.8749 (t0) cc_final: 0.7904 (t0) REVERT: B 891 MET cc_start: 0.9104 (tpp) cc_final: 0.8330 (tpp) REVERT: B 901 PHE cc_start: 0.7518 (m-80) cc_final: 0.6936 (m-80) REVERT: B 934 LYS cc_start: 0.9323 (tttm) cc_final: 0.9104 (ptmm) REVERT: B 959 ILE cc_start: 0.9267 (tp) cc_final: 0.8853 (pt) REVERT: B 971 MET cc_start: 0.9269 (mtp) cc_final: 0.8989 (mtm) REVERT: B 995 HIS cc_start: 0.7514 (m170) cc_final: 0.7189 (m-70) REVERT: B 1011 LEU cc_start: 0.8977 (tp) cc_final: 0.8101 (tp) REVERT: B 1015 PHE cc_start: 0.9414 (m-80) cc_final: 0.8804 (m-80) REVERT: A 40 THR cc_start: 0.9442 (m) cc_final: 0.9166 (p) REVERT: A 185 MET cc_start: 0.9273 (tpp) cc_final: 0.9028 (tpt) REVERT: A 437 MET cc_start: 0.9480 (mmm) cc_final: 0.8720 (mmm) REVERT: A 460 PHE cc_start: 0.8925 (m-10) cc_final: 0.7977 (t80) REVERT: A 537 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7319 (mtm-85) REVERT: A 696 MET cc_start: 0.9279 (tmm) cc_final: 0.9066 (tmm) REVERT: A 789 ASN cc_start: 0.8873 (t0) cc_final: 0.8613 (t0) REVERT: A 807 ASP cc_start: 0.8655 (t0) cc_final: 0.8388 (t0) REVERT: A 835 ASP cc_start: 0.8733 (m-30) cc_final: 0.8475 (m-30) REVERT: A 916 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8331 (p0) REVERT: C 34 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8168 (pt0) REVERT: C 88 MET cc_start: 0.9364 (tmm) cc_final: 0.9152 (tmm) REVERT: C 106 ASP cc_start: 0.8979 (m-30) cc_final: 0.8417 (m-30) REVERT: C 347 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8494 (pt0) REVERT: C 412 ILE cc_start: 0.9029 (mt) cc_final: 0.8680 (mt) REVERT: C 469 GLN cc_start: 0.9060 (mm110) cc_final: 0.8849 (mm110) REVERT: C 853 TRP cc_start: 0.7154 (m100) cc_final: 0.6379 (m100) REVERT: C 871 PHE cc_start: 0.8919 (m-10) cc_final: 0.8636 (m-10) REVERT: C 877 PHE cc_start: 0.8810 (m-80) cc_final: 0.8505 (m-80) REVERT: C 881 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9109 (mp) REVERT: C 1021 TYR cc_start: 0.8894 (t80) cc_final: 0.8652 (t80) REVERT: C 1029 TRP cc_start: 0.8415 (t60) cc_final: 0.8010 (t60) outliers start: 80 outliers final: 60 residues processed: 389 average time/residue: 0.3020 time to fit residues: 196.2393 Evaluate side-chains 380 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 314 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 366 THR Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 537 ARG Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1009 SER Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 74 ASP Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 426 ASN Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 52 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 286 optimal weight: 0.7980 chunk 31 optimal weight: 0.0670 chunk 131 optimal weight: 0.0670 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 GLN A 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.093651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.071455 restraints weight = 53336.885| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.80 r_work: 0.2877 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24390 Z= 0.119 Angle : 0.534 12.863 33132 Z= 0.274 Chirality : 0.042 0.233 3942 Planarity : 0.004 0.051 4200 Dihedral : 4.497 56.603 3314 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.59 % Allowed : 15.26 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.15), residues: 3090 helix: 2.29 (0.12), residues: 1742 sheet: -0.13 (0.23), residues: 448 loop : -0.07 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B1029 HIS 0.002 0.001 HIS C 582 PHE 0.027 0.001 PHE B 879 TYR 0.018 0.001 TYR C1021 ARG 0.004 0.000 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 1586) hydrogen bonds : angle 4.33238 ( 4689) covalent geometry : bond 0.00273 (24390) covalent geometry : angle 0.53431 (33132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 352 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5306 (mtp) cc_final: 0.4151 (ptp) REVERT: B 185 MET cc_start: 0.9078 (tpp) cc_final: 0.8044 (tpp) REVERT: B 274 GLU cc_start: 0.8636 (tt0) cc_final: 0.8406 (pt0) REVERT: B 415 GLU cc_start: 0.8847 (tp30) cc_final: 0.8617 (tp30) REVERT: B 530 TYR cc_start: 0.8341 (t80) cc_final: 0.8093 (t80) REVERT: B 537 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8089 (ptp90) REVERT: B 540 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8225 (pp) REVERT: B 731 TYR cc_start: 0.9084 (t80) cc_final: 0.8833 (t80) REVERT: B 807 ASP cc_start: 0.8714 (t0) cc_final: 0.7901 (t0) REVERT: B 891 MET cc_start: 0.9150 (tpp) cc_final: 0.8394 (tpp) REVERT: B 971 MET cc_start: 0.9277 (mtp) cc_final: 0.9021 (mtm) REVERT: B 995 HIS cc_start: 0.7542 (m170) cc_final: 0.7200 (m-70) REVERT: A 40 THR cc_start: 0.9429 (m) cc_final: 0.9154 (p) REVERT: A 185 MET cc_start: 0.9280 (tpp) cc_final: 0.9010 (tpt) REVERT: A 460 PHE cc_start: 0.8899 (m-10) cc_final: 0.7995 (t80) REVERT: A 480 VAL cc_start: 0.9223 (t) cc_final: 0.9001 (p) REVERT: A 532 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9019 (mm) REVERT: A 537 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7290 (mtm-85) REVERT: A 544 ILE cc_start: 0.9345 (mm) cc_final: 0.9121 (mm) REVERT: A 696 MET cc_start: 0.9234 (tmm) cc_final: 0.9009 (tmm) REVERT: A 789 ASN cc_start: 0.8811 (t0) cc_final: 0.8524 (t0) REVERT: A 807 ASP cc_start: 0.8630 (t0) cc_final: 0.8348 (t0) REVERT: A 835 ASP cc_start: 0.8688 (m-30) cc_final: 0.8442 (m-30) REVERT: A 916 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8346 (p0) REVERT: C 34 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: C 106 ASP cc_start: 0.8978 (m-30) cc_final: 0.8437 (m-30) REVERT: C 347 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8495 (pt0) REVERT: C 356 MET cc_start: 0.9145 (mtp) cc_final: 0.8814 (ttp) REVERT: C 412 ILE cc_start: 0.9017 (mt) cc_final: 0.8654 (mt) REVERT: C 469 GLN cc_start: 0.9014 (mm110) cc_final: 0.8774 (mm110) REVERT: C 564 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7873 (mm-30) REVERT: C 853 TRP cc_start: 0.6985 (m100) cc_final: 0.6290 (m100) REVERT: C 871 PHE cc_start: 0.8930 (m-10) cc_final: 0.8709 (m-10) REVERT: C 877 PHE cc_start: 0.8820 (m-80) cc_final: 0.8574 (m-80) REVERT: C 881 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9123 (mp) REVERT: C 1010 THR cc_start: 0.9150 (t) cc_final: 0.8807 (p) REVERT: C 1021 TYR cc_start: 0.8841 (t80) cc_final: 0.8618 (t80) REVERT: C 1029 TRP cc_start: 0.8385 (t60) cc_final: 0.8055 (t60) outliers start: 68 outliers final: 50 residues processed: 397 average time/residue: 0.2918 time to fit residues: 193.5343 Evaluate side-chains 384 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 327 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 537 ARG Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 543 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 891 MET Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 282 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 242 optimal weight: 0.9990 chunk 188 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 299 optimal weight: 0.6980 chunk 149 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.092002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.069601 restraints weight = 54129.242| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.82 r_work: 0.2834 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 24390 Z= 0.186 Angle : 0.579 12.604 33132 Z= 0.295 Chirality : 0.043 0.261 3942 Planarity : 0.004 0.096 4200 Dihedral : 4.556 56.509 3314 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.44 % Allowed : 15.91 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.15), residues: 3090 helix: 2.24 (0.12), residues: 1742 sheet: -0.12 (0.24), residues: 438 loop : -0.17 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B1029 HIS 0.003 0.001 HIS B 582 PHE 0.026 0.001 PHE B 879 TYR 0.018 0.001 TYR C1021 ARG 0.006 0.000 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 1586) hydrogen bonds : angle 4.42572 ( 4689) covalent geometry : bond 0.00434 (24390) covalent geometry : angle 0.57939 (33132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6180 Ramachandran restraints generated. 3090 Oldfield, 0 Emsley, 3090 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 329 time to evaluate : 3.159 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5313 (mtp) cc_final: 0.4075 (ptp) REVERT: B 185 MET cc_start: 0.9133 (tpp) cc_final: 0.8212 (tpp) REVERT: B 274 GLU cc_start: 0.8722 (tt0) cc_final: 0.8458 (pt0) REVERT: B 415 GLU cc_start: 0.8889 (tp30) cc_final: 0.8665 (tp30) REVERT: B 505 LYS cc_start: 0.7234 (mtpt) cc_final: 0.6848 (pttm) REVERT: B 530 TYR cc_start: 0.8398 (t80) cc_final: 0.8187 (t80) REVERT: B 537 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8084 (ptp90) REVERT: B 540 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8242 (pp) REVERT: B 807 ASP cc_start: 0.8785 (t0) cc_final: 0.7944 (t0) REVERT: B 891 MET cc_start: 0.9058 (tpp) cc_final: 0.8348 (tpp) REVERT: B 901 PHE cc_start: 0.7842 (m-10) cc_final: 0.7446 (m-10) REVERT: B 971 MET cc_start: 0.9299 (mtp) cc_final: 0.9026 (mtm) REVERT: B 994 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7273 (mtm-85) REVERT: B 995 HIS cc_start: 0.7615 (m170) cc_final: 0.7312 (m-70) REVERT: A 40 THR cc_start: 0.9446 (m) cc_final: 0.9170 (p) REVERT: A 460 PHE cc_start: 0.8950 (m-10) cc_final: 0.7981 (t80) REVERT: A 480 VAL cc_start: 0.9329 (t) cc_final: 0.9077 (p) REVERT: A 532 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9068 (mm) REVERT: A 544 ILE cc_start: 0.9359 (mm) cc_final: 0.9138 (mm) REVERT: A 696 MET cc_start: 0.9287 (tmm) cc_final: 0.9055 (tmm) REVERT: A 789 ASN cc_start: 0.8920 (t0) cc_final: 0.8654 (t0) REVERT: A 807 ASP cc_start: 0.8711 (t0) cc_final: 0.8414 (t0) REVERT: A 835 ASP cc_start: 0.8732 (m-30) cc_final: 0.8462 (m-30) REVERT: A 916 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8404 (p0) REVERT: C 34 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: C 106 ASP cc_start: 0.8991 (m-30) cc_final: 0.8571 (m-30) REVERT: C 412 ILE cc_start: 0.9019 (mt) cc_final: 0.8666 (mt) REVERT: C 469 GLN cc_start: 0.9025 (mm110) cc_final: 0.8764 (mm110) REVERT: C 564 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7913 (mm-30) REVERT: C 853 TRP cc_start: 0.6835 (m100) cc_final: 0.6121 (m100) REVERT: C 871 PHE cc_start: 0.8955 (m-10) cc_final: 0.8735 (m-10) REVERT: C 877 PHE cc_start: 0.8817 (m-80) cc_final: 0.8518 (m-80) REVERT: C 881 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9116 (mp) REVERT: C 945 GLU cc_start: 0.9344 (tp30) cc_final: 0.9089 (tp30) REVERT: C 1029 TRP cc_start: 0.8438 (t60) cc_final: 0.8003 (t60) outliers start: 64 outliers final: 52 residues processed: 369 average time/residue: 0.3133 time to fit residues: 193.5496 Evaluate side-chains 375 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 317 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 125 LEU Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 519 TRP Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 553 PHE Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 653 ARG Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 757 MET Chi-restraints excluded: chain B residue 864 LYS Chi-restraints excluded: chain B residue 880 LEU Chi-restraints excluded: chain B residue 909 LEU Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 931 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 456 ILE Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 743 ILE Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 916 ASP Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 987 THR Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 881 ILE Chi-restraints excluded: chain C residue 996 SER Chi-restraints excluded: chain C residue 1018 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 87 optimal weight: 0.9990 chunk 123 optimal weight: 0.3980 chunk 170 optimal weight: 3.9990 chunk 306 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 228 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 105 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 ASN C 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.093477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.071192 restraints weight = 53180.594| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.80 r_work: 0.2869 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 24390 Z= 0.131 Angle : 0.560 12.499 33132 Z= 0.286 Chirality : 0.043 0.235 3942 Planarity : 0.004 0.048 4200 Dihedral : 4.520 56.404 3314 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.32 % Allowed : 16.06 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.15), residues: 3090 helix: 2.23 (0.12), residues: 1743 sheet: -0.19 (0.24), residues: 438 loop : -0.14 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B1029 HIS 0.002 0.001 HIS A 995 PHE 0.025 0.001 PHE B 879 TYR 0.026 0.001 TYR C1021 ARG 0.006 0.000 ARG B 994 Details of bonding type rmsd hydrogen bonds : bond 0.03750 ( 1586) hydrogen bonds : angle 4.38223 ( 4689) covalent geometry : bond 0.00300 (24390) covalent geometry : angle 0.56043 (33132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10934.83 seconds wall clock time: 190 minutes 28.85 seconds (11428.85 seconds total)