Starting phenix.real_space_refine on Fri Jun 20 16:47:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gjj_40091/06_2025/8gjj_40091.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gjj_40091/06_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_40091/06_2025/8gjj_40091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gjj_40091/06_2025/8gjj_40091.map" model { file = "/net/cci-nas-00/data/ceres_data/8gjj_40091/06_2025/8gjj_40091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gjj_40091/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 14.28, per 1000 atoms: 0.60 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: 6.24 Conformation dependent library (CDL) restraints added in 3.2 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: 3.26 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: 9.90 Time building geometry restraints manager: 7.33 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: 3.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 56.700 Find NCS groups from input model: 1.050 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.710 ------------------------------------------------------------------------------- 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 : 2.728 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: 0.3337 time to fit residues: 315.2358 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 : 2.997 ------------------------------------------------------------------------------- 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 = 0.069630 restraints weight = 53405.671| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.84 r_work: 0.2831 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 : 2.854 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: 0.5394 (mtp) cc_final: 0.4457 (ptp) REVERT: B 185 MET cc_start: 0.9130 (tpp) cc_final: 0.8123 (tpp) REVERT: B 405 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8459 (tp) REVERT: B 408 ASP cc_start: 0.8873 (t0) cc_final: 0.8484 (t0) REVERT: B 415 GLU cc_start: 0.8762 (tp30) cc_final: 0.8469 (mt-10) REVERT: B 534 ARG cc_start: 0.7793 (mmm160) cc_final: 0.7435 (mmm160) REVERT: B 540 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8464 (pp) REVERT: B 891 MET cc_start: 0.8967 (tpp) cc_final: 0.8592 (tpp) REVERT: B 901 PHE cc_start: 0.7399 (m-80) cc_final: 0.7119 (m-10) REVERT: B 934 LYS cc_start: 0.9394 (tttm) cc_final: 0.9099 (tttm) REVERT: B 955 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.7743 (t80) REVERT: B 1011 LEU cc_start: 0.9253 (tp) cc_final: 0.8598 (tp) REVERT: B 1015 PHE cc_start: 0.9350 (m-80) cc_final: 0.8851 (m-80) REVERT: B 1021 TYR cc_start: 0.8365 (t80) cc_final: 0.8014 (t80) REVERT: A 40 THR cc_start: 0.9491 (m) cc_final: 0.9263 (p) REVERT: A 409 ASP cc_start: 0.9133 (m-30) cc_final: 0.8930 (m-30) REVERT: A 460 PHE cc_start: 0.8906 (m-10) cc_final: 0.7915 (t80) REVERT: A 532 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8882 (mm) REVERT: A 676 MET cc_start: 0.9054 (ttm) cc_final: 0.8765 (ttm) REVERT: A 848 GLU cc_start: 0.8401 (mp0) cc_final: 0.8184 (pm20) REVERT: C 106 ASP cc_start: 0.9014 (m-30) cc_final: 0.8652 (m-30) REVERT: C 347 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8414 (pt0) REVERT: C 412 ILE cc_start: 0.9025 (mt) cc_final: 0.8689 (mt) REVERT: C 469 GLN cc_start: 0.9091 (mt0) cc_final: 0.8561 (mm-40) REVERT: C 474 LEU cc_start: 0.9202 (mt) cc_final: 0.8937 (mt) REVERT: C 881 ILE cc_start: 0.9314 (mt) cc_final: 0.9051 (mp) REVERT: C 944 MET cc_start: 0.9146 (mmm) cc_final: 0.8887 (mmm) REVERT: C 1010 THR cc_start: 0.8989 (t) cc_final: 0.8559 (p) outliers start: 87 outliers final: 46 residues processed: 448 average time/residue: 0.3085 time to fit residues: 230.5633 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 : 3.158 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.091124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.068739 restraints weight = 53662.008| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.82 r_work: 0.2818 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 24390 Z= 0.172 Angle : 0.542 10.020 33132 Z= 0.281 Chirality : 0.043 0.286 3942 Planarity : 0.004 0.060 4200 Dihedral : 4.935 57.534 3324 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.08 % Allowed : 12.14 % 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: 1.73 (0.15), residues: 3090 helix: 2.18 (0.12), residues: 1747 sheet: -0.16 (0.23), residues: 453 loop : -0.14 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1029 HIS 0.002 0.001 HIS C 582 PHE 0.016 0.001 PHE C 674 TYR 0.022 0.001 TYR B 36 ARG 0.003 0.000 ARG B 965 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 1586) hydrogen bonds : angle 4.61277 ( 4689) covalent geometry : bond 0.00390 (24390) covalent geometry : angle 0.54232 (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 426 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 345 time to evaluate : 2.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5345 (mtp) cc_final: 0.4395 (ptp) REVERT: B 185 MET cc_start: 0.9169 (tpp) cc_final: 0.8209 (tpp) REVERT: B 405 ILE cc_start: 0.8761 (tp) cc_final: 0.8514 (tp) REVERT: B 408 ASP cc_start: 0.8852 (t0) cc_final: 0.8259 (t0) REVERT: B 422 HIS cc_start: 0.8612 (m90) cc_final: 0.8118 (m90) REVERT: B 534 ARG cc_start: 0.7858 (mmm160) cc_final: 0.7481 (mmm160) REVERT: B 540 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8334 (pp) REVERT: B 807 ASP cc_start: 0.8806 (t0) cc_final: 0.7923 (t0) REVERT: B 891 MET cc_start: 0.8962 (tpp) cc_final: 0.8742 (tpp) REVERT: B 934 LYS cc_start: 0.9394 (tttm) cc_final: 0.9021 (tttm) REVERT: B 955 PHE cc_start: 0.9001 (OUTLIER) cc_final: 0.7807 (t80) REVERT: B 1011 LEU cc_start: 0.9219 (tp) cc_final: 0.8783 (tp) REVERT: B 1015 PHE cc_start: 0.9392 (m-80) cc_final: 0.9088 (m-80) REVERT: B 1021 TYR cc_start: 0.8259 (t80) cc_final: 0.8018 (t80) REVERT: A 40 THR cc_start: 0.9482 (m) cc_final: 0.9235 (p) REVERT: A 99 ASP cc_start: 0.8639 (t0) cc_final: 0.8362 (t70) REVERT: A 313 GLU cc_start: 0.9014 (tp30) cc_final: 0.8655 (tp30) REVERT: A 409 ASP cc_start: 0.9147 (m-30) cc_final: 0.8907 (m-30) REVERT: A 460 PHE cc_start: 0.8944 (m-10) cc_final: 0.7970 (t80) REVERT: A 532 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8916 (mm) REVERT: A 789 ASN cc_start: 0.8844 (t0) cc_final: 0.8620 (t0) REVERT: A 807 ASP cc_start: 0.8706 (t0) cc_final: 0.8368 (t0) REVERT: A 835 ASP cc_start: 0.8733 (m-30) cc_final: 0.8520 (m-30) REVERT: A 847 ASP cc_start: 0.8958 (p0) cc_final: 0.8617 (p0) REVERT: C 34 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8212 (pt0) REVERT: C 106 ASP cc_start: 0.9043 (m-30) cc_final: 0.8830 (m-30) REVERT: C 347 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8432 (pt0) REVERT: C 412 ILE cc_start: 0.9059 (mt) cc_final: 0.8703 (mt) REVERT: C 474 LEU cc_start: 0.9178 (mt) cc_final: 0.8966 (mt) REVERT: C 598 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8650 (mtm) REVERT: C 676 MET cc_start: 0.8113 (ttm) cc_final: 0.7892 (ttm) REVERT: C 881 ILE cc_start: 0.9351 (OUTLIER) cc_final: 0.9076 (mp) REVERT: C 1005 MET cc_start: 0.9077 (tpt) cc_final: 0.8875 (tpt) REVERT: C 1010 THR cc_start: 0.9059 (t) cc_final: 0.8606 (p) outliers start: 81 outliers final: 47 residues processed: 400 average time/residue: 0.3070 time to fit residues: 203.8798 Evaluate side-chains 356 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 303 time to evaluate : 2.733 ------------------------------------------------------------------------------- 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: 0.0070 chunk 67 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 227 optimal weight: 0.4980 chunk 306 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 308 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 301 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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 C 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.092731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.070324 restraints weight = 53722.604| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.89 r_work: 0.2850 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 24390 Z= 0.121 Angle : 0.515 9.307 33132 Z= 0.265 Chirality : 0.042 0.281 3942 Planarity : 0.004 0.048 4200 Dihedral : 4.768 57.628 3321 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.82 % Allowed : 12.60 % Favored : 84.58 % 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: 1.80 (0.15), residues: 3090 helix: 2.25 (0.12), residues: 1738 sheet: -0.21 (0.23), residues: 447 loop : -0.09 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1029 HIS 0.002 0.001 HIS C 582 PHE 0.028 0.001 PHE B 345 TYR 0.022 0.001 TYR C1021 ARG 0.010 0.000 ARG C 653 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 1586) hydrogen bonds : angle 4.43864 ( 4689) covalent geometry : bond 0.00270 (24390) covalent geometry : angle 0.51481 (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 421 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 347 time to evaluate : 2.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5281 (mtp) cc_final: 0.4328 (ptp) REVERT: B 185 MET cc_start: 0.9126 (tpp) cc_final: 0.8119 (tpp) REVERT: B 408 ASP cc_start: 0.8821 (t0) cc_final: 0.8352 (t0) REVERT: B 422 HIS cc_start: 0.8611 (m90) cc_final: 0.8064 (m90) REVERT: B 534 ARG cc_start: 0.7766 (mmm160) cc_final: 0.7375 (mmm160) REVERT: B 540 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8380 (pp) REVERT: B 807 ASP cc_start: 0.8752 (t0) cc_final: 0.7873 (t0) REVERT: B 891 MET cc_start: 0.9088 (tpp) cc_final: 0.8688 (tpp) REVERT: B 955 PHE cc_start: 0.9050 (OUTLIER) cc_final: 0.7913 (t80) REVERT: B 959 ILE cc_start: 0.9176 (tp) cc_final: 0.8795 (pt) REVERT: B 995 HIS cc_start: 0.7586 (m170) cc_final: 0.7346 (m-70) REVERT: B 1011 LEU cc_start: 0.9199 (tp) cc_final: 0.8636 (tp) REVERT: B 1015 PHE cc_start: 0.9397 (m-80) cc_final: 0.9129 (m-80) REVERT: A 40 THR cc_start: 0.9456 (m) cc_final: 0.9182 (p) REVERT: A 64 THR cc_start: 0.9087 (m) cc_final: 0.8875 (p) REVERT: A 99 ASP cc_start: 0.8711 (t0) cc_final: 0.8460 (t0) REVERT: A 185 MET cc_start: 0.9262 (tpp) cc_final: 0.9022 (tpt) REVERT: A 409 ASP cc_start: 0.9082 (m-30) cc_final: 0.8774 (m-30) REVERT: A 437 MET cc_start: 0.9325 (mmm) cc_final: 0.8936 (mmm) REVERT: A 460 PHE cc_start: 0.8928 (m-10) cc_final: 0.7976 (t80) REVERT: A 532 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8802 (mm) REVERT: A 789 ASN cc_start: 0.8853 (t0) cc_final: 0.8539 (t0) REVERT: A 807 ASP cc_start: 0.8745 (t0) cc_final: 0.8521 (t0) REVERT: A 835 ASP cc_start: 0.8737 (m-30) cc_final: 0.8529 (m-30) REVERT: C 34 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8164 (pt0) REVERT: C 88 MET cc_start: 0.9462 (tmm) cc_final: 0.9202 (tmm) REVERT: C 106 ASP cc_start: 0.9107 (m-30) cc_final: 0.8810 (m-30) REVERT: C 347 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8499 (pt0) REVERT: C 412 ILE cc_start: 0.9011 (mt) cc_final: 0.8657 (mt) REVERT: C 469 GLN cc_start: 0.9073 (mm-40) cc_final: 0.8588 (mp10) REVERT: C 474 LEU cc_start: 0.9157 (mt) cc_final: 0.8872 (mt) REVERT: C 508 TYR cc_start: 0.8785 (t80) cc_final: 0.8583 (t80) REVERT: C 881 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9053 (mp) REVERT: C 919 ILE cc_start: 0.9121 (tp) cc_final: 0.8440 (tp) REVERT: C 1021 TYR cc_start: 0.8876 (t80) cc_final: 0.8627 (t80) REVERT: C 1029 TRP cc_start: 0.8307 (t60) cc_final: 0.7883 (t60) outliers start: 74 outliers final: 46 residues processed: 396 average time/residue: 0.3027 time to fit residues: 201.2161 Evaluate side-chains 366 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 315 time to evaluate : 2.662 ------------------------------------------------------------------------------- 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 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 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 125 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 426 ASN 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 984 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 164 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 752 VAL 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: 3.9990 chunk 180 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 679 GLN B 789 ASN C 277 ASN C 317 ASN C 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.091584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.069254 restraints weight = 53830.778| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.81 r_work: 0.2829 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 24390 Z= 0.168 Angle : 0.529 12.500 33132 Z= 0.273 Chirality : 0.042 0.221 3942 Planarity : 0.004 0.047 4200 Dihedral : 4.716 57.698 3316 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.08 % Allowed : 13.17 % Favored : 83.75 % 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: 1.81 (0.15), residues: 3090 helix: 2.29 (0.12), residues: 1735 sheet: -0.19 (0.23), residues: 451 loop : -0.14 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1029 HIS 0.002 0.001 HIS C 582 PHE 0.029 0.001 PHE B 345 TYR 0.019 0.001 TYR A 886 ARG 0.006 0.000 ARG C 653 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 1586) hydrogen bonds : angle 4.44559 ( 4689) covalent geometry : bond 0.00387 (24390) covalent geometry : angle 0.52942 (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 409 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 328 time to evaluate : 5.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5316 (mtp) cc_final: 0.4224 (ptp) REVERT: B 185 MET cc_start: 0.9131 (tpp) cc_final: 0.8180 (tpp) REVERT: B 274 GLU cc_start: 0.8685 (tt0) cc_final: 0.8420 (pt0) REVERT: B 408 ASP cc_start: 0.8786 (t0) cc_final: 0.8403 (t0) REVERT: B 422 HIS cc_start: 0.8611 (m90) cc_final: 0.8040 (m90) REVERT: B 534 ARG cc_start: 0.7831 (mmm160) cc_final: 0.7404 (mmm160) REVERT: B 537 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8257 (ptp90) REVERT: B 540 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8304 (pp) REVERT: B 807 ASP cc_start: 0.8760 (t0) cc_final: 0.7877 (t0) REVERT: B 891 MET cc_start: 0.9099 (tpp) cc_final: 0.8442 (tpp) REVERT: B 934 LYS cc_start: 0.9340 (tttm) cc_final: 0.9057 (tttm) REVERT: B 966 PHE cc_start: 0.9140 (t80) cc_final: 0.8877 (t80) REVERT: B 995 HIS cc_start: 0.7581 (m170) cc_final: 0.7332 (m-70) REVERT: B 1011 LEU cc_start: 0.9053 (tp) cc_final: 0.8258 (tp) REVERT: B 1015 PHE cc_start: 0.9425 (m-80) cc_final: 0.8925 (m-80) REVERT: A 40 THR cc_start: 0.9470 (m) cc_final: 0.9192 (p) REVERT: A 64 THR cc_start: 0.9106 (m) cc_final: 0.8900 (p) REVERT: A 185 MET cc_start: 0.9260 (tpp) cc_final: 0.9027 (tpt) REVERT: A 409 ASP cc_start: 0.9073 (m-30) cc_final: 0.8788 (m-30) REVERT: A 437 MET cc_start: 0.9388 (mmm) cc_final: 0.8564 (mmm) REVERT: A 460 PHE cc_start: 0.8931 (m-10) cc_final: 0.7976 (t80) REVERT: A 532 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8901 (mm) REVERT: A 789 ASN cc_start: 0.8854 (t0) cc_final: 0.8511 (t0) REVERT: A 807 ASP cc_start: 0.8726 (t0) cc_final: 0.8355 (t0) REVERT: A 835 ASP cc_start: 0.8742 (m-30) cc_final: 0.8508 (m-30) REVERT: C 34 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: C 88 MET cc_start: 0.9431 (tmm) cc_final: 0.9140 (tmm) REVERT: C 106 ASP cc_start: 0.9076 (m-30) cc_final: 0.8848 (m-30) REVERT: C 347 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8492 (pt0) REVERT: C 358 LEU cc_start: 0.9092 (mt) cc_final: 0.8707 (tp) REVERT: C 412 ILE cc_start: 0.9043 (mt) cc_final: 0.8683 (mt) REVERT: C 469 GLN cc_start: 0.9064 (mm110) cc_final: 0.8696 (mm110) REVERT: C 474 LEU cc_start: 0.9114 (mt) cc_final: 0.8871 (mt) REVERT: C 871 PHE cc_start: 0.8952 (m-10) cc_final: 0.8720 (m-10) REVERT: C 881 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9121 (mp) REVERT: C 919 ILE cc_start: 0.9141 (tp) cc_final: 0.8833 (tp) REVERT: C 1029 TRP cc_start: 0.8367 (t60) cc_final: 0.7883 (t60) outliers start: 81 outliers final: 55 residues processed: 384 average time/residue: 0.3127 time to fit residues: 201.8246 Evaluate side-chains 377 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 317 time to evaluate : 2.589 ------------------------------------------------------------------------------- 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 401 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 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 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 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 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 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 532 LEU Chi-restraints excluded: chain C residue 545 MET Chi-restraints excluded: chain C residue 596 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 83 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 293 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 307 optimal weight: 0.1980 chunk 251 optimal weight: 0.2980 chunk 240 optimal weight: 0.8980 chunk 276 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.093183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.070905 restraints weight = 53305.567| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.84 r_work: 0.2863 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2684 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= 0.119 Angle : 0.511 11.331 33132 Z= 0.264 Chirality : 0.042 0.243 3942 Planarity : 0.004 0.042 4200 Dihedral : 4.559 57.156 3314 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.05 % Allowed : 13.40 % Favored : 83.56 % 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: 2.27 (0.12), residues: 1743 sheet: -0.18 (0.23), residues: 447 loop : -0.03 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 853 HIS 0.002 0.001 HIS A 995 PHE 0.032 0.001 PHE B 345 TYR 0.024 0.001 TYR C1021 ARG 0.004 0.000 ARG B 947 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 1586) hydrogen bonds : angle 4.34419 ( 4689) covalent geometry : bond 0.00265 (24390) covalent geometry : angle 0.51057 (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 431 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 351 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5105 (mtp) cc_final: 0.3982 (ptp) REVERT: B 185 MET cc_start: 0.9107 (tpp) cc_final: 0.8096 (tpp) REVERT: B 274 GLU cc_start: 0.8689 (tt0) cc_final: 0.8423 (pt0) REVERT: B 340 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8708 (tp30) REVERT: B 408 ASP cc_start: 0.8737 (t0) cc_final: 0.8433 (t0) REVERT: B 530 TYR cc_start: 0.8222 (t80) cc_final: 0.7940 (t80) REVERT: B 537 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8012 (ptp90) REVERT: B 540 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8234 (pp) REVERT: B 807 ASP cc_start: 0.8751 (t0) cc_final: 0.7882 (t0) REVERT: B 891 MET cc_start: 0.9089 (tpp) cc_final: 0.8775 (tpp) REVERT: B 966 PHE cc_start: 0.9203 (t80) cc_final: 0.8984 (t80) REVERT: B 971 MET cc_start: 0.9233 (mtp) cc_final: 0.9024 (mtm) REVERT: B 995 HIS cc_start: 0.7546 (m170) cc_final: 0.7293 (m-70) REVERT: A 40 THR cc_start: 0.9451 (m) cc_final: 0.9180 (p) REVERT: A 64 THR cc_start: 0.9079 (m) cc_final: 0.8875 (p) REVERT: A 185 MET cc_start: 0.9282 (tpp) cc_final: 0.9042 (tpt) REVERT: A 409 ASP cc_start: 0.9068 (m-30) cc_final: 0.8735 (m-30) REVERT: A 437 MET cc_start: 0.9380 (mmm) cc_final: 0.8654 (mmm) REVERT: A 460 PHE cc_start: 0.8936 (m-10) cc_final: 0.7988 (t80) REVERT: A 532 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8861 (mm) REVERT: A 696 MET cc_start: 0.9295 (tmm) cc_final: 0.8665 (tmm) REVERT: A 789 ASN cc_start: 0.8854 (t0) cc_final: 0.8547 (t0) REVERT: A 807 ASP cc_start: 0.8734 (t0) cc_final: 0.8354 (t0) REVERT: A 835 ASP cc_start: 0.8739 (m-30) cc_final: 0.8488 (m-30) REVERT: A 916 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8202 (p0) REVERT: C 34 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8154 (pt0) REVERT: C 88 MET cc_start: 0.9389 (tmm) cc_final: 0.9181 (tmm) REVERT: C 106 ASP cc_start: 0.9068 (m-30) cc_final: 0.8790 (m-30) REVERT: C 347 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8489 (pt0) REVERT: C 358 LEU cc_start: 0.9058 (mt) cc_final: 0.8705 (tp) REVERT: C 412 ILE cc_start: 0.8990 (mt) cc_final: 0.8641 (mt) REVERT: C 467 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8901 (mm-30) REVERT: C 474 LEU cc_start: 0.9080 (mt) cc_final: 0.8688 (mt) REVERT: C 853 TRP cc_start: 0.7302 (m100) cc_final: 0.6492 (m100) REVERT: C 871 PHE cc_start: 0.8978 (m-10) cc_final: 0.8711 (m-10) REVERT: C 881 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9092 (mp) REVERT: C 1021 TYR cc_start: 0.8828 (t80) cc_final: 0.8567 (t80) REVERT: C 1029 TRP cc_start: 0.8405 (t60) cc_final: 0.8033 (t60) outliers start: 80 outliers final: 51 residues processed: 403 average time/residue: 0.3024 time to fit residues: 204.7646 Evaluate side-chains 383 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 326 time to evaluate : 2.901 ------------------------------------------------------------------------------- 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 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 A residue 1 MET 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 272 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 0.4980 chunk 279 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 303 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 235 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 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 566 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.092878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.070626 restraints weight = 53648.725| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.83 r_work: 0.2862 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2804 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= 0.127 Angle : 0.528 14.252 33132 Z= 0.270 Chirality : 0.042 0.282 3942 Planarity : 0.004 0.039 4200 Dihedral : 4.520 57.072 3314 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.59 % Allowed : 14.62 % Favored : 82.79 % 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: 1.87 (0.15), residues: 3090 helix: 2.29 (0.12), residues: 1745 sheet: -0.17 (0.23), residues: 445 loop : -0.05 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B1029 HIS 0.002 0.001 HIS C 582 PHE 0.036 0.001 PHE B 472 TYR 0.019 0.001 TYR C1021 ARG 0.004 0.000 ARG C 653 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 1586) hydrogen bonds : angle 4.32997 ( 4689) covalent geometry : bond 0.00292 (24390) covalent geometry : angle 0.52816 (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 411 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 343 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5123 (mtp) cc_final: 0.4122 (ptp) REVERT: B 185 MET cc_start: 0.9078 (tpp) cc_final: 0.8122 (tpp) REVERT: B 274 GLU cc_start: 0.8641 (tt0) cc_final: 0.8426 (pt0) REVERT: B 530 TYR cc_start: 0.8264 (t80) cc_final: 0.8013 (t80) REVERT: B 537 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8108 (ptp90) REVERT: B 540 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8230 (pp) REVERT: B 807 ASP cc_start: 0.8721 (t0) cc_final: 0.7891 (t0) REVERT: B 891 MET cc_start: 0.9131 (tpp) cc_final: 0.8469 (tpp) REVERT: B 901 PHE cc_start: 0.7949 (m-10) cc_final: 0.7624 (m-80) REVERT: B 925 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8284 (mp) REVERT: B 995 HIS cc_start: 0.7659 (m170) cc_final: 0.7386 (m-70) REVERT: A 40 THR cc_start: 0.9443 (m) cc_final: 0.9164 (p) REVERT: A 64 THR cc_start: 0.9067 (m) cc_final: 0.8692 (p) REVERT: A 88 MET cc_start: 0.9341 (tmm) cc_final: 0.9128 (tmm) REVERT: A 185 MET cc_start: 0.9263 (tpp) cc_final: 0.9013 (tpt) REVERT: A 437 MET cc_start: 0.9412 (mmm) cc_final: 0.8701 (mmm) REVERT: A 460 PHE cc_start: 0.8908 (m-10) cc_final: 0.8010 (t80) REVERT: A 544 ILE cc_start: 0.9373 (mm) cc_final: 0.9151 (mm) REVERT: A 789 ASN cc_start: 0.8797 (t0) cc_final: 0.8479 (t0) REVERT: A 807 ASP cc_start: 0.8690 (t0) cc_final: 0.8331 (t0) REVERT: A 835 ASP cc_start: 0.8706 (m-30) cc_final: 0.8452 (m-30) REVERT: A 916 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8248 (p0) REVERT: C 34 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8192 (pt0) REVERT: C 88 MET cc_start: 0.9351 (tmm) cc_final: 0.9150 (tmm) REVERT: C 106 ASP cc_start: 0.9016 (m-30) cc_final: 0.8767 (m-30) REVERT: C 347 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8510 (pt0) REVERT: C 358 LEU cc_start: 0.9053 (mt) cc_final: 0.8704 (tp) REVERT: C 412 ILE cc_start: 0.9015 (mt) cc_final: 0.8663 (mt) REVERT: C 467 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8855 (mm-30) REVERT: C 474 LEU cc_start: 0.9090 (mt) cc_final: 0.8869 (mt) REVERT: C 871 PHE cc_start: 0.8923 (m-10) cc_final: 0.8648 (m-10) REVERT: C 877 PHE cc_start: 0.8829 (m-80) cc_final: 0.8515 (m-80) REVERT: C 881 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9124 (mp) REVERT: C 945 GLU cc_start: 0.9314 (tp30) cc_final: 0.9073 (tp30) REVERT: C 1021 TYR cc_start: 0.8864 (t80) cc_final: 0.8500 (t80) REVERT: C 1029 TRP cc_start: 0.8405 (t60) cc_final: 0.8040 (t60) outliers start: 68 outliers final: 51 residues processed: 388 average time/residue: 0.3193 time to fit residues: 206.1423 Evaluate side-chains 373 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 316 time to evaluate : 2.892 ------------------------------------------------------------------------------- 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 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 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 371 ILE 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 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 118 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 291 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 285 optimal weight: 0.0060 chunk 261 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 212 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.093347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.071109 restraints weight = 53525.671| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.80 r_work: 0.2869 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24390 Z= 0.125 Angle : 0.531 13.474 33132 Z= 0.270 Chirality : 0.042 0.211 3942 Planarity : 0.004 0.039 4200 Dihedral : 4.481 57.089 3314 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.66 % Allowed : 14.54 % Favored : 82.79 % 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: 1.87 (0.15), residues: 3090 helix: 2.28 (0.12), residues: 1745 sheet: -0.14 (0.23), residues: 445 loop : -0.06 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP C 853 HIS 0.002 0.001 HIS C 582 PHE 0.051 0.001 PHE B 472 TYR 0.019 0.001 TYR C1021 ARG 0.004 0.000 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.03655 ( 1586) hydrogen bonds : angle 4.31104 ( 4689) covalent geometry : bond 0.00284 (24390) covalent geometry : angle 0.53082 (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 406 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 336 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5361 (mtp) cc_final: 0.4276 (ptp) REVERT: B 185 MET cc_start: 0.9061 (tpp) cc_final: 0.8105 (tpp) REVERT: B 274 GLU cc_start: 0.8646 (tt0) cc_final: 0.8444 (pt0) REVERT: B 408 ASP cc_start: 0.8766 (t70) cc_final: 0.8549 (t0) REVERT: B 530 TYR cc_start: 0.8291 (t80) cc_final: 0.8046 (t80) REVERT: B 537 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8126 (ptp90) REVERT: B 540 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8230 (pp) REVERT: B 807 ASP cc_start: 0.8707 (t0) cc_final: 0.7881 (t0) REVERT: B 891 MET cc_start: 0.9090 (tpp) cc_final: 0.8455 (tpp) REVERT: B 925 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8398 (mp) REVERT: B 995 HIS cc_start: 0.7512 (m170) cc_final: 0.7194 (m-70) REVERT: A 40 THR cc_start: 0.9425 (m) cc_final: 0.9145 (p) REVERT: A 64 THR cc_start: 0.9007 (m) cc_final: 0.8756 (p) REVERT: A 88 MET cc_start: 0.9358 (tmm) cc_final: 0.9141 (tmm) REVERT: A 185 MET cc_start: 0.9273 (tpp) cc_final: 0.9025 (tpt) REVERT: A 437 MET cc_start: 0.9428 (mmm) cc_final: 0.8735 (mmm) REVERT: A 460 PHE cc_start: 0.8908 (m-10) cc_final: 0.7997 (t80) REVERT: A 532 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8938 (mm) REVERT: A 544 ILE cc_start: 0.9343 (mm) cc_final: 0.9116 (mm) REVERT: A 696 MET cc_start: 0.9262 (tmm) cc_final: 0.9059 (tmm) REVERT: A 789 ASN cc_start: 0.8784 (t0) cc_final: 0.8497 (t0) REVERT: A 807 ASP cc_start: 0.8684 (t0) cc_final: 0.8330 (t0) REVERT: A 835 ASP cc_start: 0.8709 (m-30) cc_final: 0.8449 (m-30) REVERT: A 916 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8288 (p0) REVERT: C 34 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8176 (pt0) REVERT: C 106 ASP cc_start: 0.9024 (m-30) cc_final: 0.8760 (m-30) REVERT: C 347 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8511 (pt0) REVERT: C 358 LEU cc_start: 0.9012 (mt) cc_final: 0.8685 (tp) REVERT: C 412 ILE cc_start: 0.9034 (mt) cc_final: 0.8672 (mt) REVERT: C 467 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8836 (mm-30) REVERT: C 871 PHE cc_start: 0.8948 (m-10) cc_final: 0.8676 (m-10) REVERT: C 877 PHE cc_start: 0.8811 (m-80) cc_final: 0.8505 (m-80) REVERT: C 881 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9118 (mp) REVERT: C 945 GLU cc_start: 0.9320 (tp30) cc_final: 0.9079 (tp30) REVERT: C 1021 TYR cc_start: 0.8859 (t80) cc_final: 0.8516 (t80) REVERT: C 1029 TRP cc_start: 0.8387 (t60) cc_final: 0.8045 (t60) outliers start: 70 outliers final: 52 residues processed: 382 average time/residue: 0.2954 time to fit residues: 188.6711 Evaluate side-chains 377 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 318 time to evaluate : 2.578 ------------------------------------------------------------------------------- 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 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 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 A residue 1 MET 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 371 ILE 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 545 MET 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 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 151 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 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: 10.0000 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 0.3980 chunk 122 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 286 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.093513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.071276 restraints weight = 53420.954| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 2.80 r_work: 0.2872 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 24390 Z= 0.125 Angle : 0.543 13.058 33132 Z= 0.276 Chirality : 0.042 0.219 3942 Planarity : 0.004 0.062 4200 Dihedral : 4.460 57.043 3314 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.63 % Allowed : 14.81 % Favored : 82.57 % 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: 1.84 (0.15), residues: 3090 helix: 2.26 (0.12), residues: 1742 sheet: -0.11 (0.24), residues: 445 loop : -0.07 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 853 HIS 0.002 0.001 HIS B 582 PHE 0.032 0.001 PHE B 345 TYR 0.018 0.001 TYR C1021 ARG 0.004 0.000 ARG A 634 Details of bonding type rmsd hydrogen bonds : bond 0.03666 ( 1586) hydrogen bonds : angle 4.33812 ( 4689) covalent geometry : bond 0.00286 (24390) covalent geometry : angle 0.54312 (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 408 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 339 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5262 (mtp) cc_final: 0.4145 (ptp) REVERT: B 99 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8070 (t70) REVERT: B 185 MET cc_start: 0.9055 (tpp) cc_final: 0.8099 (tpp) REVERT: B 530 TYR cc_start: 0.8341 (t80) cc_final: 0.8073 (t80) REVERT: B 537 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8108 (ptp90) REVERT: B 540 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8242 (pp) REVERT: B 731 TYR cc_start: 0.9120 (t80) cc_final: 0.8852 (t80) REVERT: B 807 ASP cc_start: 0.8717 (t0) cc_final: 0.7889 (t0) REVERT: B 891 MET cc_start: 0.9110 (tpp) cc_final: 0.8430 (tpp) REVERT: B 925 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8407 (mp) REVERT: B 995 HIS cc_start: 0.7611 (m170) cc_final: 0.7261 (m-70) REVERT: A 40 THR cc_start: 0.9417 (m) cc_final: 0.9128 (p) REVERT: A 64 THR cc_start: 0.8989 (m) cc_final: 0.8728 (p) REVERT: A 88 MET cc_start: 0.9360 (tmm) cc_final: 0.9155 (tmm) REVERT: A 185 MET cc_start: 0.9278 (tpp) cc_final: 0.9029 (tpt) REVERT: A 437 MET cc_start: 0.9431 (mmm) cc_final: 0.8702 (mmm) REVERT: A 460 PHE cc_start: 0.8880 (m-10) cc_final: 0.7996 (t80) REVERT: A 532 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9009 (mm) REVERT: A 696 MET cc_start: 0.9252 (tmm) cc_final: 0.9019 (tmm) REVERT: A 789 ASN cc_start: 0.8826 (t0) cc_final: 0.8549 (t0) REVERT: A 835 ASP cc_start: 0.8689 (m-30) cc_final: 0.8429 (m-30) REVERT: A 916 ASP cc_start: 0.8670 (OUTLIER) cc_final: 0.8362 (p0) REVERT: C 34 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8186 (pt0) REVERT: C 106 ASP cc_start: 0.9019 (m-30) cc_final: 0.8733 (m-30) REVERT: C 347 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8497 (pt0) REVERT: C 358 LEU cc_start: 0.9028 (mt) cc_final: 0.8727 (tp) REVERT: C 412 ILE cc_start: 0.9023 (mt) cc_final: 0.8656 (mt) REVERT: C 467 GLU cc_start: 0.9138 (mm-30) cc_final: 0.8848 (mm-30) REVERT: C 853 TRP cc_start: 0.7235 (m100) cc_final: 0.6368 (m100) REVERT: C 871 PHE cc_start: 0.8936 (m-10) cc_final: 0.8707 (m-10) REVERT: C 877 PHE cc_start: 0.8821 (m-80) cc_final: 0.8566 (m-80) REVERT: C 881 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9121 (mp) REVERT: C 1010 THR cc_start: 0.9120 (t) cc_final: 0.8765 (p) REVERT: C 1021 TYR cc_start: 0.8848 (t80) cc_final: 0.8621 (t80) REVERT: C 1029 TRP cc_start: 0.8382 (t60) cc_final: 0.8041 (t60) outliers start: 69 outliers final: 50 residues processed: 385 average time/residue: 0.3055 time to fit residues: 197.2032 Evaluate side-chains 384 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 326 time to evaluate : 2.600 ------------------------------------------------------------------------------- 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 225 VAL 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 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 A residue 1 MET 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 371 ILE 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 545 MET 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 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 151 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 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: 3.9990 chunk 76 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 240 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 154 optimal weight: 0.9980 chunk 299 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.092731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.070411 restraints weight = 53997.206| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.81 r_work: 0.2854 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 24390 Z= 0.154 Angle : 0.562 12.857 33132 Z= 0.286 Chirality : 0.043 0.253 3942 Planarity : 0.004 0.046 4200 Dihedral : 4.474 57.246 3314 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.28 % Allowed : 15.45 % Favored : 82.26 % 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: 1.81 (0.15), residues: 3090 helix: 2.24 (0.12), residues: 1743 sheet: -0.10 (0.24), residues: 445 loop : -0.12 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B1029 HIS 0.002 0.001 HIS B 582 PHE 0.076 0.001 PHE B 472 TYR 0.017 0.001 TYR C1021 ARG 0.007 0.000 ARG B 994 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 1586) hydrogen bonds : angle 4.39858 ( 4689) covalent geometry : bond 0.00358 (24390) covalent geometry : angle 0.56198 (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 388 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 328 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.5139 (mtp) cc_final: 0.4195 (ptp) REVERT: B 185 MET cc_start: 0.9083 (tpp) cc_final: 0.8165 (tpp) REVERT: B 530 TYR cc_start: 0.8375 (t80) cc_final: 0.8121 (t80) REVERT: B 537 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8084 (ptp90) REVERT: B 540 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8257 (pp) REVERT: B 731 TYR cc_start: 0.9142 (t80) cc_final: 0.8868 (t80) REVERT: B 807 ASP cc_start: 0.8745 (t0) cc_final: 0.7911 (t0) REVERT: B 891 MET cc_start: 0.9109 (tpp) cc_final: 0.8425 (tpp) REVERT: B 925 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8326 (mp) REVERT: B 995 HIS cc_start: 0.7611 (m170) cc_final: 0.7234 (m-70) REVERT: A 40 THR cc_start: 0.9419 (m) cc_final: 0.9137 (p) REVERT: A 64 THR cc_start: 0.9021 (m) cc_final: 0.8763 (p) REVERT: A 88 MET cc_start: 0.9366 (tmm) cc_final: 0.9145 (tmm) REVERT: A 185 MET cc_start: 0.9271 (tpp) cc_final: 0.9048 (tpt) REVERT: A 437 MET cc_start: 0.9437 (mmm) cc_final: 0.8710 (mmm) REVERT: A 460 PHE cc_start: 0.8907 (m-10) cc_final: 0.7988 (t80) REVERT: A 480 VAL cc_start: 0.9276 (t) cc_final: 0.9060 (p) REVERT: A 532 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9071 (mm) REVERT: A 696 MET cc_start: 0.9275 (tmm) cc_final: 0.9045 (tmm) REVERT: A 789 ASN cc_start: 0.8862 (t0) cc_final: 0.8576 (t0) REVERT: A 835 ASP cc_start: 0.8719 (m-30) cc_final: 0.8455 (m-30) REVERT: A 916 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8404 (p0) REVERT: C 34 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8198 (pt0) REVERT: C 106 ASP cc_start: 0.9071 (m-30) cc_final: 0.8826 (m-30) REVERT: C 347 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8475 (pt0) REVERT: C 358 LEU cc_start: 0.9042 (mt) cc_final: 0.8717 (tp) REVERT: C 412 ILE cc_start: 0.9012 (mt) cc_final: 0.8658 (mt) REVERT: C 467 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8818 (mm-30) REVERT: C 853 TRP cc_start: 0.6866 (m100) cc_final: 0.6027 (m100) REVERT: C 871 PHE cc_start: 0.9020 (m-10) cc_final: 0.8767 (m-10) REVERT: C 877 PHE cc_start: 0.8830 (m-80) cc_final: 0.8579 (m-80) REVERT: C 881 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9121 (mp) REVERT: C 945 GLU cc_start: 0.9329 (tp30) cc_final: 0.9086 (tp30) REVERT: C 1021 TYR cc_start: 0.8894 (t80) cc_final: 0.8621 (t80) REVERT: C 1029 TRP cc_start: 0.8391 (t60) cc_final: 0.8025 (t60) outliers start: 60 outliers final: 48 residues processed: 367 average time/residue: 0.3653 time to fit residues: 226.1229 Evaluate side-chains 370 residues out of total 2631 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 315 time to evaluate : 2.780 ------------------------------------------------------------------------------- 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 225 VAL 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 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 A residue 1 MET 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 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 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 151 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 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: 0.8980 chunk 123 optimal weight: 0.8980 chunk 170 optimal weight: 4.9990 chunk 306 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 228 optimal weight: 5.9990 chunk 55 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 131 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 ASN C 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.093059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.070799 restraints weight = 53128.779| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.80 r_work: 0.2866 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3073 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= 0.137 Angle : 0.555 12.725 33132 Z= 0.283 Chirality : 0.043 0.297 3942 Planarity : 0.004 0.055 4200 Dihedral : 4.474 57.523 3314 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.32 % Allowed : 15.53 % 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: 1.82 (0.15), residues: 3090 helix: 2.24 (0.12), residues: 1744 sheet: -0.10 (0.24), residues: 445 loop : -0.10 (0.21), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B1029 HIS 0.002 0.001 HIS A 995 PHE 0.029 0.001 PHE B 345 TYR 0.018 0.001 TYR C1021 ARG 0.005 0.000 ARG C 653 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 1586) hydrogen bonds : angle 4.37543 ( 4689) covalent geometry : bond 0.00318 (24390) covalent geometry : angle 0.55526 (33132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11092.09 seconds wall clock time: 195 minutes 24.42 seconds (11724.42 seconds total)