Starting phenix.real_space_refine on Sun Sep 13 15:37:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vks_21228/09_2026/6vks_21228.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vks_21228/09_2026/6vks_21228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vks_21228/09_2026/6vks_21228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vks_21228/09_2026/6vks_21228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vks_21228/09_2026/6vks_21228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vks_21228/09_2026/6vks_21228.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vks_21228/09_2026/6vks_21228.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vks_21228/09_2026/6vks_21228.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 137 5.16 5 C 15458 2.51 5 N 3920 2.21 5 O 4504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24034 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 7864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 7864 Classifications: {'peptide': 1049} Link IDs: {'PTRANS': 40, 'TRANS': 1008} Chain: "B" Number of atoms: 7788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 7788 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 40, 'TRANS': 999} Chain: "C" Number of atoms: 7806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1042, 7806 Classifications: {'peptide': 1042} Link IDs: {'PTRANS': 40, 'TRANS': 1001} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 101 Unusual residues: {'PTY': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PTY:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 201 Unusual residues: {'AIX': 1, 'PTY': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'AIX:plan-4': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 274 Unusual residues: {'PTY': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PTY:plan-2': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 5.39, per 1000 atoms: 0.22 Number of scatterers: 24034 At special positions: 0 Unit cell: (123.2, 116.6, 147.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 137 16.00 P 15 15.00 O 4504 8.00 N 3920 7.00 C 15458 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5704 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 21 sheets defined 55.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 8 through 29 removed outlier: 4.088A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 69 removed outlier: 3.717A pdb=" N SER A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N SER A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 113 Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.939A pdb=" N LEU A 118 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.681A pdb=" N TYR A 125 " --> pdb=" O THR A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.682A pdb=" N LEU A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 187 through 192' Processing helix chain 'A' and resid 197 through 209 removed outlier: 3.516A pdb=" N VAL A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 259 through 263 removed outlier: 4.296A pdb=" N VAL A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 263' Processing helix chain 'A' and resid 298 through 311 Processing helix chain 'A' and resid 327 through 358 removed outlier: 4.052A pdb=" N VAL A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 365 through 384 Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 389 through 422 removed outlier: 3.620A pdb=" N MET A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A 394 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 452 removed outlier: 5.607A pdb=" N GLY A 438 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA A 439 " --> pdb=" O GLN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 456 removed outlier: 3.805A pdb=" N MET A 456 " --> pdb=" O PRO A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 461 through 494 removed outlier: 3.543A pdb=" N TYR A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Proline residue: A 488 - end of helix removed outlier: 3.558A pdb=" N MET A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 533 removed outlier: 4.185A pdb=" N ALA A 529 " --> pdb=" O GLU A 525 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS A 530 " --> pdb=" O GLY A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 554 removed outlier: 3.575A pdb=" N VAL A 540 " --> pdb=" O PHE A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 596 removed outlier: 3.848A pdb=" N THR A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 653 removed outlier: 3.618A pdb=" N GLY A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 671 removed outlier: 3.570A pdb=" N LEU A 670 " --> pdb=" O ILE A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 704 Processing helix chain 'A' and resid 729 through 734 Processing helix chain 'A' and resid 740 through 751 removed outlier: 4.337A pdb=" N LEU A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 847 removed outlier: 3.534A pdb=" N ALA A 837 " --> pdb=" O SER A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 864 removed outlier: 4.156A pdb=" N GLU A 862 " --> pdb=" O GLY A 858 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 863 " --> pdb=" O GLN A 859 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 864 " --> pdb=" O SER A 860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 858 through 864' Processing helix chain 'A' and resid 869 through 890 removed outlier: 4.135A pdb=" N ALA A 875 " --> pdb=" O ILE A 871 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU A 876 " --> pdb=" O ALA A 872 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 878 " --> pdb=" O TYR A 874 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 879 " --> pdb=" O ALA A 875 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 899 removed outlier: 4.002A pdb=" N ALA A 897 " --> pdb=" O SER A 893 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 920 removed outlier: 4.276A pdb=" N LEU A 906 " --> pdb=" O MET A 902 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU A 918 " --> pdb=" O THR A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 958 removed outlier: 3.864A pdb=" N GLN A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 937 " --> pdb=" O ILE A 933 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY A 938 " --> pdb=" O TYR A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 990 removed outlier: 3.532A pdb=" N LEU A 972 " --> pdb=" O VAL A 968 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ARG A 980 " --> pdb=" O ARG A 976 " (cutoff:3.500A) Proline residue: A 981 - end of helix Processing helix chain 'A' and resid 993 through 999 Processing helix chain 'A' and resid 1004 through 1041 removed outlier: 4.060A pdb=" N THR A1022 " --> pdb=" O MET A1018 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1026 " --> pdb=" O THR A1022 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A1029 " --> pdb=" O SER A1025 " (cutoff:3.500A) Proline residue: A1030 - end of helix Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.699A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 67 removed outlier: 5.427A pdb=" N SER B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 115 removed outlier: 3.964A pdb=" N GLU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 119 through 126 removed outlier: 3.661A pdb=" N GLN B 123 " --> pdb=" O PRO B 119 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR B 125 " --> pdb=" O THR B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 160 removed outlier: 3.549A pdb=" N MET B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.547A pdb=" N GLN B 165 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 194 removed outlier: 3.551A pdb=" N LEU B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 240 through 245 Processing helix chain 'B' and resid 297 through 313 removed outlier: 3.571A pdb=" N LYS B 302 " --> pdb=" O MET B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 357 removed outlier: 4.039A pdb=" N GLU B 332 " --> pdb=" O SER B 328 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 333 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER B 334 " --> pdb=" O PHE B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 384 removed outlier: 4.227A pdb=" N THR B 367 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Proline residue: B 371 - end of helix Processing helix chain 'B' and resid 389 through 399 Processing helix chain 'B' and resid 399 through 421 removed outlier: 3.790A pdb=" N ASP B 406 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 410 " --> pdb=" O ASP B 406 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 411 " --> pdb=" O ALA B 407 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 452 removed outlier: 5.711A pdb=" N GLY B 438 " --> pdb=" O GLY B 434 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ALA B 439 " --> pdb=" O GLN B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 457 removed outlier: 3.579A pdb=" N MET B 456 " --> pdb=" O PRO B 453 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE B 457 " --> pdb=" O LEU B 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 457' Processing helix chain 'B' and resid 459 through 494 removed outlier: 4.138A pdb=" N GLN B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) Proline residue: B 488 - end of helix Processing helix chain 'B' and resid 508 through 532 removed outlier: 4.250A pdb=" N TRP B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE B 513 " --> pdb=" O PHE B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 555 removed outlier: 3.549A pdb=" N MET B 538 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 596 removed outlier: 3.732A pdb=" N THR B 584 " --> pdb=" O THR B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 654 removed outlier: 3.519A pdb=" N GLY B 652 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 704 Processing helix chain 'B' and resid 729 through 735 Processing helix chain 'B' and resid 740 through 751 removed outlier: 3.572A pdb=" N ARG B 744 " --> pdb=" O PHE B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 847 removed outlier: 3.780A pdb=" N ALA B 837 " --> pdb=" O SER B 833 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU B 839 " --> pdb=" O GLY B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 864 removed outlier: 3.681A pdb=" N GLU B 863 " --> pdb=" O GLN B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 890 Processing helix chain 'B' and resid 893 through 899 Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.864A pdb=" N GLY B 905 " --> pdb=" O VAL B 901 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 906 " --> pdb=" O MET B 902 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B 922 " --> pdb=" O LEU B 918 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 923 " --> pdb=" O PHE B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 959 removed outlier: 3.666A pdb=" N ASP B 959 " --> pdb=" O GLU B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 998 removed outlier: 5.179A pdb=" N ARG B 980 " --> pdb=" O ARG B 976 " (cutoff:3.500A) Proline residue: B 981 - end of helix Proline residue: B 995 - end of helix removed outlier: 3.527A pdb=" N ILE B 998 " --> pdb=" O VAL B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1040 removed outlier: 3.750A pdb=" N GLN B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR B1013 " --> pdb=" O ALA B1009 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N PHE B1027 " --> pdb=" O LEU B1023 " (cutoff:3.500A) Proline residue: B1030 - end of helix Processing helix chain 'C' and resid 3 through 8 removed outlier: 4.280A pdb=" N ASP C 7 " --> pdb=" O LYS C 3 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG C 8 " --> pdb=" O PHE C 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3 through 8' Processing helix chain 'C' and resid 8 through 28 removed outlier: 3.932A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.677A pdb=" N ILE C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 112 removed outlier: 4.002A pdb=" N ALA C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 108 " --> pdb=" O GLN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 115 No H-bonds generated for 'chain 'C' and resid 113 through 115' Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.633A pdb=" N TYR C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.834A pdb=" N MET C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 166 removed outlier: 3.665A pdb=" N GLU C 163 " --> pdb=" O ASN C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.566A pdb=" N LEU C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 208 Processing helix chain 'C' and resid 240 through 245 removed outlier: 3.552A pdb=" N GLY C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 312 removed outlier: 3.631A pdb=" N LYS C 302 " --> pdb=" O MET C 298 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 330 through 358 removed outlier: 3.989A pdb=" N GLU C 336 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL C 349 " --> pdb=" O ALA C 345 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE C 350 " --> pdb=" O MET C 346 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 384 removed outlier: 3.936A pdb=" N THR C 363 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU C 364 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE C 365 " --> pdb=" O ARG C 361 " (cutoff:3.500A) Proline residue: C 366 - end of helix removed outlier: 4.144A pdb=" N VAL C 369 " --> pdb=" O ILE C 365 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 370 " --> pdb=" O PRO C 366 " (cutoff:3.500A) Proline residue: C 371 - end of helix removed outlier: 3.553A pdb=" N MET C 384 " --> pdb=" O PHE C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 401 removed outlier: 3.519A pdb=" N MET C 393 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 416 removed outlier: 3.566A pdb=" N GLU C 412 " --> pdb=" O ILE C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 424 through 436 removed outlier: 3.516A pdb=" N THR C 429 " --> pdb=" O PRO C 425 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 430 " --> pdb=" O LYS C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 449 removed outlier: 3.643A pdb=" N GLY C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 456 removed outlier: 3.593A pdb=" N MET C 456 " --> pdb=" O PRO C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 494 removed outlier: 4.037A pdb=" N THR C 471 " --> pdb=" O GLN C 467 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N THR C 487 " --> pdb=" O ALA C 483 " (cutoff:3.500A) Proline residue: C 488 - end of helix Processing helix chain 'C' and resid 508 through 532 removed outlier: 3.582A pdb=" N TRP C 512 " --> pdb=" O GLY C 508 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 526 " --> pdb=" O HIS C 522 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 529 " --> pdb=" O GLU C 525 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS C 530 " --> pdb=" O GLY C 526 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 531 " --> pdb=" O ARG C 527 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 532 " --> pdb=" O VAL C 528 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 555 removed outlier: 3.562A pdb=" N ARG C 555 " --> pdb=" O PHE C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 596 removed outlier: 3.760A pdb=" N THR C 584 " --> pdb=" O THR C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 654 removed outlier: 3.515A pdb=" N LYS C 645 " --> pdb=" O ALA C 641 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR C 647 " --> pdb=" O ALA C 643 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY C 648 " --> pdb=" O GLY C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 703 Processing helix chain 'C' and resid 729 through 737 Processing helix chain 'C' and resid 739 through 750 removed outlier: 4.195A pdb=" N ILE C 743 " --> pdb=" O SER C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 780 through 785 removed outlier: 3.542A pdb=" N LEU C 784 " --> pdb=" O PRO C 780 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 801 removed outlier: 4.158A pdb=" N ILE C 801 " --> pdb=" O PRO C 797 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 797 through 801' Processing helix chain 'C' and resid 833 through 846 removed outlier: 3.850A pdb=" N ALA C 837 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP C 846 " --> pdb=" O GLN C 842 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 866 removed outlier: 3.696A pdb=" N GLU C 862 " --> pdb=" O GLY C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 889 removed outlier: 3.813A pdb=" N ALA C 872 " --> pdb=" O SER C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 899 removed outlier: 3.876A pdb=" N ALA C 897 " --> pdb=" O SER C 893 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 898 " --> pdb=" O ILE C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 924 Processing helix chain 'C' and resid 932 through 962 removed outlier: 3.926A pdb=" N ILE C 953 " --> pdb=" O ASN C 949 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 959 " --> pdb=" O GLU C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 998 removed outlier: 3.845A pdb=" N GLU C 973 " --> pdb=" O GLU C 969 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG C 980 " --> pdb=" O ARG C 976 " (cutoff:3.500A) Proline residue: C 981 - end of helix removed outlier: 3.724A pdb=" N ALA C 988 " --> pdb=" O MET C 984 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 989 " --> pdb=" O THR C 985 " (cutoff:3.500A) Proline residue: C 995 - end of helix Processing helix chain 'C' and resid 1004 through 1040 removed outlier: 3.930A pdb=" N ARG C1008 " --> pdb=" O SER C1004 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR C1013 " --> pdb=" O ALA C1009 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE C1027 " --> pdb=" O LEU C1023 " (cutoff:3.500A) Proline residue: C1030 - end of helix removed outlier: 4.013A pdb=" N VAL C1034 " --> pdb=" O PRO C1030 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.921A pdb=" N SER A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A 83 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 175 removed outlier: 6.947A pdb=" N VAL A 170 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N SER A 292 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 172 " --> pdb=" O MET A 290 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A 287 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 140 " --> pdb=" O MET A 287 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET A 138 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU A 291 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE A 136 " --> pdb=" O LEU A 291 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N LEU A 137 " --> pdb=" O ASP A 326 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASP A 326 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE A 139 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 322 " --> pdb=" O MET A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 264 through 270 removed outlier: 8.390A pdb=" N ARG A 180 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG A 767 " --> pdb=" O ARG A 180 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER A 757 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N VAL A 770 " --> pdb=" O TYR A 755 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR A 755 " --> pdb=" O VAL A 770 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 215 through 217 removed outlier: 4.014A pdb=" N GLY A 215 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 282 through 284 removed outlier: 3.673A pdb=" N VAL A 282 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR A 277 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 276 " --> pdb=" O SER A 608 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N MET A 619 " --> pdb=" O GLY A 609 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET A 570 " --> pdb=" O VAL A 662 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 662 " --> pdb=" O MET A 570 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 676 through 680 removed outlier: 4.249A pdb=" N LEU A 676 " --> pdb=" O GLY A 826 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY A 826 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 805 through 809 removed outlier: 5.014A pdb=" N THR C 231 " --> pdb=" O PRO A 722 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY C 215 " --> pdb=" O VAL C 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'B' and resid 47 through 48 removed outlier: 5.160A pdb=" N SER B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP B 83 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 175 removed outlier: 6.972A pdb=" N MET B 290 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B 173 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA B 288 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B 287 " --> pdb=" O VAL B 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 264 through 269 removed outlier: 3.838A pdb=" N ARG B 764 " --> pdb=" O ASN B 761 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER B 757 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL B 770 " --> pdb=" O TYR B 755 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N TYR B 755 " --> pdb=" O VAL B 770 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 216 through 217 removed outlier: 6.404A pdb=" N THR B 231 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE C 726 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR B 233 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE C 728 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER C 721 " --> pdb=" O GLY C 809 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 809 " --> pdb=" O SER C 721 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 282 through 283 removed outlier: 3.545A pdb=" N VAL B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET B 570 " --> pdb=" O VAL B 662 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 681 through 682 Processing sheet with id=AB6, first strand: chain 'B' and resid 721 through 723 Processing sheet with id=AB7, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.772A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP C 83 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 77 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 11.452A pdb=" N GLN C 812 " --> pdb=" O GLU C 823 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N GLU C 823 " --> pdb=" O GLN C 812 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL C 814 " --> pdb=" O ALA C 821 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.772A pdb=" N SER C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP C 83 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 77 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 11.452A pdb=" N GLN C 812 " --> pdb=" O GLU C 823 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N GLU C 823 " --> pdb=" O GLN C 812 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL C 814 " --> pdb=" O ALA C 821 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 170 through 173 removed outlier: 7.154A pdb=" N MET C 290 " --> pdb=" O GLY C 171 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL C 173 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ALA C 288 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET C 138 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE C 139 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 264 through 270 removed outlier: 7.764A pdb=" N ARG C 180 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N MET C 769 " --> pdb=" O ARG C 180 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N MET C 182 " --> pdb=" O MET C 769 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLN C 771 " --> pdb=" O MET C 182 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE C 184 " --> pdb=" O GLN C 771 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER C 757 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 770 " --> pdb=" O TYR C 755 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N TYR C 755 " --> pdb=" O VAL C 770 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.825A pdb=" N ARG C 250 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 282 through 283 removed outlier: 3.704A pdb=" N VAL C 282 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE C 623 " --> pdb=" O ILE C 605 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL C 573 " --> pdb=" O ALA C 620 " (cutoff:3.500A) 1332 hydrogen bonds defined for protein. 3891 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.40 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3888 1.31 - 1.44: 6083 1.44 - 1.56: 14173 1.56 - 1.69: 32 1.69 - 1.81: 270 Bond restraints: 24446 Sorted by residual: bond pdb=" C6 AIX B1106 " pdb=" S1 AIX B1106 " ideal model delta sigma weight residual 1.851 1.474 0.377 2.00e-02 2.50e+03 3.56e+02 bond pdb=" C8 PTY C1108 " pdb=" O10 PTY C1108 " ideal model delta sigma weight residual 1.205 1.451 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C13 AIX B1106 " pdb=" N3 AIX B1106 " ideal model delta sigma weight residual 1.447 1.667 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C13 AIX B1106 " pdb=" S1 AIX B1106 " ideal model delta sigma weight residual 1.855 1.654 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C12 AIX B1106 " pdb=" C6 AIX B1106 " ideal model delta sigma weight residual 1.560 1.706 -0.146 2.00e-02 2.50e+03 5.36e+01 ... (remaining 24441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 32441 2.93 - 5.86: 503 5.86 - 8.79: 74 8.79 - 11.72: 22 11.72 - 14.65: 7 Bond angle restraints: 33047 Sorted by residual: angle pdb=" O11 PTY B1104 " pdb=" P1 PTY B1104 " pdb=" O14 PTY B1104 " ideal model delta sigma weight residual 92.90 107.55 -14.65 3.00e+00 1.11e-01 2.38e+01 angle pdb=" C13 AIX B1106 " pdb=" S1 AIX B1106 " pdb=" C6 AIX B1106 " ideal model delta sigma weight residual 93.36 106.69 -13.33 3.00e+00 1.11e-01 1.97e+01 angle pdb=" O11 PTY B1101 " pdb=" P1 PTY B1101 " pdb=" O14 PTY B1101 " ideal model delta sigma weight residual 92.90 105.87 -12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" O11 PTY B1103 " pdb=" P1 PTY B1103 " pdb=" O14 PTY B1103 " ideal model delta sigma weight residual 92.90 105.63 -12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" O11 PTY A1103 " pdb=" P1 PTY A1103 " pdb=" O14 PTY A1103 " ideal model delta sigma weight residual 92.90 105.58 -12.68 3.00e+00 1.11e-01 1.79e+01 ... (remaining 33042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 14348 35.27 - 70.55: 236 70.55 - 105.82: 33 105.82 - 141.09: 8 141.09 - 176.36: 7 Dihedral angle restraints: 14632 sinusoidal: 5728 harmonic: 8904 Sorted by residual: dihedral pdb=" C3 PTY B1103 " pdb=" O11 PTY B1103 " pdb=" P1 PTY B1103 " pdb=" O12 PTY B1103 " ideal model delta sinusoidal sigma weight residual -59.77 116.59 -176.36 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 PTY B1105 " pdb=" O11 PTY B1105 " pdb=" P1 PTY B1105 " pdb=" O12 PTY B1105 " ideal model delta sinusoidal sigma weight residual 300.23 124.45 175.78 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N1 PTY B1101 " pdb=" C2 PTY B1101 " pdb=" C3 PTY B1101 " pdb=" O11 PTY B1101 " ideal model delta sinusoidal sigma weight residual 65.33 -128.71 -165.96 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 14629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 3156 0.058 - 0.117: 592 0.117 - 0.175: 81 0.175 - 0.234: 16 0.234 - 0.292: 6 Chirality restraints: 3851 Sorted by residual: chirality pdb=" CA ASP C 97 " pdb=" N ASP C 97 " pdb=" C ASP C 97 " pdb=" CB ASP C 97 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA LEU B 707 " pdb=" N LEU B 707 " pdb=" C LEU B 707 " pdb=" CB LEU B 707 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA LYS B 507 " pdb=" N LYS B 507 " pdb=" C LYS B 507 " pdb=" CB LYS B 507 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3848 not shown) Planarity restraints: 4158 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 902 " 0.069 5.00e-02 4.00e+02 1.08e-01 1.85e+01 pdb=" N PRO A 903 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 903 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 903 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1046 " -0.020 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLU A1046 " 0.073 2.00e-02 2.50e+03 pdb=" O GLU A1046 " -0.028 2.00e-02 2.50e+03 pdb=" N HIS A1047 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 861 " -0.268 9.50e-02 1.11e+02 1.20e-01 8.86e+00 pdb=" NE ARG B 861 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 861 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 861 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 861 " -0.010 2.00e-02 2.50e+03 ... (remaining 4155 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 133 2.54 - 3.13: 16649 3.13 - 3.72: 35583 3.72 - 4.31: 49514 4.31 - 4.90: 84328 Nonbonded interactions: 186207 Sorted by model distance: nonbonded pdb=" O10 PTY A1103 " pdb=" O10 PTY C1104 " model vdw 1.946 3.040 nonbonded pdb=" O12 PTY C1102 " pdb=" O10 PTY C1107 " model vdw 2.053 3.040 nonbonded pdb=" NE2 GLN A 358 " pdb=" CE LYS A 507 " model vdw 2.065 3.520 nonbonded pdb=" OE1 GLN C 961 " pdb=" OH TYR C1033 " model vdw 2.188 3.040 nonbonded pdb=" NE2 GLN A 358 " pdb=" CD LYS A 507 " model vdw 2.232 3.520 ... (remaining 186202 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 1040 or (resid 1101 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C5 or nam \ e C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or na \ me O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'B' and (resid 1 through 1040 or (resid 1104 and (name C1 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 \ or name C19 or name C2 or name C3 or name C30 or name C31 or name C32 or name C \ 33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C5 or nam \ e C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or na \ me O14 or name O30 or name O4 or name O7 or name P1 )))) selection = (chain 'C' and (resid 1 through 1040 or resid 1107)) } 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: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.050 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 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 : 0.009 0.897 24448 Z= 0.687 Angle : 0.894 14.651 33047 Z= 0.462 Chirality : 0.048 0.292 3851 Planarity : 0.008 0.120 4158 Dihedral : 15.155 176.364 8928 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.11), residues: 3125 helix: -2.47 (0.09), residues: 1532 sheet: -1.98 (0.24), residues: 402 loop : -2.69 (0.14), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 744 TYR 0.010 0.001 TYR B 77 PHE 0.016 0.001 PHE B 18 TRP 0.009 0.001 TRP A1016 HIS 0.008 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.38 (24446) covalent geometry : angle 0.89389 / 0.46 (33047) hydrogen bonds : bond 0.15264 / 10.09 ( 1308) hydrogen bonds : angle 6.52348 / 4.53 ( 3891) Misc. bond : bond 0.63455 / 33.39 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 400 ILE cc_start: 0.7386 (mt) cc_final: 0.7043 (mt) REVERT: A 943 MET cc_start: 0.7015 (ptm) cc_final: 0.6421 (ptt) REVERT: B 66 GLU cc_start: 0.6914 (tt0) cc_final: 0.6613 (tt0) REVERT: B 554 MET cc_start: 0.6375 (tpp) cc_final: 0.6150 (tpp) REVERT: B 1010 ILE cc_start: 0.7545 (pt) cc_final: 0.7318 (pt) REVERT: C 838 MET cc_start: 0.8583 (mtm) cc_final: 0.8350 (mtt) REVERT: C 1023 LEU cc_start: 0.7446 (mt) cc_final: 0.7208 (mt) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.1575 time to fit residues: 135.0010 Evaluate side-chains 347 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN A 211 GLN A 226 GLN A 574 GLN A 617 GLN A 685 ASN A 762 GLN B 109 ASN B 147 GLN B 463 ASN B 593 GLN B 672 ASN B 859 GLN B 917 ASN B1007 GLN C 101 ASN C 179 GLN C 252 ASN C 283 ASN C 293 ASN C 566 GLN C 617 GLN C 685 ASN C 696 ASN C 762 GLN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 836 GLN C 859 GLN C 936 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.122378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105559 restraints weight = 41019.337| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.49 r_work: 0.3379 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24448 Z= 0.130 Angle : 0.554 8.328 33047 Z= 0.281 Chirality : 0.041 0.207 3851 Planarity : 0.005 0.067 4158 Dihedral : 12.632 176.589 3680 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.12 % Allowed : 10.77 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.14), residues: 3125 helix: -0.25 (0.12), residues: 1582 sheet: -1.68 (0.23), residues: 433 loop : -2.21 (0.16), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 744 TYR 0.016 0.001 TYR C 77 PHE 0.018 0.001 PHE A1015 TRP 0.014 0.001 TRP C 512 HIS 0.006 0.001 HIS B 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (24446) covalent geometry : angle 0.55430 / 0.28 (33047) hydrogen bonds : bond 0.03624 / 2.38 ( 1308) hydrogen bonds : angle 4.25387 / 2.95 ( 3891) Misc. bond : bond 0.00760 / 0.40 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 361 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 29 SER cc_start: 0.8649 (p) cc_final: 0.8364 (p) REVERT: A 182 MET cc_start: 0.8712 (tpp) cc_final: 0.8457 (tpt) REVERT: A 356 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.6593 (t80) REVERT: A 400 ILE cc_start: 0.7608 (mt) cc_final: 0.7219 (mt) REVERT: A 649 MET cc_start: 0.8068 (mtp) cc_final: 0.7670 (mtm) REVERT: A 701 LYS cc_start: 0.7650 (tttt) cc_final: 0.7417 (mtmt) REVERT: A 778 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7921 (mmm) REVERT: A 1019 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8779 (mm) REVERT: B 141 MET cc_start: 0.7994 (mmm) cc_final: 0.7409 (mmm) REVERT: B 174 ARG cc_start: 0.7908 (ttt180) cc_final: 0.7630 (ttt-90) REVERT: B 306 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8222 (mt-10) REVERT: B 353 MET cc_start: 0.8367 (mmm) cc_final: 0.7852 (mmt) REVERT: B 554 MET cc_start: 0.7617 (tpp) cc_final: 0.6920 (tpp) REVERT: B 668 LEU cc_start: 0.7315 (mt) cc_final: 0.7091 (pp) REVERT: C 141 MET cc_start: 0.8252 (mmt) cc_final: 0.7959 (mmt) REVERT: C 354 TYR cc_start: 0.8450 (t80) cc_final: 0.8109 (t80) REVERT: C 468 PHE cc_start: 0.8157 (t80) cc_final: 0.7926 (t80) REVERT: C 838 MET cc_start: 0.8720 (mtm) cc_final: 0.8510 (mtt) REVERT: C 987 PHE cc_start: 0.8079 (m-80) cc_final: 0.7833 (m-10) outliers start: 28 outliers final: 11 residues processed: 383 average time/residue: 0.1358 time to fit residues: 86.6045 Evaluate side-chains 331 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 316 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain C residue 399 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 7 optimal weight: 4.9990 chunk 253 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 185 optimal weight: 0.9980 chunk 242 optimal weight: 0.9980 chunk 276 optimal weight: 0.4980 chunk 71 optimal weight: 8.9990 chunk 196 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 221 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 685 ASN B 672 ASN C 101 ASN C 108 GLN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.118475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.101348 restraints weight = 40910.993| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.48 r_work: 0.3308 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24448 Z= 0.123 Angle : 0.512 7.948 33047 Z= 0.261 Chirality : 0.041 0.183 3851 Planarity : 0.004 0.057 4158 Dihedral : 11.350 171.102 3680 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.72 % Allowed : 11.89 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.15), residues: 3125 helix: 0.77 (0.13), residues: 1592 sheet: -1.26 (0.25), residues: 437 loop : -1.92 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 815 TYR 0.012 0.001 TYR A 49 PHE 0.025 0.001 PHE A 658 TRP 0.015 0.001 TRP A1016 HIS 0.004 0.001 HIS A 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (24446) covalent geometry : angle 0.51235 / 0.26 (33047) hydrogen bonds : bond 0.03507 / 2.33 ( 1308) hydrogen bonds : angle 3.92635 / 2.73 ( 3891) Misc. bond : bond 0.00188 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 331 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: A 152 MET cc_start: 0.8230 (mtm) cc_final: 0.7988 (mtm) REVERT: A 182 MET cc_start: 0.8738 (tpp) cc_final: 0.8471 (tpt) REVERT: A 400 ILE cc_start: 0.7749 (mt) cc_final: 0.7362 (mt) REVERT: A 412 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7587 (mt-10) REVERT: A 457 PHE cc_start: 0.7575 (p90) cc_final: 0.7139 (p90) REVERT: A 649 MET cc_start: 0.8140 (mtp) cc_final: 0.7870 (mtm) REVERT: A 701 LYS cc_start: 0.7575 (tttt) cc_final: 0.7234 (mtmt) REVERT: A 778 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8057 (mmm) REVERT: A 899 LEU cc_start: 0.8582 (mt) cc_final: 0.8372 (mt) REVERT: A 1019 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8672 (mm) REVERT: B 174 ARG cc_start: 0.7937 (ttt180) cc_final: 0.7650 (ttt-90) REVERT: B 353 MET cc_start: 0.8233 (mmm) cc_final: 0.8023 (mmm) REVERT: B 668 LEU cc_start: 0.7370 (mt) cc_final: 0.7158 (pp) REVERT: B 846 ASP cc_start: 0.8382 (t70) cc_final: 0.8157 (t0) REVERT: C 141 MET cc_start: 0.8322 (mmt) cc_final: 0.8008 (mmt) REVERT: C 798 LEU cc_start: 0.8700 (tp) cc_final: 0.8491 (tp) REVERT: C 987 PHE cc_start: 0.8181 (m-80) cc_final: 0.7874 (m-10) outliers start: 43 outliers final: 21 residues processed: 358 average time/residue: 0.1402 time to fit residues: 82.8746 Evaluate side-chains 328 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 305 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 994 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 117 optimal weight: 1.9990 chunk 294 optimal weight: 0.6980 chunk 206 optimal weight: 0.7980 chunk 258 optimal weight: 0.0020 chunk 211 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 305 optimal weight: 0.9980 chunk 80 optimal weight: 0.0980 chunk 12 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 295 optimal weight: 2.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 413 ASN A 685 ASN B 672 ASN C 101 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.118698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101495 restraints weight = 40958.468| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.53 r_work: 0.3310 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24448 Z= 0.096 Angle : 0.480 7.543 33047 Z= 0.243 Chirality : 0.040 0.155 3851 Planarity : 0.003 0.050 4158 Dihedral : 10.562 171.166 3680 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.88 % Allowed : 12.97 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.15), residues: 3125 helix: 1.24 (0.13), residues: 1587 sheet: -0.97 (0.26), residues: 435 loop : -1.70 (0.17), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 744 TYR 0.010 0.001 TYR B 934 PHE 0.014 0.001 PHE A 25 TRP 0.012 0.001 TRP A1016 HIS 0.002 0.000 HIS A 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (24446) covalent geometry : angle 0.48030 / 0.24 (33047) hydrogen bonds : bond 0.03080 / 2.05 ( 1308) hydrogen bonds : angle 3.77305 / 2.62 ( 3891) Misc. bond : bond 0.00137 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 322 time to evaluate : 0.882 Fit side-chains REVERT: A 152 MET cc_start: 0.8152 (mtm) cc_final: 0.7915 (mtm) REVERT: A 182 MET cc_start: 0.8722 (tpp) cc_final: 0.8458 (tpt) REVERT: A 400 ILE cc_start: 0.7639 (mt) cc_final: 0.7223 (mt) REVERT: A 413 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8320 (t0) REVERT: A 457 PHE cc_start: 0.7600 (p90) cc_final: 0.7249 (p90) REVERT: A 701 LYS cc_start: 0.7560 (tttt) cc_final: 0.7227 (mtmt) REVERT: A 778 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7917 (mmm) REVERT: A 899 LEU cc_start: 0.8651 (mt) cc_final: 0.8420 (mt) REVERT: A 1019 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8645 (mm) REVERT: B 60 SER cc_start: 0.7829 (m) cc_final: 0.7595 (m) REVERT: B 353 MET cc_start: 0.8242 (mmm) cc_final: 0.7832 (mmt) REVERT: B 554 MET cc_start: 0.7742 (tpp) cc_final: 0.7108 (tpp) REVERT: B 846 ASP cc_start: 0.8399 (t70) cc_final: 0.8197 (t0) REVERT: B 902 MET cc_start: 0.8056 (mmm) cc_final: 0.7837 (mmm) REVERT: C 141 MET cc_start: 0.8359 (mmt) cc_final: 0.8045 (mmt) REVERT: C 798 LEU cc_start: 0.8675 (tp) cc_final: 0.8453 (tp) REVERT: C 839 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7571 (pt0) REVERT: C 987 PHE cc_start: 0.8090 (m-80) cc_final: 0.7782 (m-10) outliers start: 47 outliers final: 27 residues processed: 349 average time/residue: 0.1368 time to fit residues: 80.3319 Evaluate side-chains 337 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 307 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 413 ASN Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 987 PHE Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 994 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 259 optimal weight: 0.9980 chunk 308 optimal weight: 3.9990 chunk 264 optimal weight: 0.8980 chunk 222 optimal weight: 7.9990 chunk 198 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 211 GLN A 358 GLN B 672 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.096098 restraints weight = 40976.919| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.42 r_work: 0.3236 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24448 Z= 0.161 Angle : 0.540 8.306 33047 Z= 0.276 Chirality : 0.042 0.190 3851 Planarity : 0.004 0.050 4158 Dihedral : 10.291 171.545 3680 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.11 % Allowed : 13.81 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 3125 helix: 1.37 (0.13), residues: 1608 sheet: -0.94 (0.26), residues: 431 loop : -1.58 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 416 TYR 0.017 0.002 TYR A 49 PHE 0.024 0.002 PHE B 919 TRP 0.015 0.001 TRP A1016 HIS 0.003 0.001 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (24446) covalent geometry : angle 0.53970 / 0.28 (33047) hydrogen bonds : bond 0.03937 / 2.65 ( 1308) hydrogen bonds : angle 3.87317 / 2.69 ( 3891) Misc. bond : bond 0.00078 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 312 time to evaluate : 0.934 Fit side-chains REVERT: A 182 MET cc_start: 0.8953 (tpp) cc_final: 0.8709 (tpt) REVERT: A 353 MET cc_start: 0.8556 (mmm) cc_final: 0.8354 (mmp) REVERT: A 386 MET cc_start: 0.8509 (mmm) cc_final: 0.8201 (mtt) REVERT: A 400 ILE cc_start: 0.7884 (mt) cc_final: 0.7470 (mt) REVERT: A 457 PHE cc_start: 0.7724 (p90) cc_final: 0.7451 (p90) REVERT: A 463 ASN cc_start: 0.8322 (p0) cc_final: 0.8039 (p0) REVERT: A 536 PHE cc_start: 0.6052 (t80) cc_final: 0.5824 (t80) REVERT: A 701 LYS cc_start: 0.7638 (tttt) cc_final: 0.7329 (mtmt) REVERT: A 778 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8177 (mmp) REVERT: A 1019 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8688 (mm) REVERT: B 348 LEU cc_start: 0.8991 (mt) cc_final: 0.8649 (tp) REVERT: B 353 MET cc_start: 0.8501 (mmm) cc_final: 0.8275 (mmm) REVERT: B 906 LEU cc_start: 0.8579 (tp) cc_final: 0.8363 (tp) REVERT: C 57 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8007 (tpp) REVERT: C 141 MET cc_start: 0.8604 (mmt) cc_final: 0.8330 (mmt) REVERT: C 839 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7869 (pt0) REVERT: C 1023 LEU cc_start: 0.8317 (mt) cc_final: 0.8085 (mp) outliers start: 53 outliers final: 39 residues processed: 347 average time/residue: 0.1402 time to fit residues: 81.2661 Evaluate side-chains 334 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 854 LEU Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 994 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 58 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 260 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 249 optimal weight: 0.6980 chunk 281 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 GLN B 672 ASN C 208 GLN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.114390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.097304 restraints weight = 40989.859| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.42 r_work: 0.3255 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24448 Z= 0.112 Angle : 0.499 7.803 33047 Z= 0.254 Chirality : 0.041 0.150 3851 Planarity : 0.003 0.045 4158 Dihedral : 9.939 169.499 3680 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.00 % Allowed : 14.80 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.16), residues: 3125 helix: 1.56 (0.13), residues: 1608 sheet: -0.85 (0.26), residues: 418 loop : -1.42 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 744 TYR 0.016 0.001 TYR A 934 PHE 0.023 0.001 PHE C 939 TRP 0.013 0.001 TRP A1016 HIS 0.002 0.000 HIS A 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (24446) covalent geometry : angle 0.49925 / 0.25 (33047) hydrogen bonds : bond 0.03363 / 2.24 ( 1308) hydrogen bonds : angle 3.80459 / 2.64 ( 3891) Misc. bond : bond 0.00074 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 0.602 Fit side-chains REVERT: A 182 MET cc_start: 0.8980 (tpp) cc_final: 0.8735 (tpt) REVERT: A 400 ILE cc_start: 0.7856 (mt) cc_final: 0.7433 (mt) REVERT: A 457 PHE cc_start: 0.7665 (p90) cc_final: 0.7457 (p90) REVERT: A 536 PHE cc_start: 0.6090 (t80) cc_final: 0.5869 (t80) REVERT: A 551 PHE cc_start: 0.8384 (t80) cc_final: 0.8152 (t80) REVERT: A 701 LYS cc_start: 0.7631 (tttt) cc_final: 0.7283 (mtmt) REVERT: A 778 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8000 (mmm) REVERT: A 1018 MET cc_start: 0.8731 (mmm) cc_final: 0.8474 (mmm) REVERT: B 348 LEU cc_start: 0.8991 (mt) cc_final: 0.8665 (tp) REVERT: B 353 MET cc_start: 0.8356 (mmm) cc_final: 0.7946 (mmt) REVERT: B 456 MET cc_start: 0.8523 (mmm) cc_final: 0.8300 (mtp) REVERT: B 906 LEU cc_start: 0.8554 (tp) cc_final: 0.8271 (tp) REVERT: C 141 MET cc_start: 0.8575 (mmt) cc_final: 0.8292 (mmt) REVERT: C 839 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7767 (pt0) REVERT: C 1023 LEU cc_start: 0.8300 (mt) cc_final: 0.8091 (mp) outliers start: 50 outliers final: 38 residues processed: 334 average time/residue: 0.1377 time to fit residues: 76.5486 Evaluate side-chains 335 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 296 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 966 SER Chi-restraints excluded: chain C residue 994 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 231 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 213 optimal weight: 0.0870 chunk 113 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 ASN B 672 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 859 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.113573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.095774 restraints weight = 40988.975| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.49 r_work: 0.3220 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24448 Z= 0.134 Angle : 0.520 7.886 33047 Z= 0.265 Chirality : 0.041 0.187 3851 Planarity : 0.004 0.047 4158 Dihedral : 9.671 169.699 3680 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.15 % Allowed : 14.88 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 3125 helix: 1.65 (0.13), residues: 1608 sheet: -0.93 (0.25), residues: 449 loop : -1.29 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 224 TYR 0.013 0.001 TYR A 49 PHE 0.031 0.001 PHE B 919 TRP 0.012 0.001 TRP A1016 HIS 0.003 0.001 HIS A 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (24446) covalent geometry : angle 0.51971 / 0.26 (33047) hydrogen bonds : bond 0.03670 / 2.44 ( 1308) hydrogen bonds : angle 3.80957 / 2.65 ( 3891) Misc. bond : bond 0.00065 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 306 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 182 MET cc_start: 0.8816 (tpp) cc_final: 0.8569 (tpt) REVERT: A 400 ILE cc_start: 0.7754 (mt) cc_final: 0.7354 (mt) REVERT: A 470 LEU cc_start: 0.8836 (mt) cc_final: 0.8476 (mt) REVERT: A 551 PHE cc_start: 0.8311 (t80) cc_final: 0.8077 (t80) REVERT: A 902 MET cc_start: 0.7669 (mmp) cc_final: 0.7153 (ptp) REVERT: B 348 LEU cc_start: 0.8932 (mt) cc_final: 0.8594 (tp) REVERT: B 554 MET cc_start: 0.7736 (tpp) cc_final: 0.7267 (tpp) REVERT: C 141 MET cc_start: 0.8286 (mmt) cc_final: 0.8024 (mmt) REVERT: C 224 ARG cc_start: 0.6348 (mmm160) cc_final: 0.6146 (mmp-170) outliers start: 54 outliers final: 47 residues processed: 340 average time/residue: 0.1383 time to fit residues: 78.6756 Evaluate side-chains 340 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 293 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 563 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 983 ILE Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 966 SER Chi-restraints excluded: chain C residue 994 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 149 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 109 optimal weight: 0.0980 chunk 206 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 130 optimal weight: 0.7980 chunk 248 optimal weight: 7.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 672 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.112963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.095989 restraints weight = 40816.422| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.39 r_work: 0.3234 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24448 Z= 0.122 Angle : 0.516 8.800 33047 Z= 0.261 Chirality : 0.041 0.206 3851 Planarity : 0.003 0.046 4158 Dihedral : 9.468 168.436 3680 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.92 % Allowed : 15.68 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 3125 helix: 1.74 (0.13), residues: 1606 sheet: -0.79 (0.26), residues: 432 loop : -1.26 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 416 TYR 0.018 0.001 TYR A 934 PHE 0.026 0.001 PHE A 457 TRP 0.012 0.001 TRP A1016 HIS 0.002 0.000 HIS B 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (24446) covalent geometry : angle 0.51608 / 0.26 (33047) hydrogen bonds : bond 0.03491 / 2.33 ( 1308) hydrogen bonds : angle 3.80234 / 2.64 ( 3891) Misc. bond : bond 0.00075 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 301 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8632 (mp0) cc_final: 0.8253 (mp0) REVERT: A 182 MET cc_start: 0.8978 (tpp) cc_final: 0.8750 (tpt) REVERT: A 400 ILE cc_start: 0.7834 (mt) cc_final: 0.7414 (mt) REVERT: A 536 PHE cc_start: 0.6124 (t80) cc_final: 0.5908 (t80) REVERT: A 551 PHE cc_start: 0.8393 (t80) cc_final: 0.8155 (t80) REVERT: A 902 MET cc_start: 0.7843 (mmp) cc_final: 0.7327 (ptp) REVERT: B 348 LEU cc_start: 0.9014 (mt) cc_final: 0.8690 (tp) REVERT: B 554 MET cc_start: 0.7821 (tpp) cc_final: 0.7344 (tpp) REVERT: C 141 MET cc_start: 0.8569 (mmt) cc_final: 0.8287 (mmt) outliers start: 48 outliers final: 46 residues processed: 333 average time/residue: 0.1357 time to fit residues: 75.4958 Evaluate side-chains 343 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LYS Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 952 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 896 LEU Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 983 ILE Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 966 SER Chi-restraints excluded: chain C residue 994 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 160 optimal weight: 0.0370 chunk 5 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 245 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 139 optimal weight: 4.9990 chunk 187 optimal weight: 0.6980 chunk 228 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 0.0270 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 685 ASN B 672 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.115405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.098405 restraints weight = 40963.983| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.40 r_work: 0.3269 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24448 Z= 0.095 Angle : 0.493 8.629 33047 Z= 0.249 Chirality : 0.040 0.199 3851 Planarity : 0.003 0.045 4158 Dihedral : 9.024 167.880 3680 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.96 % Allowed : 16.00 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.16), residues: 3125 helix: 1.85 (0.13), residues: 1609 sheet: -0.61 (0.27), residues: 410 loop : -1.21 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 416 TYR 0.011 0.001 TYR B 314 PHE 0.029 0.001 PHE B 919 TRP 0.009 0.001 TRP A1016 HIS 0.001 0.000 HIS A 688 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (24446) covalent geometry : angle 0.49320 / 0.25 (33047) hydrogen bonds : bond 0.03052 / 2.03 ( 1308) hydrogen bonds : angle 3.69826 / 2.57 ( 3891) Misc. bond : bond 0.00073 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 320 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8418 (mp0) cc_final: 0.8049 (mp0) REVERT: A 182 MET cc_start: 0.8805 (tpp) cc_final: 0.8543 (tpt) REVERT: A 307 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7944 (tpp80) REVERT: A 400 ILE cc_start: 0.7645 (mt) cc_final: 0.7224 (mt) REVERT: A 778 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.7975 (mmm) REVERT: A 902 MET cc_start: 0.7530 (mmp) cc_final: 0.7190 (ptp) REVERT: B 538 MET cc_start: 0.8385 (mmm) cc_final: 0.8012 (mmm) REVERT: B 554 MET cc_start: 0.7670 (tpp) cc_final: 0.7230 (tpp) REVERT: B 862 GLU cc_start: 0.7770 (pm20) cc_final: 0.7558 (pm20) REVERT: B 1018 MET cc_start: 0.7631 (tpp) cc_final: 0.7233 (mmm) REVERT: C 141 MET cc_start: 0.8248 (mmt) cc_final: 0.7960 (mmt) outliers start: 49 outliers final: 41 residues processed: 352 average time/residue: 0.1405 time to fit residues: 82.1668 Evaluate side-chains 341 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 299 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 966 SER Chi-restraints excluded: chain C residue 994 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 200 optimal weight: 2.9990 chunk 49 optimal weight: 0.0270 chunk 17 optimal weight: 5.9990 chunk 175 optimal weight: 0.4980 chunk 152 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 204 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 232 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 685 ASN B 672 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.114875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.098093 restraints weight = 40890.066| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.41 r_work: 0.3265 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 24448 Z= 0.102 Angle : 0.516 10.385 33047 Z= 0.258 Chirality : 0.041 0.217 3851 Planarity : 0.003 0.045 4158 Dihedral : 8.854 167.688 3680 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.96 % Allowed : 16.40 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.16), residues: 3125 helix: 1.86 (0.13), residues: 1609 sheet: -0.55 (0.27), residues: 409 loop : -1.16 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 416 TYR 0.016 0.001 TYR A 934 PHE 0.030 0.001 PHE B 919 TRP 0.010 0.001 TRP A1016 HIS 0.002 0.000 HIS B 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (24446) covalent geometry : angle 0.51584 / 0.26 (33047) hydrogen bonds : bond 0.03159 / 2.10 ( 1308) hydrogen bonds : angle 3.72003 / 2.59 ( 3891) Misc. bond : bond 0.00072 / 0.04 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6250 Ramachandran restraints generated. 3125 Oldfield, 0 Emsley, 3125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 304 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8434 (mp0) cc_final: 0.8054 (mp0) REVERT: A 182 MET cc_start: 0.8825 (tpp) cc_final: 0.8570 (tpt) REVERT: A 400 ILE cc_start: 0.7638 (mt) cc_final: 0.7225 (mt) REVERT: A 778 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7949 (mmm) REVERT: A 902 MET cc_start: 0.7535 (mmp) cc_final: 0.7275 (ptp) REVERT: B 538 MET cc_start: 0.8424 (mmm) cc_final: 0.8037 (mmm) REVERT: B 862 GLU cc_start: 0.7786 (pm20) cc_final: 0.7550 (pm20) REVERT: B 1018 MET cc_start: 0.7707 (tpp) cc_final: 0.7352 (mmm) REVERT: C 141 MET cc_start: 0.8293 (mmt) cc_final: 0.7998 (mmt) outliers start: 49 outliers final: 42 residues processed: 337 average time/residue: 0.1322 time to fit residues: 75.3554 Evaluate side-chains 343 residues out of total 2506 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 300 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 340 HIS Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 778 MET Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 896 LEU Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 994 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 452 VAL Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 503 HIS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 918 LEU Chi-restraints excluded: chain B residue 994 VAL Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 406 ASP Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 633 THR Chi-restraints excluded: chain C residue 738 VAL Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 845 VAL Chi-restraints excluded: chain C residue 966 SER Chi-restraints excluded: chain C residue 994 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 310 optimal weight: 0.5980 chunk 204 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 267 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 296 optimal weight: 5.9990 chunk 120 optimal weight: 0.0670 chunk 240 optimal weight: 0.9980 chunk 220 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 685 ASN B 672 ASN ** C 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.115054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098010 restraints weight = 40904.697| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.40 r_work: 0.3266 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 24448 Z= 0.100 Angle : 0.507 10.746 33047 Z= 0.255 Chirality : 0.041 0.209 3851 Planarity : 0.003 0.045 4158 Dihedral : 8.575 166.688 3680 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.88 % Allowed : 16.32 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.16), residues: 3125 helix: 1.90 (0.13), residues: 1609 sheet: -0.61 (0.27), residues: 418 loop : -1.09 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 224 TYR 0.010 0.001 TYR B 314 PHE 0.033 0.001 PHE B 919 TRP 0.009 0.001 TRP A1016 HIS 0.002 0.000 HIS B 503 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (24446) covalent geometry : angle 0.50675 / 0.25 (33047) hydrogen bonds : bond 0.03121 / 2.08 ( 1308) hydrogen bonds : angle 3.71002 / 2.58 ( 3891) Misc. bond : bond 0.00078 / 0.04 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4701.64 seconds wall clock time: 81 minutes 35.70 seconds (4895.70 seconds total)