Starting phenix.real_space_refine on Tue Aug 26 01:35:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bk7_16091/08_2025/8bk7_16091.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bk7_16091/08_2025/8bk7_16091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bk7_16091/08_2025/8bk7_16091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bk7_16091/08_2025/8bk7_16091.map" model { file = "/net/cci-nas-00/data/ceres_data/8bk7_16091/08_2025/8bk7_16091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bk7_16091/08_2025/8bk7_16091.cif" } resolution = 3.3 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 152 5.16 5 C 20552 2.51 5 N 5760 2.21 5 O 6036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 248 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32500 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8125 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 945} Restraints were copied for chains: B, C, D Time building chain proxies: 9.41, per 1000 atoms: 0.29 Number of scatterers: 32500 At special positions: 0 Unit cell: (194.666, 150.086, 105.506, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 152 16.00 O 6036 8.00 N 5760 7.00 C 20552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 238.4 nanoseconds 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7520 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 52 sheets defined 16.9% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.687A pdb=" N ASN A 18 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.608A pdb=" N GLY A 94 " --> pdb=" O GLN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.862A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 395 through 406 removed outlier: 4.030A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.758A pdb=" N ARG A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.670A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.653A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 614 through 623 removed outlier: 4.137A pdb=" N THR A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 619 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 814 Processing helix chain 'A' and resid 923 through 926 removed outlier: 3.564A pdb=" N TYR A 926 " --> pdb=" O SER A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 1004 through 1008 removed outlier: 3.641A pdb=" N GLN A1008 " --> pdb=" O ALA A1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.687A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 89 through 94 removed outlier: 3.608A pdb=" N GLY B 94 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 136 removed outlier: 3.862A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 395 through 406 removed outlier: 4.030A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.758A pdb=" N ARG B 442 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.670A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 removed outlier: 3.654A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 614 through 623 removed outlier: 4.137A pdb=" N THR B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 814 Processing helix chain 'B' and resid 923 through 926 removed outlier: 3.564A pdb=" N TYR B 926 " --> pdb=" O SER B 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 923 through 926' Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'B' and resid 1004 through 1008 removed outlier: 3.641A pdb=" N GLN B1008 " --> pdb=" O ALA B1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.687A pdb=" N ASN C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.608A pdb=" N GLY C 94 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.863A pdb=" N LEU C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 368 through 382 Processing helix chain 'C' and resid 395 through 406 removed outlier: 4.030A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 447 removed outlier: 3.758A pdb=" N ARG C 442 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.671A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 removed outlier: 3.653A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 Processing helix chain 'C' and resid 614 through 623 removed outlier: 4.138A pdb=" N THR C 618 " --> pdb=" O HIS C 614 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 814 Processing helix chain 'C' and resid 923 through 926 removed outlier: 3.564A pdb=" N TYR C 926 " --> pdb=" O SER C 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 923 through 926' Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 972 through 976 Processing helix chain 'C' and resid 1004 through 1008 removed outlier: 3.640A pdb=" N GLN C1008 " --> pdb=" O ALA C1005 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.687A pdb=" N ASN D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 89 through 94 removed outlier: 3.607A pdb=" N GLY D 94 " --> pdb=" O GLN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.862A pdb=" N LEU D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 395 through 406 removed outlier: 4.030A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 447 removed outlier: 3.758A pdb=" N ARG D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.670A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 525 removed outlier: 3.653A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 614 through 623 removed outlier: 4.138A pdb=" N THR D 618 " --> pdb=" O HIS D 614 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU D 619 " --> pdb=" O PRO D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 814 Processing helix chain 'D' and resid 923 through 926 removed outlier: 3.564A pdb=" N TYR D 926 " --> pdb=" O SER D 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 923 through 926' Processing helix chain 'D' and resid 963 through 970 Processing helix chain 'D' and resid 972 through 976 Processing helix chain 'D' and resid 1004 through 1008 removed outlier: 3.641A pdb=" N GLN D1008 " --> pdb=" O ALA D1005 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.781A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 129 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100 removed outlier: 3.679A pdb=" N ILE A 99 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 230 removed outlier: 3.519A pdb=" N CYS A 247 " --> pdb=" O GLN A 221 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN A 245 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE A 225 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU A 243 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A 227 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU A 241 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR A 229 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 239 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 273 removed outlier: 6.772A pdb=" N LEU A 260 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 258 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR A 271 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL A 256 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU A 254 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR A 317 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU A 322 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA7, first strand: chain 'A' and resid 484 through 485 removed outlier: 7.994A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL A 409 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TRP A 456 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASP A 411 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU A 412 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 386 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 356 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AB1, first strand: chain 'A' and resid 661 through 669 removed outlier: 6.168A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 664 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY A 692 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU A 724 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU A 694 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLN A 702 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 714 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.085A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 776 through 783 removed outlier: 5.837A pdb=" N GLN A 887 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.459A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.683A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.542A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 850 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 833 " --> pdb=" O LEU A 830 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA A 820 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 776 through 783 removed outlier: 5.837A pdb=" N GLN A 887 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR A 941 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 900 " --> pdb=" O THR A 941 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 23 through 24 removed outlier: 6.782A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 129 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'B' and resid 99 through 100 removed outlier: 3.679A pdb=" N ILE B 99 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 221 through 230 removed outlier: 3.519A pdb=" N CYS B 247 " --> pdb=" O GLN B 221 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLN B 245 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE B 225 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU B 243 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL B 227 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU B 241 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR B 229 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 239 " --> pdb=" O THR B 229 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 265 through 273 removed outlier: 6.773A pdb=" N LEU B 260 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER B 269 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 258 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR B 271 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 256 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU B 254 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR B 317 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B 322 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=AC2, first strand: chain 'B' and resid 484 through 485 removed outlier: 7.995A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL B 409 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TRP B 456 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ASP B 411 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU B 412 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 386 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 356 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU B 533 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N PHE B 566 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 535 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 575 through 578 Processing sheet with id=AC4, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AC5, first strand: chain 'B' and resid 661 through 669 removed outlier: 6.168A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 664 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY B 692 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU B 724 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU B 694 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B 716 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLN B 702 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE B 714 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.085A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 776 through 783 removed outlier: 5.837A pdb=" N GLN B 887 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.900A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.459A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.683A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.542A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 850 " --> pdb=" O TRP B 842 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 833 " --> pdb=" O LEU B 830 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA B 820 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 776 through 783 removed outlier: 5.837A pdb=" N GLN B 887 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.900A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR B 941 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU B 900 " --> pdb=" O THR B 941 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.781A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL C 129 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AD2, first strand: chain 'C' and resid 99 through 100 removed outlier: 3.679A pdb=" N ILE C 99 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 221 through 230 removed outlier: 3.519A pdb=" N CYS C 247 " --> pdb=" O GLN C 221 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN C 245 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE C 225 " --> pdb=" O GLU C 243 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLU C 243 " --> pdb=" O PHE C 225 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL C 227 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU C 241 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR C 229 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL C 239 " --> pdb=" O THR C 229 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 265 through 273 removed outlier: 6.773A pdb=" N LEU C 260 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER C 269 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 258 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR C 271 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL C 256 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU C 254 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR C 317 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 322 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AD6, first strand: chain 'C' and resid 484 through 485 removed outlier: 7.995A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL C 409 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TRP C 456 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASP C 411 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU C 412 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA C 386 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 356 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 575 through 578 Processing sheet with id=AD8, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AD9, first strand: chain 'C' and resid 661 through 669 removed outlier: 6.168A pdb=" N LEU C 658 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 664 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY C 692 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU C 724 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU C 694 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLN C 702 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE C 714 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 739 through 742 removed outlier: 6.085A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 776 through 783 removed outlier: 5.836A pdb=" N GLN C 887 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.440A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.460A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.683A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.542A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 850 " --> pdb=" O TRP C 842 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA C 833 " --> pdb=" O LEU C 830 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ALA C 820 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 776 through 783 removed outlier: 5.836A pdb=" N GLN C 887 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR C 941 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU C 900 " --> pdb=" O THR C 941 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 23 through 24 removed outlier: 6.781A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL D 129 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AE6, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.679A pdb=" N ILE D 99 " --> pdb=" O ARG D 204 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 221 through 230 removed outlier: 3.519A pdb=" N CYS D 247 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN D 245 " --> pdb=" O SER D 223 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N PHE D 225 " --> pdb=" O GLU D 243 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU D 243 " --> pdb=" O PHE D 225 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL D 227 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU D 241 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR D 229 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL D 239 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 265 through 273 removed outlier: 6.772A pdb=" N LEU D 260 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER D 269 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL D 258 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR D 271 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 256 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N LEU D 254 " --> pdb=" O PRO D 273 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR D 317 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AF1, first strand: chain 'D' and resid 484 through 485 removed outlier: 7.994A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL D 409 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TRP D 456 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASP D 411 " --> pdb=" O TRP D 456 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU D 412 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA D 386 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG D 356 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU D 533 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N PHE D 566 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU D 535 " --> pdb=" O PHE D 566 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 575 through 578 Processing sheet with id=AF3, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AF4, first strand: chain 'D' and resid 661 through 669 removed outlier: 6.168A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA D 664 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY D 692 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU D 724 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU D 694 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA D 716 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLN D 702 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE D 714 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 739 through 742 removed outlier: 6.085A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 776 through 783 removed outlier: 5.836A pdb=" N GLN D 887 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.460A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.683A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.542A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE D 850 " --> pdb=" O TRP D 842 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA D 833 " --> pdb=" O LEU D 830 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 776 through 783 removed outlier: 5.836A pdb=" N GLN D 887 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.899A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR D 941 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU D 900 " --> pdb=" O THR D 941 " (cutoff:3.500A) 1232 hydrogen bonds defined for protein. 3228 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: 7.38 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10968 1.34 - 1.46: 7919 1.46 - 1.58: 14333 1.58 - 1.70: 8 1.70 - 1.82: 240 Bond restraints: 33468 Sorted by residual: bond pdb=" CB PRO C 596 " pdb=" CG PRO C 596 " ideal model delta sigma weight residual 1.506 1.617 -0.111 3.90e-02 6.57e+02 8.11e+00 bond pdb=" CB PRO B 596 " pdb=" CG PRO B 596 " ideal model delta sigma weight residual 1.506 1.616 -0.110 3.90e-02 6.57e+02 8.00e+00 bond pdb=" CB PRO D 596 " pdb=" CG PRO D 596 " ideal model delta sigma weight residual 1.506 1.616 -0.110 3.90e-02 6.57e+02 7.97e+00 bond pdb=" CB PRO A 596 " pdb=" CG PRO A 596 " ideal model delta sigma weight residual 1.506 1.616 -0.110 3.90e-02 6.57e+02 7.92e+00 bond pdb=" CB PRO A 32 " pdb=" CG PRO A 32 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.40e+00 ... (remaining 33463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 45146 2.94 - 5.87: 414 5.87 - 8.81: 80 8.81 - 11.75: 16 11.75 - 14.69: 4 Bond angle restraints: 45660 Sorted by residual: angle pdb=" CA PRO B 596 " pdb=" N PRO B 596 " pdb=" CD PRO B 596 " ideal model delta sigma weight residual 111.50 96.81 14.69 1.40e+00 5.10e-01 1.10e+02 angle pdb=" CA PRO A 596 " pdb=" N PRO A 596 " pdb=" CD PRO A 596 " ideal model delta sigma weight residual 111.50 96.87 14.63 1.40e+00 5.10e-01 1.09e+02 angle pdb=" CA PRO D 596 " pdb=" N PRO D 596 " pdb=" CD PRO D 596 " ideal model delta sigma weight residual 111.50 96.87 14.63 1.40e+00 5.10e-01 1.09e+02 angle pdb=" CA PRO C 596 " pdb=" N PRO C 596 " pdb=" CD PRO C 596 " ideal model delta sigma weight residual 111.50 96.90 14.60 1.40e+00 5.10e-01 1.09e+02 angle pdb=" CA PRO C 32 " pdb=" N PRO C 32 " pdb=" CD PRO C 32 " ideal model delta sigma weight residual 112.00 100.97 11.03 1.40e+00 5.10e-01 6.21e+01 ... (remaining 45655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 16600 17.80 - 35.61: 2125 35.61 - 53.41: 683 53.41 - 71.21: 128 71.21 - 89.02: 60 Dihedral angle restraints: 19596 sinusoidal: 7912 harmonic: 11684 Sorted by residual: dihedral pdb=" CA ASP B 598 " pdb=" C ASP B 598 " pdb=" N ARG B 599 " pdb=" CA ARG B 599 " ideal model delta harmonic sigma weight residual -180.00 -148.93 -31.07 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CA ASP A 598 " pdb=" C ASP A 598 " pdb=" N ARG A 599 " pdb=" CA ARG A 599 " ideal model delta harmonic sigma weight residual -180.00 -148.96 -31.04 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA ASP C 598 " pdb=" C ASP C 598 " pdb=" N ARG C 599 " pdb=" CA ARG C 599 " ideal model delta harmonic sigma weight residual -180.00 -148.97 -31.03 0 5.00e+00 4.00e-02 3.85e+01 ... (remaining 19593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3979 0.059 - 0.119: 671 0.119 - 0.178: 88 0.178 - 0.237: 6 0.237 - 0.296: 8 Chirality restraints: 4752 Sorted by residual: chirality pdb=" CA PRO B 32 " pdb=" N PRO B 32 " pdb=" C PRO B 32 " pdb=" CB PRO B 32 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA PRO A 32 " pdb=" N PRO A 32 " pdb=" C PRO A 32 " pdb=" CB PRO A 32 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA PRO C 32 " pdb=" N PRO C 32 " pdb=" C PRO C 32 " pdb=" CB PRO C 32 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 4749 not shown) Planarity restraints: 6036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 682 " -0.099 5.00e-02 4.00e+02 1.46e-01 3.41e+01 pdb=" N PRO B 683 " 0.252 5.00e-02 4.00e+02 pdb=" CA PRO B 683 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO B 683 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 682 " 0.099 5.00e-02 4.00e+02 1.46e-01 3.41e+01 pdb=" N PRO C 683 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO C 683 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO C 683 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 682 " 0.099 5.00e-02 4.00e+02 1.46e-01 3.40e+01 pdb=" N PRO A 683 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO A 683 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO A 683 " 0.075 5.00e-02 4.00e+02 ... (remaining 6033 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1284 2.71 - 3.26: 29293 3.26 - 3.81: 56401 3.81 - 4.35: 70145 4.35 - 4.90: 121069 Nonbonded interactions: 278192 Sorted by model distance: nonbonded pdb=" OE2 GLU B 724 " pdb=" OG SER C 874 " model vdw 2.168 3.040 nonbonded pdb=" OE2 GLU A 724 " pdb=" OG SER D 874 " model vdw 2.168 3.040 nonbonded pdb=" OG SER B 874 " pdb=" OE2 GLU C 724 " model vdw 2.168 3.040 nonbonded pdb=" OG SER A 874 " pdb=" OE2 GLU D 724 " model vdw 2.168 3.040 nonbonded pdb=" OD2 ASP C 234 " pdb=" OG SER C 236 " model vdw 2.250 3.040 ... (remaining 278187 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.940 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.004 0.111 33468 Z= 0.173 Angle : 0.775 14.687 45660 Z= 0.420 Chirality : 0.047 0.296 4752 Planarity : 0.008 0.146 6036 Dihedral : 18.141 89.017 12076 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.95 % Allowed : 27.03 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.13), residues: 4036 helix: -1.03 (0.22), residues: 444 sheet: 0.45 (0.14), residues: 1420 loop : -0.86 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 230 TYR 0.034 0.002 TYR C 100 PHE 0.019 0.002 PHE C 231 TRP 0.054 0.002 TRP B 654 HIS 0.013 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00424 (33468) covalent geometry : angle 0.77451 (45660) hydrogen bonds : bond 0.22162 ( 1164) hydrogen bonds : angle 8.10981 ( 3228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 605 time to evaluate : 1.167 Fit side-chains REVERT: A 249 GLU cc_start: 0.5290 (mm-30) cc_final: 0.4867 (tm-30) REVERT: A 277 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6589 (mm-30) REVERT: A 334 GLU cc_start: 0.8134 (pp20) cc_final: 0.7808 (pt0) REVERT: A 395 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.6416 (t-90) REVERT: A 424 ASN cc_start: 0.8393 (p0) cc_final: 0.7952 (p0) REVERT: A 502 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7867 (mpp) REVERT: A 781 ARG cc_start: 0.8156 (ptm160) cc_final: 0.7417 (ptp90) REVERT: A 835 LEU cc_start: 0.8138 (tm) cc_final: 0.7923 (tp) REVERT: A 970 THR cc_start: 0.7702 (m) cc_final: 0.7129 (p) REVERT: A 1022 GLN cc_start: 0.7126 (mm-40) cc_final: 0.6370 (tm-30) REVERT: B 249 GLU cc_start: 0.5258 (mm-30) cc_final: 0.4828 (tm-30) REVERT: B 277 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6482 (mm-30) REVERT: B 334 GLU cc_start: 0.8092 (pp20) cc_final: 0.7762 (pt0) REVERT: B 395 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.6376 (t-90) REVERT: B 424 ASN cc_start: 0.8386 (p0) cc_final: 0.7948 (p0) REVERT: B 487 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6841 (tm-30) REVERT: B 502 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7884 (mpp) REVERT: B 781 ARG cc_start: 0.8177 (ptm160) cc_final: 0.7406 (ptp90) REVERT: B 835 LEU cc_start: 0.8162 (tm) cc_final: 0.7951 (tp) REVERT: B 970 THR cc_start: 0.7712 (m) cc_final: 0.7138 (p) REVERT: B 1022 GLN cc_start: 0.7109 (mm-40) cc_final: 0.6382 (tm-30) REVERT: C 33 PHE cc_start: 0.7931 (m-80) cc_final: 0.7702 (m-10) REVERT: C 249 GLU cc_start: 0.5282 (mm-30) cc_final: 0.4847 (tm-30) REVERT: C 277 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6473 (mm-30) REVERT: C 334 GLU cc_start: 0.8082 (pp20) cc_final: 0.7762 (pt0) REVERT: C 395 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.6338 (t-90) REVERT: C 424 ASN cc_start: 0.8390 (p0) cc_final: 0.7966 (p0) REVERT: C 502 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7873 (mpp) REVERT: C 781 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7406 (ptp90) REVERT: C 835 LEU cc_start: 0.8199 (tm) cc_final: 0.7979 (tp) REVERT: C 970 THR cc_start: 0.7702 (m) cc_final: 0.7109 (p) REVERT: C 1022 GLN cc_start: 0.7093 (mm-40) cc_final: 0.6341 (tm-30) REVERT: D 249 GLU cc_start: 0.5315 (mm-30) cc_final: 0.4890 (tm-30) REVERT: D 277 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6192 (mm-30) REVERT: D 334 GLU cc_start: 0.8131 (pp20) cc_final: 0.7808 (pt0) REVERT: D 388 ARG cc_start: 0.8640 (ttt180) cc_final: 0.8340 (ttt180) REVERT: D 395 HIS cc_start: 0.7734 (OUTLIER) cc_final: 0.6376 (t-90) REVERT: D 424 ASN cc_start: 0.8400 (p0) cc_final: 0.7970 (p0) REVERT: D 476 LYS cc_start: 0.8257 (tptp) cc_final: 0.8052 (mmmt) REVERT: D 487 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6816 (tm-30) REVERT: D 502 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7862 (mpp) REVERT: D 781 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7386 (ptp90) REVERT: D 835 LEU cc_start: 0.8158 (tm) cc_final: 0.7941 (tp) REVERT: D 970 THR cc_start: 0.7698 (m) cc_final: 0.7109 (p) REVERT: D 1022 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6321 (tm-30) outliers start: 102 outliers final: 68 residues processed: 677 average time/residue: 0.1953 time to fit residues: 211.3048 Evaluate side-chains 639 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 558 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 689 GLU Chi-restraints excluded: chain A residue 690 SER Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 1002 SER Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain B residue 525 SER Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 1002 SER Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 246 MET Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 277 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 502 MET Chi-restraints excluded: chain C residue 525 SER Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 689 GLU Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 1002 SER Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 277 GLU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain D residue 472 TYR Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 502 MET Chi-restraints excluded: chain D residue 525 SER Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 689 GLU Chi-restraints excluded: chain D residue 690 SER Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 1002 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 623 GLN A 634 GLN B 147 ASN B 623 GLN B 634 GLN B 653 HIS C 147 ASN C 623 GLN C 634 GLN C 653 HIS D 147 ASN D 623 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.142845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.126108 restraints weight = 46469.431| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.61 r_work: 0.3193 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33468 Z= 0.152 Angle : 0.568 8.447 45660 Z= 0.300 Chirality : 0.045 0.177 4752 Planarity : 0.006 0.090 6036 Dihedral : 6.975 58.986 4571 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.89 % Allowed : 23.03 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.13), residues: 4036 helix: -0.39 (0.22), residues: 492 sheet: 0.82 (0.14), residues: 1388 loop : -0.64 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 230 TYR 0.017 0.002 TYR D 100 PHE 0.010 0.001 PHE D 150 TRP 0.021 0.001 TRP D 654 HIS 0.004 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00347 (33468) covalent geometry : angle 0.56760 (45660) hydrogen bonds : bond 0.04100 ( 1164) hydrogen bonds : angle 5.64710 ( 3228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 685 time to evaluate : 1.196 Fit side-chains REVERT: A 67 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 177 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8046 (tp) REVERT: A 202 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8196 (pmm) REVERT: A 264 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.7947 (pm20) REVERT: A 336 ARG cc_start: 0.7958 (ptt-90) cc_final: 0.7492 (ptt-90) REVERT: A 338 GLU cc_start: 0.7856 (pt0) cc_final: 0.7131 (pt0) REVERT: A 781 ARG cc_start: 0.8319 (ptm160) cc_final: 0.7505 (ptp90) REVERT: A 852 SER cc_start: 0.9018 (p) cc_final: 0.8779 (p) REVERT: A 863 GLN cc_start: 0.7447 (OUTLIER) cc_final: 0.7115 (mt0) REVERT: A 969 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: A 970 THR cc_start: 0.7881 (m) cc_final: 0.7380 (p) REVERT: A 980 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6703 (mm-30) REVERT: A 1022 GLN cc_start: 0.7171 (mm-40) cc_final: 0.6641 (tm-30) REVERT: B 67 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7955 (mm-30) REVERT: B 177 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8071 (tp) REVERT: B 202 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8134 (pmm) REVERT: B 264 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.7938 (pm20) REVERT: B 334 GLU cc_start: 0.8198 (pp20) cc_final: 0.7894 (pt0) REVERT: B 336 ARG cc_start: 0.7950 (ptt-90) cc_final: 0.7473 (ptt-90) REVERT: B 338 GLU cc_start: 0.7829 (pt0) cc_final: 0.7114 (pt0) REVERT: B 781 ARG cc_start: 0.8259 (ptm160) cc_final: 0.7362 (ptp90) REVERT: B 863 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7105 (mt0) REVERT: B 969 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: B 970 THR cc_start: 0.8011 (m) cc_final: 0.7457 (p) REVERT: B 980 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6568 (mm-30) REVERT: B 1022 GLN cc_start: 0.7289 (mm-40) cc_final: 0.6667 (tm-30) REVERT: C 67 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7860 (mm-30) REVERT: C 177 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8052 (tp) REVERT: C 202 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8156 (pmm) REVERT: C 264 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: C 336 ARG cc_start: 0.7942 (ptt-90) cc_final: 0.7456 (ptt-90) REVERT: C 338 GLU cc_start: 0.7817 (pt0) cc_final: 0.7076 (pt0) REVERT: C 781 ARG cc_start: 0.8290 (ptm160) cc_final: 0.7368 (ptp90) REVERT: C 863 GLN cc_start: 0.7379 (OUTLIER) cc_final: 0.7045 (mt0) REVERT: C 969 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: C 970 THR cc_start: 0.7910 (m) cc_final: 0.7410 (p) REVERT: C 980 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6715 (mm-30) REVERT: C 1022 GLN cc_start: 0.7211 (mm-40) cc_final: 0.6709 (tm-30) REVERT: D 67 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7864 (mm-30) REVERT: D 177 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8058 (tp) REVERT: D 202 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8329 (pmm) REVERT: D 264 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: D 336 ARG cc_start: 0.7963 (ptt-90) cc_final: 0.7507 (ptt-90) REVERT: D 338 GLU cc_start: 0.7873 (pt0) cc_final: 0.7172 (pt0) REVERT: D 617 LEU cc_start: 0.9505 (tp) cc_final: 0.9301 (tp) REVERT: D 781 ARG cc_start: 0.8316 (ptm160) cc_final: 0.7466 (ptp90) REVERT: D 852 SER cc_start: 0.9003 (p) cc_final: 0.8738 (p) REVERT: D 863 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.7006 (mt0) REVERT: D 969 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: D 970 THR cc_start: 0.7908 (m) cc_final: 0.7394 (p) REVERT: D 980 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6665 (mm-30) REVERT: D 1022 GLN cc_start: 0.7212 (mm-40) cc_final: 0.6699 (tm-30) outliers start: 169 outliers final: 80 residues processed: 785 average time/residue: 0.1901 time to fit residues: 235.0764 Evaluate side-chains 743 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 643 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 934 GLU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 472 TYR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 765 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 934 GLU Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain B residue 991 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 934 GLU Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 991 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 934 GLU Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 991 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 400 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 178 optimal weight: 8.9990 chunk 362 optimal weight: 9.9990 chunk 64 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 387 optimal weight: 10.0000 chunk 172 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 163 GLN A 221 GLN A 370 GLN A 604 ASN A 713 HIS B 147 ASN B 163 GLN B 221 GLN B 604 ASN B 713 HIS C 147 ASN C 163 GLN C 221 GLN C 370 GLN C 604 ASN C 713 HIS C 949 HIS D 147 ASN D 163 GLN D 221 GLN D 370 GLN D 604 ASN D 634 GLN D 713 HIS D 949 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.132661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.116297 restraints weight = 47355.834| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.58 r_work: 0.3058 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.046 33468 Z= 0.377 Angle : 0.734 7.018 45660 Z= 0.389 Chirality : 0.052 0.184 4752 Planarity : 0.007 0.079 6036 Dihedral : 6.454 55.153 4466 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 6.60 % Allowed : 21.53 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.13), residues: 4036 helix: -0.74 (0.22), residues: 488 sheet: 0.69 (0.14), residues: 1400 loop : -0.78 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 599 TYR 0.023 0.003 TYR A1016 PHE 0.024 0.003 PHE C 274 TRP 0.021 0.002 TRP B 720 HIS 0.011 0.002 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00873 (33468) covalent geometry : angle 0.73394 (45660) hydrogen bonds : bond 0.04894 ( 1164) hydrogen bonds : angle 5.58372 ( 3228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 667 time to evaluate : 0.930 Fit side-chains REVERT: A 46 ARG cc_start: 0.7047 (mtt90) cc_final: 0.6714 (mtt90) REVERT: A 131 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7231 (mm-30) REVERT: A 177 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8152 (tp) REVERT: A 202 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8187 (pmm) REVERT: A 395 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.6525 (t70) REVERT: A 423 MET cc_start: 0.8571 (ttm) cc_final: 0.8274 (ttm) REVERT: A 442 ARG cc_start: 0.9149 (mtp-110) cc_final: 0.8929 (mtp85) REVERT: A 502 MET cc_start: 0.8567 (mtp) cc_final: 0.8338 (mtt) REVERT: A 781 ARG cc_start: 0.8369 (ptm160) cc_final: 0.7490 (ptp90) REVERT: A 852 SER cc_start: 0.8965 (p) cc_final: 0.8757 (p) REVERT: A 969 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: A 980 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7070 (mm-30) REVERT: A 1022 GLN cc_start: 0.7374 (mm-40) cc_final: 0.6589 (tm-30) REVERT: B 46 ARG cc_start: 0.7029 (mtt90) cc_final: 0.6701 (mtt90) REVERT: B 67 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8341 (mm-30) REVERT: B 177 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8160 (tp) REVERT: B 202 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8156 (pmm) REVERT: B 334 GLU cc_start: 0.8470 (pp20) cc_final: 0.8169 (pt0) REVERT: B 336 ARG cc_start: 0.8165 (ptt-90) cc_final: 0.7640 (ptt-90) REVERT: B 338 GLU cc_start: 0.8466 (pt0) cc_final: 0.7604 (pt0) REVERT: B 395 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.6531 (t70) REVERT: B 423 MET cc_start: 0.8602 (ttm) cc_final: 0.8308 (ttm) REVERT: B 442 ARG cc_start: 0.9153 (mtp-110) cc_final: 0.8931 (mtp85) REVERT: B 502 MET cc_start: 0.8579 (mtp) cc_final: 0.8334 (mtt) REVERT: B 781 ARG cc_start: 0.8322 (ptm160) cc_final: 0.7445 (ptp90) REVERT: B 903 GLN cc_start: 0.8601 (mm-40) cc_final: 0.8246 (mt0) REVERT: B 1022 GLN cc_start: 0.7433 (mm-40) cc_final: 0.6614 (tm-30) REVERT: C 46 ARG cc_start: 0.7036 (mtt90) cc_final: 0.6707 (mtt90) REVERT: C 202 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8158 (pmm) REVERT: C 338 GLU cc_start: 0.8426 (pt0) cc_final: 0.8224 (pt0) REVERT: C 395 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.6492 (t70) REVERT: C 423 MET cc_start: 0.8577 (ttm) cc_final: 0.8277 (ttm) REVERT: C 442 ARG cc_start: 0.9160 (mtp-110) cc_final: 0.8942 (mtp85) REVERT: C 502 MET cc_start: 0.8600 (mtp) cc_final: 0.8359 (mtt) REVERT: C 781 ARG cc_start: 0.8329 (ptm160) cc_final: 0.7412 (ptp90) REVERT: C 852 SER cc_start: 0.8975 (p) cc_final: 0.8770 (p) REVERT: C 969 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8054 (mp0) REVERT: C 980 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7082 (mm-30) REVERT: C 1022 GLN cc_start: 0.7455 (mm-40) cc_final: 0.6535 (tm-30) REVERT: D 131 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7256 (mm-30) REVERT: D 202 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8188 (pmm) REVERT: D 395 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.6518 (t70) REVERT: D 423 MET cc_start: 0.8582 (ttm) cc_final: 0.8276 (ttm) REVERT: D 442 ARG cc_start: 0.9157 (mtp-110) cc_final: 0.8936 (mtp85) REVERT: D 502 MET cc_start: 0.8593 (mtp) cc_final: 0.8354 (mtt) REVERT: D 781 ARG cc_start: 0.8393 (ptm160) cc_final: 0.7474 (ptp90) REVERT: D 852 SER cc_start: 0.8986 (p) cc_final: 0.8780 (p) REVERT: D 969 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: D 980 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7158 (mm-30) REVERT: D 1022 GLN cc_start: 0.7460 (mm-40) cc_final: 0.6529 (tm-30) outliers start: 228 outliers final: 149 residues processed: 802 average time/residue: 0.1971 time to fit residues: 247.6865 Evaluate side-chains 788 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 626 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 952 ARG Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 545 SER Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 838 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 952 ARG Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 991 MET Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 147 ASN Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 545 SER Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 838 THR Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 952 ARG Chi-restraints excluded: chain C residue 960 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 991 MET Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 545 SER Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 898 LEU Chi-restraints excluded: chain D residue 952 ARG Chi-restraints excluded: chain D residue 960 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 991 MET Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 345 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 393 optimal weight: 3.9990 chunk 197 optimal weight: 10.0000 chunk 390 optimal weight: 0.0270 overall best weight: 2.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 370 GLN A 573 GLN A 604 ASN A 634 GLN A 949 HIS A 990 HIS B 147 ASN B 573 GLN B 604 ASN B 634 GLN B 949 HIS C 147 ASN C 370 GLN C 573 GLN C 604 ASN C 634 GLN D 147 ASN D 370 GLN D 573 GLN D 604 ASN D 634 GLN D 990 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.136373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.120120 restraints weight = 46685.824| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.59 r_work: 0.3107 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33468 Z= 0.138 Angle : 0.554 6.958 45660 Z= 0.292 Chirality : 0.045 0.174 4752 Planarity : 0.005 0.066 6036 Dihedral : 5.943 57.017 4460 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.30 % Allowed : 22.40 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.13), residues: 4036 helix: -0.32 (0.23), residues: 488 sheet: 0.79 (0.14), residues: 1364 loop : -0.73 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 599 TYR 0.015 0.002 TYR A 100 PHE 0.013 0.001 PHE C 274 TRP 0.025 0.001 TRP B 553 HIS 0.003 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00315 (33468) covalent geometry : angle 0.55351 (45660) hydrogen bonds : bond 0.03690 ( 1164) hydrogen bonds : angle 5.19120 ( 3228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 690 time to evaluate : 0.951 Fit side-chains REVERT: A 46 ARG cc_start: 0.7099 (mtt90) cc_final: 0.6774 (mtt90) REVERT: A 131 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7370 (mm-30) REVERT: A 177 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7942 (tp) REVERT: A 202 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8178 (pmm) REVERT: A 264 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: A 287 ASP cc_start: 0.8379 (p0) cc_final: 0.7885 (p0) REVERT: A 502 MET cc_start: 0.8475 (mtp) cc_final: 0.8234 (mtm) REVERT: A 781 ARG cc_start: 0.8169 (ptm160) cc_final: 0.7363 (ptp90) REVERT: A 852 SER cc_start: 0.8931 (p) cc_final: 0.8718 (p) REVERT: A 968 MET cc_start: 0.8023 (mtp) cc_final: 0.7652 (mtp) REVERT: A 969 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: A 980 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6920 (mm-30) REVERT: A 1013 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6681 (mtm110) REVERT: A 1022 GLN cc_start: 0.7390 (mm-40) cc_final: 0.6580 (tm-30) REVERT: B 46 ARG cc_start: 0.7043 (mtt90) cc_final: 0.6724 (mtt90) REVERT: B 177 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7953 (tp) REVERT: B 202 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8155 (pmm) REVERT: B 264 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7746 (pm20) REVERT: B 287 ASP cc_start: 0.8404 (p0) cc_final: 0.7894 (p0) REVERT: B 502 MET cc_start: 0.8372 (mtp) cc_final: 0.8048 (mtm) REVERT: B 781 ARG cc_start: 0.8249 (ptm160) cc_final: 0.7404 (ptp90) REVERT: B 965 GLN cc_start: 0.7332 (tp40) cc_final: 0.6468 (tp40) REVERT: B 969 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: B 980 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6921 (mm-30) REVERT: B 1013 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6663 (mtm110) REVERT: B 1022 GLN cc_start: 0.7397 (mm-40) cc_final: 0.6589 (tm-30) REVERT: C 46 ARG cc_start: 0.7001 (mtt90) cc_final: 0.6684 (mtt90) REVERT: C 202 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8161 (pmm) REVERT: C 264 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7796 (pm20) REVERT: C 287 ASP cc_start: 0.8391 (p0) cc_final: 0.7897 (p0) REVERT: C 502 MET cc_start: 0.8418 (mtp) cc_final: 0.8088 (mtm) REVERT: C 781 ARG cc_start: 0.8228 (ptm160) cc_final: 0.7376 (ptp90) REVERT: C 863 GLN cc_start: 0.7488 (OUTLIER) cc_final: 0.7185 (mt0) REVERT: C 968 MET cc_start: 0.7997 (mtp) cc_final: 0.7625 (mtp) REVERT: C 969 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: C 980 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6898 (mm-30) REVERT: C 1013 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6687 (mtm110) REVERT: C 1022 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6597 (tm-30) REVERT: D 131 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7352 (mm-30) REVERT: D 202 MET cc_start: 0.8933 (OUTLIER) cc_final: 0.8166 (pmm) REVERT: D 264 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7750 (pm20) REVERT: D 287 ASP cc_start: 0.8368 (p0) cc_final: 0.7883 (p0) REVERT: D 502 MET cc_start: 0.8398 (mtp) cc_final: 0.8077 (mtm) REVERT: D 599 ARG cc_start: 0.8264 (pmm-80) cc_final: 0.8034 (mtm180) REVERT: D 781 ARG cc_start: 0.8203 (ptm160) cc_final: 0.7374 (ptp90) REVERT: D 852 SER cc_start: 0.8951 (p) cc_final: 0.8737 (p) REVERT: D 968 MET cc_start: 0.7989 (mtp) cc_final: 0.7619 (mtp) REVERT: D 969 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: D 980 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6976 (mm-30) REVERT: D 1013 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6684 (mtm110) REVERT: D 1022 GLN cc_start: 0.7439 (mm-40) cc_final: 0.6627 (tm-30) outliers start: 183 outliers final: 100 residues processed: 806 average time/residue: 0.1948 time to fit residues: 247.8210 Evaluate side-chains 768 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 649 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 102 ASN Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain B residue 1013 ARG Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 863 GLN Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 960 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 1013 ARG Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 960 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1013 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 177 optimal weight: 9.9990 chunk 307 optimal weight: 9.9990 chunk 358 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 132 optimal weight: 0.0470 chunk 210 optimal weight: 7.9990 chunk 312 optimal weight: 10.0000 chunk 191 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 241 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 overall best weight: 3.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 719 GLN A 949 HIS B 102 ASN B 719 GLN B 949 HIS C 102 ASN C 370 GLN C 719 GLN C 949 HIS D 370 GLN D 719 GLN D 949 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.135391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.119128 restraints weight = 46850.172| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.60 r_work: 0.3093 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 33468 Z= 0.194 Angle : 0.579 8.488 45660 Z= 0.304 Chirality : 0.046 0.169 4752 Planarity : 0.005 0.069 6036 Dihedral : 5.710 47.494 4456 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.05 % Allowed : 20.25 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.13), residues: 4036 helix: -0.27 (0.23), residues: 488 sheet: 0.74 (0.14), residues: 1372 loop : -0.75 (0.14), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 288 TYR 0.028 0.002 TYR C 100 PHE 0.013 0.002 PHE B 274 TRP 0.024 0.002 TRP C 553 HIS 0.005 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00451 (33468) covalent geometry : angle 0.57893 (45660) hydrogen bonds : bond 0.03750 ( 1164) hydrogen bonds : angle 5.11082 ( 3228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 692 time to evaluate : 1.261 Fit side-chains REVERT: A 131 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 177 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.8001 (tp) REVERT: A 202 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8115 (pmm) REVERT: A 250 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6712 (tt) REVERT: A 287 ASP cc_start: 0.8401 (p0) cc_final: 0.7773 (p0) REVERT: A 502 MET cc_start: 0.8528 (mtp) cc_final: 0.8190 (mtt) REVERT: A 781 ARG cc_start: 0.8103 (ptm160) cc_final: 0.7287 (ptp90) REVERT: A 852 SER cc_start: 0.8898 (p) cc_final: 0.8691 (p) REVERT: A 952 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8220 (ttp-170) REVERT: A 969 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: A 987 ASP cc_start: 0.8465 (m-30) cc_final: 0.8192 (m-30) REVERT: A 1013 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6970 (mtm110) REVERT: A 1022 GLN cc_start: 0.7436 (mm-40) cc_final: 0.6686 (tm-30) REVERT: B 26 ARG cc_start: 0.8436 (ttp-170) cc_final: 0.7967 (ttm170) REVERT: B 177 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.8009 (tp) REVERT: B 202 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8098 (pmm) REVERT: B 250 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6612 (tt) REVERT: B 287 ASP cc_start: 0.8443 (p0) cc_final: 0.7828 (p0) REVERT: B 336 ARG cc_start: 0.8067 (ptt-90) cc_final: 0.7854 (ptt-90) REVERT: B 502 MET cc_start: 0.8454 (mtp) cc_final: 0.8125 (mtm) REVERT: B 781 ARG cc_start: 0.8154 (ptm160) cc_final: 0.7328 (ptp90) REVERT: B 969 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: B 1013 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6948 (mtm110) REVERT: B 1022 GLN cc_start: 0.7386 (mm-40) cc_final: 0.6676 (tm-30) REVERT: C 202 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8083 (pmm) REVERT: C 250 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6696 (tt) REVERT: C 287 ASP cc_start: 0.8426 (p0) cc_final: 0.7800 (p0) REVERT: C 502 MET cc_start: 0.8492 (mtp) cc_final: 0.8159 (mtm) REVERT: C 654 TRP cc_start: 0.7486 (p90) cc_final: 0.7260 (p90) REVERT: C 740 LEU cc_start: 0.8236 (tp) cc_final: 0.7994 (tp) REVERT: C 781 ARG cc_start: 0.8134 (ptm160) cc_final: 0.7291 (ptp90) REVERT: C 829 THR cc_start: 0.7672 (t) cc_final: 0.7158 (m) REVERT: C 969 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: C 1013 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6955 (mtm110) REVERT: C 1022 GLN cc_start: 0.7443 (mm-40) cc_final: 0.6687 (tm-30) REVERT: D 131 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7530 (mm-30) REVERT: D 202 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8092 (pmm) REVERT: D 250 LEU cc_start: 0.7050 (OUTLIER) cc_final: 0.6328 (tt) REVERT: D 287 ASP cc_start: 0.8398 (p0) cc_final: 0.7818 (p0) REVERT: D 484 VAL cc_start: 0.9386 (OUTLIER) cc_final: 0.9126 (t) REVERT: D 502 MET cc_start: 0.8469 (mtp) cc_final: 0.8136 (mtm) REVERT: D 781 ARG cc_start: 0.8116 (ptm160) cc_final: 0.7298 (ptp90) REVERT: D 969 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: D 980 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6903 (mm-30) REVERT: D 987 ASP cc_start: 0.8446 (m-30) cc_final: 0.8175 (m-30) REVERT: D 1013 ARG cc_start: 0.7394 (OUTLIER) cc_final: 0.6947 (mtm110) REVERT: D 1022 GLN cc_start: 0.7451 (mm-40) cc_final: 0.6683 (tm-30) outliers start: 209 outliers final: 154 residues processed: 814 average time/residue: 0.2299 time to fit residues: 293.4599 Evaluate side-chains 834 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 660 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 952 ARG Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain B residue 991 MET Chi-restraints excluded: chain B residue 1013 ARG Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 677 LYS Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 960 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 1013 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 706 THR Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 960 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1013 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 127 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 318 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 283 optimal weight: 8.9990 chunk 383 optimal weight: 3.9990 chunk 167 optimal weight: 0.8980 chunk 351 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 372 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 395 HIS A 573 GLN A 949 HIS A 964 GLN B 395 HIS B 573 GLN B 949 HIS C 370 GLN C 395 HIS C 573 GLN C 863 GLN C 949 HIS D 370 GLN D 395 HIS D 573 GLN D 949 HIS D 964 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.136056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.119965 restraints weight = 46776.212| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.60 r_work: 0.3102 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33468 Z= 0.170 Angle : 0.563 8.786 45660 Z= 0.294 Chirality : 0.045 0.171 4752 Planarity : 0.005 0.059 6036 Dihedral : 5.610 46.967 4456 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.96 % Allowed : 20.57 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.13), residues: 4036 helix: -0.23 (0.23), residues: 488 sheet: 0.69 (0.14), residues: 1372 loop : -0.68 (0.14), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 952 TYR 0.022 0.002 TYR D 100 PHE 0.011 0.001 PHE B 274 TRP 0.025 0.001 TRP C 553 HIS 0.004 0.001 HIS D 151 Details of bonding type rmsd covalent geometry : bond 0.00394 (33468) covalent geometry : angle 0.56325 (45660) hydrogen bonds : bond 0.03599 ( 1164) hydrogen bonds : angle 5.03350 ( 3228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 701 time to evaluate : 1.252 Fit side-chains REVERT: A 131 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7442 (mm-30) REVERT: A 177 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7982 (tp) REVERT: A 202 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8093 (pmm) REVERT: A 250 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6948 (tt) REVERT: A 264 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8055 (pm20) REVERT: A 287 ASP cc_start: 0.8403 (p0) cc_final: 0.7786 (p0) REVERT: A 438 GLU cc_start: 0.8081 (pp20) cc_final: 0.7649 (pp20) REVERT: A 502 MET cc_start: 0.8591 (mtp) cc_final: 0.8168 (mtm) REVERT: A 781 ARG cc_start: 0.8062 (ptm160) cc_final: 0.7232 (ptp90) REVERT: A 852 SER cc_start: 0.8905 (p) cc_final: 0.8698 (p) REVERT: A 969 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: A 980 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6955 (mm-30) REVERT: A 987 ASP cc_start: 0.8441 (m-30) cc_final: 0.8196 (m-30) REVERT: A 1013 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6833 (mtm110) REVERT: A 1022 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6681 (tm-30) REVERT: B 177 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.8006 (tp) REVERT: B 202 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8059 (pmm) REVERT: B 250 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6639 (tt) REVERT: B 264 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8052 (pm20) REVERT: B 287 ASP cc_start: 0.8431 (p0) cc_final: 0.7863 (p0) REVERT: B 336 ARG cc_start: 0.8061 (ptt-90) cc_final: 0.7831 (ptt-90) REVERT: B 438 GLU cc_start: 0.8070 (pp20) cc_final: 0.7645 (pp20) REVERT: B 502 MET cc_start: 0.8500 (mtp) cc_final: 0.8113 (mtm) REVERT: B 654 TRP cc_start: 0.7505 (p90) cc_final: 0.7301 (p90) REVERT: B 781 ARG cc_start: 0.8187 (ptm160) cc_final: 0.7373 (ptp90) REVERT: B 969 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: B 980 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6932 (mm-30) REVERT: B 1013 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6766 (mtm110) REVERT: B 1022 GLN cc_start: 0.7360 (mm-40) cc_final: 0.6690 (tm-30) REVERT: C 202 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8069 (pmm) REVERT: C 250 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6954 (tt) REVERT: C 264 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8067 (pm20) REVERT: C 287 ASP cc_start: 0.8423 (p0) cc_final: 0.7815 (p0) REVERT: C 438 GLU cc_start: 0.8096 (pp20) cc_final: 0.7664 (pp20) REVERT: C 484 VAL cc_start: 0.9418 (OUTLIER) cc_final: 0.9147 (t) REVERT: C 502 MET cc_start: 0.8506 (mtp) cc_final: 0.8108 (mtm) REVERT: C 740 LEU cc_start: 0.8240 (tp) cc_final: 0.8005 (tp) REVERT: C 781 ARG cc_start: 0.8119 (ptm160) cc_final: 0.7266 (ptp90) REVERT: C 829 THR cc_start: 0.7513 (t) cc_final: 0.7042 (m) REVERT: C 969 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: C 980 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6848 (mm-30) REVERT: C 1013 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6822 (mtm110) REVERT: C 1022 GLN cc_start: 0.7427 (mm-40) cc_final: 0.6701 (tm-30) REVERT: D 131 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7473 (mm-30) REVERT: D 202 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8065 (pmm) REVERT: D 250 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6460 (tt) REVERT: D 264 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8115 (pm20) REVERT: D 287 ASP cc_start: 0.8416 (p0) cc_final: 0.7844 (p0) REVERT: D 438 GLU cc_start: 0.8067 (pp20) cc_final: 0.7635 (pp20) REVERT: D 484 VAL cc_start: 0.9381 (OUTLIER) cc_final: 0.9134 (t) REVERT: D 502 MET cc_start: 0.8503 (mtp) cc_final: 0.8118 (mtm) REVERT: D 781 ARG cc_start: 0.8154 (ptm160) cc_final: 0.7348 (ptp90) REVERT: D 969 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: D 987 ASP cc_start: 0.8405 (m-30) cc_final: 0.8162 (m-30) REVERT: D 1013 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6862 (mtm110) REVERT: D 1022 GLN cc_start: 0.7427 (mm-40) cc_final: 0.6698 (tm-30) outliers start: 206 outliers final: 151 residues processed: 821 average time/residue: 0.2340 time to fit residues: 299.7030 Evaluate side-chains 847 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 672 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 964 GLN Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain B residue 1013 ARG Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 677 LYS Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 960 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 1013 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 960 SER Chi-restraints excluded: chain D residue 964 GLN Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1013 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 111 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 385 optimal weight: 20.0000 chunk 358 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 340 optimal weight: 8.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS A 573 GLN A 604 ASN A 949 HIS B 102 ASN B 226 HIS B 395 HIS B 573 GLN B 604 ASN B 949 HIS C 102 ASN ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 395 HIS C 573 GLN C 604 ASN C 949 HIS D 102 ASN D 370 GLN D 395 HIS D 573 GLN D 604 ASN D 949 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.135027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.118871 restraints weight = 46861.242| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.61 r_work: 0.3087 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 33468 Z= 0.215 Angle : 0.597 8.765 45660 Z= 0.312 Chirality : 0.046 0.175 4752 Planarity : 0.005 0.058 6036 Dihedral : 5.656 45.008 4452 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 6.31 % Allowed : 20.31 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.13), residues: 4036 helix: -0.29 (0.23), residues: 488 sheet: 0.60 (0.14), residues: 1372 loop : -0.71 (0.14), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 952 TYR 0.019 0.002 TYR D 100 PHE 0.012 0.002 PHE A 274 TRP 0.036 0.002 TRP C 654 HIS 0.006 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00502 (33468) covalent geometry : angle 0.59709 (45660) hydrogen bonds : bond 0.03776 ( 1164) hydrogen bonds : angle 5.09488 ( 3228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 691 time to evaluate : 1.352 Fit side-chains REVERT: A 26 ARG cc_start: 0.8491 (ttp-170) cc_final: 0.7945 (ttm170) REVERT: A 131 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7450 (mm-30) REVERT: A 177 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.8000 (tp) REVERT: A 202 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8094 (pmm) REVERT: A 250 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6999 (tt) REVERT: A 287 ASP cc_start: 0.8434 (p0) cc_final: 0.7783 (p0) REVERT: A 438 GLU cc_start: 0.8097 (pp20) cc_final: 0.7701 (pp20) REVERT: A 484 VAL cc_start: 0.9404 (OUTLIER) cc_final: 0.9162 (t) REVERT: A 487 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7509 (tm-30) REVERT: A 502 MET cc_start: 0.8661 (mtp) cc_final: 0.8283 (mtt) REVERT: A 781 ARG cc_start: 0.8156 (ptm160) cc_final: 0.7343 (ptp90) REVERT: A 828 ASP cc_start: 0.7052 (t0) cc_final: 0.6757 (t0) REVERT: A 852 SER cc_start: 0.8911 (p) cc_final: 0.8697 (p) REVERT: A 969 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: A 987 ASP cc_start: 0.8486 (m-30) cc_final: 0.8234 (m-30) REVERT: A 1013 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7008 (mtm110) REVERT: A 1022 GLN cc_start: 0.7457 (mm-40) cc_final: 0.6651 (tm-30) REVERT: B 26 ARG cc_start: 0.8489 (ttp-170) cc_final: 0.7946 (ttm170) REVERT: B 177 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.8006 (tp) REVERT: B 202 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8069 (pmm) REVERT: B 250 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6921 (tt) REVERT: B 287 ASP cc_start: 0.8480 (p0) cc_final: 0.7851 (p0) REVERT: B 336 ARG cc_start: 0.8067 (ptt-90) cc_final: 0.7534 (ptt-90) REVERT: B 338 GLU cc_start: 0.8339 (pt0) cc_final: 0.7571 (pt0) REVERT: B 438 GLU cc_start: 0.8113 (pp20) cc_final: 0.7726 (pp20) REVERT: B 484 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.9157 (t) REVERT: B 502 MET cc_start: 0.8512 (mtp) cc_final: 0.8164 (mtm) REVERT: B 781 ARG cc_start: 0.8188 (ptm160) cc_final: 0.7376 (ptp90) REVERT: B 969 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: B 1013 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6982 (mtm110) REVERT: B 1022 GLN cc_start: 0.7487 (mm-40) cc_final: 0.6644 (tm-30) REVERT: C 26 ARG cc_start: 0.8488 (ttp-170) cc_final: 0.7937 (ttm170) REVERT: C 202 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8052 (pmm) REVERT: C 250 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7012 (tt) REVERT: C 287 ASP cc_start: 0.8448 (p0) cc_final: 0.7794 (p0) REVERT: C 323 ILE cc_start: 0.7328 (OUTLIER) cc_final: 0.6906 (mp) REVERT: C 438 GLU cc_start: 0.8121 (pp20) cc_final: 0.7731 (pp20) REVERT: C 502 MET cc_start: 0.8608 (mtp) cc_final: 0.8242 (mtm) REVERT: C 740 LEU cc_start: 0.8311 (tp) cc_final: 0.8073 (tp) REVERT: C 781 ARG cc_start: 0.8192 (ptm160) cc_final: 0.7357 (ptp90) REVERT: C 829 THR cc_start: 0.7665 (t) cc_final: 0.7306 (m) REVERT: C 969 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: C 980 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6841 (mm-30) REVERT: C 1013 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6986 (mtm110) REVERT: C 1022 GLN cc_start: 0.7486 (mm-40) cc_final: 0.6656 (tm-30) REVERT: D 26 ARG cc_start: 0.8507 (ttp-170) cc_final: 0.7981 (ttm170) REVERT: D 131 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7456 (mm-30) REVERT: D 202 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8062 (pmm) REVERT: D 250 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6566 (tt) REVERT: D 287 ASP cc_start: 0.8429 (p0) cc_final: 0.7802 (p0) REVERT: D 502 MET cc_start: 0.8619 (mtp) cc_final: 0.8255 (mtm) REVERT: D 781 ARG cc_start: 0.8163 (ptm160) cc_final: 0.7353 (ptp90) REVERT: D 969 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: D 980 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6686 (mm-30) REVERT: D 987 ASP cc_start: 0.8454 (m-30) cc_final: 0.8199 (m-30) REVERT: D 1013 ARG cc_start: 0.7455 (OUTLIER) cc_final: 0.6996 (mtm110) REVERT: D 1022 GLN cc_start: 0.7417 (mm-40) cc_final: 0.6644 (tm-30) outliers start: 218 outliers final: 160 residues processed: 817 average time/residue: 0.2308 time to fit residues: 295.9632 Evaluate side-chains 859 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 678 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain B residue 991 MET Chi-restraints excluded: chain B residue 1013 ARG Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 960 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 1013 ARG Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 960 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1013 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 98 optimal weight: 9.9990 chunk 382 optimal weight: 7.9990 chunk 326 optimal weight: 9.9990 chunk 378 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 317 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 228 optimal weight: 0.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS A 573 GLN A 604 ASN A 949 HIS ** B 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 365 GLN B 395 HIS B 573 GLN B 604 ASN ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 395 HIS C 573 GLN C 604 ASN C 949 HIS D 102 ASN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN D 395 HIS D 573 GLN D 604 ASN D 949 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.135051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.119010 restraints weight = 46989.338| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.59 r_work: 0.3096 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 33468 Z= 0.201 Angle : 0.593 8.140 45660 Z= 0.309 Chirality : 0.046 0.178 4752 Planarity : 0.005 0.056 6036 Dihedral : 5.656 45.483 4452 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.31 % Allowed : 20.49 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.13), residues: 4036 helix: -0.28 (0.23), residues: 488 sheet: 0.55 (0.14), residues: 1372 loop : -0.73 (0.14), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 952 TYR 0.018 0.002 TYR D 100 PHE 0.010 0.001 PHE C 274 TRP 0.039 0.002 TRP B 654 HIS 0.005 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00468 (33468) covalent geometry : angle 0.59324 (45660) hydrogen bonds : bond 0.03713 ( 1164) hydrogen bonds : angle 5.09151 ( 3228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 694 time to evaluate : 1.450 Fit side-chains REVERT: A 26 ARG cc_start: 0.8486 (ttp-170) cc_final: 0.7948 (ttm170) REVERT: A 131 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7446 (mm-30) REVERT: A 177 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7983 (tp) REVERT: A 202 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8101 (pmm) REVERT: A 250 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7015 (tt) REVERT: A 277 GLU cc_start: 0.7298 (tp30) cc_final: 0.7041 (tp30) REVERT: A 287 ASP cc_start: 0.8433 (p0) cc_final: 0.7776 (p0) REVERT: A 420 MET cc_start: 0.8891 (mmt) cc_final: 0.8612 (mmt) REVERT: A 438 GLU cc_start: 0.8092 (pp20) cc_final: 0.7681 (pp20) REVERT: A 484 VAL cc_start: 0.9411 (OUTLIER) cc_final: 0.9157 (t) REVERT: A 502 MET cc_start: 0.8607 (mtp) cc_final: 0.8269 (mtm) REVERT: A 781 ARG cc_start: 0.8155 (ptm160) cc_final: 0.7335 (ptp90) REVERT: A 828 ASP cc_start: 0.7006 (t0) cc_final: 0.6590 (t0) REVERT: A 852 SER cc_start: 0.8900 (p) cc_final: 0.8694 (p) REVERT: A 969 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: A 980 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6664 (mm-30) REVERT: A 987 ASP cc_start: 0.8479 (m-30) cc_final: 0.8203 (m-30) REVERT: A 1013 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6995 (mtm110) REVERT: A 1022 GLN cc_start: 0.7455 (mm-40) cc_final: 0.6639 (tm-30) REVERT: B 26 ARG cc_start: 0.8489 (ttp-170) cc_final: 0.7950 (ttm170) REVERT: B 177 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.8004 (tp) REVERT: B 202 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8083 (pmm) REVERT: B 250 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6929 (tt) REVERT: B 287 ASP cc_start: 0.8478 (p0) cc_final: 0.7850 (p0) REVERT: B 336 ARG cc_start: 0.8071 (ptt-90) cc_final: 0.7550 (ptt-90) REVERT: B 338 GLU cc_start: 0.8313 (pt0) cc_final: 0.7558 (pt0) REVERT: B 420 MET cc_start: 0.8872 (mmt) cc_final: 0.8585 (mmt) REVERT: B 438 GLU cc_start: 0.8097 (pp20) cc_final: 0.7685 (pp20) REVERT: B 484 VAL cc_start: 0.9404 (OUTLIER) cc_final: 0.9148 (t) REVERT: B 502 MET cc_start: 0.8736 (mtp) cc_final: 0.8396 (mtm) REVERT: B 781 ARG cc_start: 0.8217 (ptm160) cc_final: 0.7368 (ptp90) REVERT: B 828 ASP cc_start: 0.6738 (t0) cc_final: 0.6400 (t0) REVERT: B 969 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: B 1013 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.6954 (mtm110) REVERT: B 1022 GLN cc_start: 0.7484 (mm-40) cc_final: 0.6632 (tm-30) REVERT: C 26 ARG cc_start: 0.8488 (ttp-170) cc_final: 0.7940 (ttm170) REVERT: C 202 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8070 (pmm) REVERT: C 250 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7033 (tt) REVERT: C 287 ASP cc_start: 0.8454 (p0) cc_final: 0.7794 (p0) REVERT: C 323 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.6887 (mp) REVERT: C 420 MET cc_start: 0.8910 (mmt) cc_final: 0.8614 (mmt) REVERT: C 438 GLU cc_start: 0.8096 (pp20) cc_final: 0.7689 (pp20) REVERT: C 502 MET cc_start: 0.8605 (mtp) cc_final: 0.8235 (mtm) REVERT: C 740 LEU cc_start: 0.8303 (tp) cc_final: 0.8081 (tp) REVERT: C 781 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7330 (ptp90) REVERT: C 829 THR cc_start: 0.7485 (t) cc_final: 0.6972 (m) REVERT: C 853 ARG cc_start: 0.8182 (mtt-85) cc_final: 0.7892 (mtt-85) REVERT: C 969 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: C 980 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6824 (mm-30) REVERT: C 1013 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6856 (mtm110) REVERT: C 1022 GLN cc_start: 0.7483 (mm-40) cc_final: 0.6631 (tm-30) REVERT: D 26 ARG cc_start: 0.8499 (ttp-170) cc_final: 0.7956 (ttm170) REVERT: D 131 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7467 (mm-30) REVERT: D 202 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8080 (pmm) REVERT: D 250 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6574 (tt) REVERT: D 420 MET cc_start: 0.8883 (mmt) cc_final: 0.8593 (mmt) REVERT: D 438 GLU cc_start: 0.8056 (pp20) cc_final: 0.7622 (pp20) REVERT: D 502 MET cc_start: 0.8596 (mtp) cc_final: 0.8227 (mtt) REVERT: D 781 ARG cc_start: 0.8134 (ptm160) cc_final: 0.7321 (ptp90) REVERT: D 969 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: D 980 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6899 (mm-30) REVERT: D 987 ASP cc_start: 0.8444 (m-30) cc_final: 0.8195 (m-30) REVERT: D 1013 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.7006 (mtm110) REVERT: D 1022 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6619 (tm-30) outliers start: 218 outliers final: 176 residues processed: 822 average time/residue: 0.2394 time to fit residues: 308.8652 Evaluate side-chains 880 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 683 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 677 LYS Chi-restraints excluded: chain A residue 729 THR Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 991 MET Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 729 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 793 ILE Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain B residue 1013 ARG Chi-restraints excluded: chain B residue 1018 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 677 LYS Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 729 THR Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 793 ILE Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 960 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 1013 ARG Chi-restraints excluded: chain C residue 1018 LEU Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 677 LYS Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 960 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1013 ARG Chi-restraints excluded: chain D residue 1018 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 188 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 252 optimal weight: 0.9980 chunk 375 optimal weight: 1.9990 chunk 283 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 323 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS A 573 GLN A 885 ASN A 949 HIS B 102 ASN B 395 HIS B 573 GLN C 102 ASN C 370 GLN C 395 HIS C 573 GLN D 102 ASN D 370 GLN D 395 HIS D 573 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.136691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.120780 restraints weight = 46493.998| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.58 r_work: 0.3122 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33468 Z= 0.138 Angle : 0.557 8.923 45660 Z= 0.288 Chirality : 0.045 0.177 4752 Planarity : 0.004 0.054 6036 Dihedral : 5.502 45.759 4452 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.41 % Allowed : 21.56 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.13), residues: 4036 helix: -0.13 (0.24), residues: 488 sheet: 0.61 (0.14), residues: 1368 loop : -0.63 (0.14), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 288 TYR 0.016 0.002 TYR B 100 PHE 0.009 0.001 PHE C 274 TRP 0.028 0.002 TRP B 720 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00320 (33468) covalent geometry : angle 0.55730 (45660) hydrogen bonds : bond 0.03381 ( 1164) hydrogen bonds : angle 4.99079 ( 3228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 722 time to evaluate : 1.398 Fit side-chains REVERT: A 131 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7461 (mm-30) REVERT: A 202 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8074 (pmm) REVERT: A 250 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6983 (tt) REVERT: A 264 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: A 277 GLU cc_start: 0.6972 (tp30) cc_final: 0.6701 (tp30) REVERT: A 287 ASP cc_start: 0.8435 (p0) cc_final: 0.7872 (p0) REVERT: A 438 GLU cc_start: 0.8071 (pp20) cc_final: 0.7680 (pp20) REVERT: A 502 MET cc_start: 0.8674 (mtp) cc_final: 0.8339 (mtm) REVERT: A 781 ARG cc_start: 0.8167 (ptm160) cc_final: 0.7299 (ptp90) REVERT: A 828 ASP cc_start: 0.6780 (t0) cc_final: 0.6390 (t0) REVERT: A 852 SER cc_start: 0.8900 (p) cc_final: 0.8686 (p) REVERT: A 969 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: A 987 ASP cc_start: 0.8409 (m-30) cc_final: 0.8179 (m-30) REVERT: A 1013 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6767 (mtm110) REVERT: A 1022 GLN cc_start: 0.7326 (mm-40) cc_final: 0.6620 (tm-30) REVERT: B 135 GLN cc_start: 0.6814 (mm110) cc_final: 0.6391 (mt0) REVERT: B 202 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8089 (pmm) REVERT: B 250 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6912 (tt) REVERT: B 264 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7727 (pm20) REVERT: B 287 ASP cc_start: 0.8454 (p0) cc_final: 0.7866 (p0) REVERT: B 336 ARG cc_start: 0.8073 (ptt-90) cc_final: 0.7533 (ptt-90) REVERT: B 338 GLU cc_start: 0.8250 (pt0) cc_final: 0.7459 (pt0) REVERT: B 420 MET cc_start: 0.8830 (mmt) cc_final: 0.8443 (mmt) REVERT: B 438 GLU cc_start: 0.8070 (pp20) cc_final: 0.7673 (pp20) REVERT: B 502 MET cc_start: 0.8576 (mtp) cc_final: 0.8233 (mtm) REVERT: B 781 ARG cc_start: 0.8152 (ptm160) cc_final: 0.7301 (ptp90) REVERT: B 828 ASP cc_start: 0.6939 (t0) cc_final: 0.6508 (t0) REVERT: B 969 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: B 1013 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6717 (mtm110) REVERT: B 1022 GLN cc_start: 0.7371 (mm-40) cc_final: 0.6632 (tm-30) REVERT: C 135 GLN cc_start: 0.6792 (mm110) cc_final: 0.6386 (mt0) REVERT: C 202 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8044 (pmm) REVERT: C 250 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7009 (tt) REVERT: C 264 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: C 287 ASP cc_start: 0.8439 (p0) cc_final: 0.7868 (p0) REVERT: C 323 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.6850 (mp) REVERT: C 336 ARG cc_start: 0.8042 (ptt-90) cc_final: 0.7653 (ptt-90) REVERT: C 438 GLU cc_start: 0.8051 (pp20) cc_final: 0.7661 (pp20) REVERT: C 502 MET cc_start: 0.8560 (mtp) cc_final: 0.8197 (mtm) REVERT: C 740 LEU cc_start: 0.8296 (tp) cc_final: 0.8074 (tp) REVERT: C 781 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7284 (ptp90) REVERT: C 829 THR cc_start: 0.7499 (t) cc_final: 0.7042 (m) REVERT: C 938 ARG cc_start: 0.8970 (mpt180) cc_final: 0.8756 (mmt90) REVERT: C 969 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: C 980 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6914 (mm-30) REVERT: C 1013 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6884 (mtm110) REVERT: C 1022 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6649 (tm-30) REVERT: D 131 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7490 (mm-30) REVERT: D 202 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8068 (pmm) REVERT: D 250 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6427 (tt) REVERT: D 264 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: D 287 ASP cc_start: 0.8478 (p0) cc_final: 0.7935 (p0) REVERT: D 438 GLU cc_start: 0.8040 (pp20) cc_final: 0.7666 (pp20) REVERT: D 446 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.9031 (ttt180) REVERT: D 502 MET cc_start: 0.8580 (mtp) cc_final: 0.8217 (mtm) REVERT: D 781 ARG cc_start: 0.8151 (ptm160) cc_final: 0.7296 (ptp90) REVERT: D 853 ARG cc_start: 0.8128 (mtt-85) cc_final: 0.7804 (mtt-85) REVERT: D 969 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: D 980 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6895 (mm-30) REVERT: D 987 ASP cc_start: 0.8376 (m-30) cc_final: 0.8150 (m-30) REVERT: D 1013 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6891 (mtm110) REVERT: D 1022 GLN cc_start: 0.7331 (mm-40) cc_final: 0.6648 (tm-30) outliers start: 187 outliers final: 141 residues processed: 834 average time/residue: 0.2329 time to fit residues: 303.7730 Evaluate side-chains 849 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 686 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 677 LYS Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain B residue 1013 ARG Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 677 LYS Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 801 ILE Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 960 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 985 ASN Chi-restraints excluded: chain C residue 1013 ARG Chi-restraints excluded: chain C residue 1018 LEU Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain D residue 801 ILE Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 960 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 1013 ARG Chi-restraints excluded: chain D residue 1018 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 79 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 358 optimal weight: 7.9990 chunk 289 optimal weight: 10.0000 chunk 374 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 206 optimal weight: 9.9990 chunk 205 optimal weight: 3.9990 chunk 284 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 102 ASN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS A 604 ASN A 719 GLN A 885 ASN B 102 ASN B 226 HIS B 395 HIS B 604 ASN B 719 GLN B 949 HIS C 226 HIS ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 HIS C 604 ASN C 719 GLN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 HIS D 604 ASN D 719 GLN D 878 HIS D 949 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.133794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.117564 restraints weight = 47376.217| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.62 r_work: 0.3070 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 33468 Z= 0.257 Angle : 0.649 8.513 45660 Z= 0.337 Chirality : 0.048 0.180 4752 Planarity : 0.005 0.058 6036 Dihedral : 5.760 46.208 4452 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.12 % Allowed : 22.16 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.13), residues: 4036 helix: -0.32 (0.23), residues: 488 sheet: 0.51 (0.14), residues: 1364 loop : -0.78 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 952 TYR 0.018 0.002 TYR C 100 PHE 0.010 0.002 PHE C 150 TRP 0.028 0.002 TRP A 720 HIS 0.007 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00600 (33468) covalent geometry : angle 0.64912 (45660) hydrogen bonds : bond 0.03956 ( 1164) hydrogen bonds : angle 5.17875 ( 3228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 678 time to evaluate : 1.184 Fit side-chains REVERT: A 26 ARG cc_start: 0.8526 (ttp-170) cc_final: 0.7983 (ttm170) REVERT: A 131 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7451 (mm-30) REVERT: A 202 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8130 (pmm) REVERT: A 250 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6907 (tt) REVERT: A 323 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.6911 (mp) REVERT: A 502 MET cc_start: 0.8775 (mtp) cc_final: 0.8445 (mtt) REVERT: A 781 ARG cc_start: 0.8143 (ptm160) cc_final: 0.7327 (ptp90) REVERT: A 791 ASN cc_start: 0.7289 (m-40) cc_final: 0.6754 (m-40) REVERT: A 828 ASP cc_start: 0.7013 (t0) cc_final: 0.6598 (t0) REVERT: A 969 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: A 987 ASP cc_start: 0.8461 (m-30) cc_final: 0.8179 (m-30) REVERT: A 1013 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7095 (mtm110) REVERT: A 1022 GLN cc_start: 0.7464 (mm-40) cc_final: 0.6628 (tm-30) REVERT: B 26 ARG cc_start: 0.8521 (ttp-170) cc_final: 0.7983 (ttm170) REVERT: B 135 GLN cc_start: 0.6880 (mm110) cc_final: 0.6461 (mm110) REVERT: B 202 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8052 (pmm) REVERT: B 250 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6995 (tt) REVERT: B 336 ARG cc_start: 0.8166 (ptt-90) cc_final: 0.7697 (ptt-90) REVERT: B 338 GLU cc_start: 0.8359 (pt0) cc_final: 0.7663 (pt0) REVERT: B 502 MET cc_start: 0.8763 (mtp) cc_final: 0.8420 (mtt) REVERT: B 781 ARG cc_start: 0.8158 (ptm160) cc_final: 0.7347 (ptp90) REVERT: B 791 ASN cc_start: 0.7264 (m-40) cc_final: 0.6807 (m-40) REVERT: B 828 ASP cc_start: 0.7108 (t0) cc_final: 0.6690 (t0) REVERT: B 965 GLN cc_start: 0.7386 (tp40) cc_final: 0.6581 (tp40) REVERT: B 969 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: B 1013 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7042 (mtm110) REVERT: B 1022 GLN cc_start: 0.7447 (mm-40) cc_final: 0.6659 (tm-30) REVERT: C 26 ARG cc_start: 0.8526 (ttp-170) cc_final: 0.7975 (ttm170) REVERT: C 202 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8083 (pmm) REVERT: C 250 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6925 (tt) REVERT: C 323 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6902 (mp) REVERT: C 336 ARG cc_start: 0.8088 (ptt-90) cc_final: 0.7734 (ptt-90) REVERT: C 502 MET cc_start: 0.8665 (mtp) cc_final: 0.8327 (mtm) REVERT: C 781 ARG cc_start: 0.8126 (ptm160) cc_final: 0.7301 (ptp90) REVERT: C 791 ASN cc_start: 0.7318 (m-40) cc_final: 0.6848 (m-40) REVERT: C 829 THR cc_start: 0.7678 (t) cc_final: 0.7358 (p) REVERT: C 969 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: C 1013 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7066 (mtm110) REVERT: C 1022 GLN cc_start: 0.7471 (mm-40) cc_final: 0.6642 (tm-30) REVERT: D 26 ARG cc_start: 0.8525 (ttp-170) cc_final: 0.7986 (ttm170) REVERT: D 131 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7459 (mm-30) REVERT: D 202 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8106 (pmm) REVERT: D 250 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6650 (tt) REVERT: D 502 MET cc_start: 0.8670 (mtp) cc_final: 0.8342 (mtt) REVERT: D 781 ARG cc_start: 0.8139 (ptm160) cc_final: 0.7326 (ptp90) REVERT: D 791 ASN cc_start: 0.7271 (m-40) cc_final: 0.6725 (m-40) REVERT: D 969 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: D 987 ASP cc_start: 0.8448 (m-30) cc_final: 0.8199 (m-30) REVERT: D 1013 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7084 (mtm110) REVERT: D 1022 GLN cc_start: 0.7395 (mm-40) cc_final: 0.6547 (tm-30) outliers start: 177 outliers final: 147 residues processed: 794 average time/residue: 0.2298 time to fit residues: 285.5175 Evaluate side-chains 825 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 660 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 MET Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 423 MET Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 583 ASN Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 824 GLN Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 904 GLU Chi-restraints excluded: chain A residue 922 LEU Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 335 VAL Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 583 ASN Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 706 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 801 ILE Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 824 GLN Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 904 GLU Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 960 SER Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 1013 ARG Chi-restraints excluded: chain B residue 1018 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 MET Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 446 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 583 ASN Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 658 LEU Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 824 GLN Chi-restraints excluded: chain C residue 858 ILE Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 960 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain C residue 1013 ARG Chi-restraints excluded: chain C residue 1018 LEU Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 247 CYS Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 372 MET Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 446 ARG Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 583 ASN Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 729 THR Chi-restraints excluded: chain D residue 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 793 ILE Chi-restraints excluded: chain D residue 797 GLU Chi-restraints excluded: chain D residue 822 LEU Chi-restraints excluded: chain D residue 824 GLN Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 858 ILE Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 960 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 1013 ARG Chi-restraints excluded: chain D residue 1018 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 234 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 403 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 325 optimal weight: 0.9990 chunk 292 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS A 573 GLN A 604 ASN B 102 ASN B 226 HIS B 395 HIS B 573 GLN B 604 ASN B 949 HIS B 964 GLN C 102 ASN C 226 HIS ** C 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 395 HIS C 573 GLN D 102 ASN ** D 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 HIS D 573 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.135085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.119150 restraints weight = 47101.047| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.58 r_work: 0.3089 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 33468 Z= 0.195 Angle : 0.609 8.287 45660 Z= 0.317 Chirality : 0.046 0.184 4752 Planarity : 0.005 0.059 6036 Dihedral : 5.699 47.151 4452 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.21 % Allowed : 22.25 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.13), residues: 4036 helix: -0.30 (0.23), residues: 488 sheet: 0.47 (0.14), residues: 1368 loop : -0.76 (0.14), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 952 TYR 0.015 0.002 TYR A 100 PHE 0.010 0.001 PHE B 127 TRP 0.027 0.002 TRP C 720 HIS 0.004 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00454 (33468) covalent geometry : angle 0.60904 (45660) hydrogen bonds : bond 0.03717 ( 1164) hydrogen bonds : angle 5.12919 ( 3228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8220.87 seconds wall clock time: 141 minutes 41.79 seconds (8501.79 seconds total)