Starting phenix.real_space_refine on Fri Jun 27 23:59:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bk7_16091/06_2025/8bk7_16091.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bk7_16091/06_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_16091/06_2025/8bk7_16091.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bk7_16091/06_2025/8bk7_16091.map" model { file = "/net/cci-nas-00/data/ceres_data/8bk7_16091/06_2025/8bk7_16091.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bk7_16091/06_2025/8bk7_16091.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 22.68, per 1000 atoms: 0.70 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: 7.63 Conformation dependent library (CDL) restraints added in 4.2 seconds 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: 5.03 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: 16.93 Time building geometry restraints manager: 9.15 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: 0.27 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.360 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: 0.050 Extract box with map and model: 1.450 Check model and map are aligned: 0.270 Set scattering table: 0.340 Process input model: 81.350 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.510 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.054 0.002 TRP B 654 HIS 0.013 0.001 HIS A 395 PHE 0.019 0.002 PHE C 231 TYR 0.034 0.002 TYR C 100 ARG 0.013 0.001 ARG C 230 Details of bonding type rmsd hydrogen bonds : bond 0.22162 ( 1164) hydrogen bonds : angle 8.10981 ( 3228) covalent geometry : bond 0.00424 (33468) covalent geometry : angle 0.77451 (45660) *********************** 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 : 3.955 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: 0.4586 time to fit residues: 494.6486 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 : 3.543 ------------------------------------------------------------------------------- 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 341 optimal weight: 10.0000 chunk 306 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 206 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 366 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN A 634 GLN B 147 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 GLN B 634 GLN C 147 ASN ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 GLN C 634 GLN C 653 HIS D 147 ASN ** D 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 GLN D 634 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.137949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.121280 restraints weight = 46677.305| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.59 r_work: 0.3126 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 33468 Z= 0.242 Angle : 0.639 8.431 45660 Z= 0.338 Chirality : 0.047 0.179 4752 Planarity : 0.006 0.092 6036 Dihedral : 7.273 54.816 4571 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 6.28 % Allowed : 22.11 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 4036 helix: -0.52 (0.22), residues: 492 sheet: 0.78 (0.14), residues: 1396 loop : -0.65 (0.14), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 654 HIS 0.007 0.001 HIS C1015 PHE 0.018 0.002 PHE C 384 TYR 0.021 0.002 TYR C 100 ARG 0.008 0.001 ARG B 230 Details of bonding type rmsd hydrogen bonds : bond 0.04331 ( 1164) hydrogen bonds : angle 5.61015 ( 3228) covalent geometry : bond 0.00560 (33468) covalent geometry : angle 0.63871 (45660) *********************** 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 902 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 685 time to evaluate : 3.930 Fit side-chains REVERT: A 67 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8140 (mm-30) REVERT: A 177 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8207 (tp) REVERT: A 202 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8260 (pmm) REVERT: A 264 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: A 336 ARG cc_start: 0.8016 (ptt-90) cc_final: 0.7549 (ptt-90) REVERT: A 338 GLU cc_start: 0.7922 (pt0) cc_final: 0.7151 (pt0) REVERT: A 395 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.6046 (t70) REVERT: A 781 ARG cc_start: 0.8331 (ptm160) cc_final: 0.7500 (ptp90) REVERT: A 852 SER cc_start: 0.9005 (p) cc_final: 0.8773 (p) REVERT: A 863 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7258 (mt0) REVERT: A 969 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: A 980 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6609 (mm-30) REVERT: A 1014 TYR cc_start: 0.8475 (m-80) cc_final: 0.8248 (m-80) REVERT: A 1022 GLN cc_start: 0.7275 (mm-40) cc_final: 0.6724 (tm-30) REVERT: B 67 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7932 (mm-30) REVERT: B 202 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8312 (pmm) REVERT: B 264 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8230 (pm20) REVERT: B 326 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7609 (mm-30) REVERT: B 334 GLU cc_start: 0.8315 (pp20) cc_final: 0.7992 (pt0) REVERT: B 336 ARG cc_start: 0.8014 (ptt-90) cc_final: 0.7543 (ptt-90) REVERT: B 338 GLU cc_start: 0.7986 (pt0) cc_final: 0.7262 (pt0) REVERT: B 395 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.6045 (t70) REVERT: B 781 ARG cc_start: 0.8327 (ptm160) cc_final: 0.7495 (ptp90) REVERT: B 852 SER cc_start: 0.8996 (p) cc_final: 0.8758 (p) REVERT: B 863 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.7279 (mt0) REVERT: B 969 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: B 980 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6599 (mm-30) REVERT: B 1014 TYR cc_start: 0.8478 (m-80) cc_final: 0.8261 (m-80) REVERT: B 1022 GLN cc_start: 0.7271 (mm-40) cc_final: 0.6726 (tm-30) REVERT: C 67 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8133 (mm-30) REVERT: C 202 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8244 (pmm) REVERT: C 264 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8226 (pm20) REVERT: C 334 GLU cc_start: 0.8287 (pp20) cc_final: 0.7989 (pt0) REVERT: C 336 ARG cc_start: 0.8005 (ptt-90) cc_final: 0.7512 (ptt-90) REVERT: C 338 GLU cc_start: 0.7970 (pt0) cc_final: 0.7190 (pt0) REVERT: C 388 ARG cc_start: 0.8889 (ttt180) cc_final: 0.8669 (ttt180) REVERT: C 395 HIS cc_start: 0.7339 (OUTLIER) cc_final: 0.6033 (t70) REVERT: C 781 ARG cc_start: 0.8313 (ptm160) cc_final: 0.7470 (ptp90) REVERT: C 852 SER cc_start: 0.9001 (p) cc_final: 0.8757 (p) REVERT: C 863 GLN cc_start: 0.7520 (OUTLIER) cc_final: 0.7173 (mt0) REVERT: C 969 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: C 980 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6584 (mm-30) REVERT: C 1014 TYR cc_start: 0.8455 (m-80) cc_final: 0.8239 (m-80) REVERT: C 1022 GLN cc_start: 0.7309 (mm-40) cc_final: 0.6702 (tm-30) REVERT: D 67 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8139 (mm-30) REVERT: D 135 GLN cc_start: 0.6734 (mm110) cc_final: 0.6500 (mt0) REVERT: D 177 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8228 (tp) REVERT: D 202 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8233 (pmm) REVERT: D 264 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8378 (pm20) REVERT: D 336 ARG cc_start: 0.8023 (ptt-90) cc_final: 0.7573 (ptt-90) REVERT: D 338 GLU cc_start: 0.7946 (pt0) cc_final: 0.7197 (pt0) REVERT: D 395 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6058 (t70) REVERT: D 781 ARG cc_start: 0.8285 (ptm160) cc_final: 0.7466 (ptp90) REVERT: D 852 SER cc_start: 0.8999 (p) cc_final: 0.8752 (p) REVERT: D 863 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7201 (mt0) REVERT: D 969 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7901 (mp0) REVERT: D 980 GLU cc_start: 0.7379 (mm-30) cc_final: 0.6713 (mm-30) REVERT: D 1014 TYR cc_start: 0.8476 (m-80) cc_final: 0.8259 (m-80) REVERT: D 1022 GLN cc_start: 0.7320 (mm-40) cc_final: 0.6747 (tm-30) outliers start: 217 outliers final: 118 residues processed: 803 average time/residue: 0.4785 time to fit residues: 606.9242 Evaluate side-chains 788 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 648 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 147 ASN 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 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 379 MET Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 583 ASN 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 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 960 SER 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 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 99 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 147 ASN 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 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 379 MET Chi-restraints excluded: chain B residue 395 HIS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 583 ASN 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 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 960 SER 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 B residue 1006 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 147 ASN 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 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 379 MET Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 583 ASN 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 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 960 SER 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 C residue 1006 GLU 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 99 ILE Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 147 ASN 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 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 379 MET Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 583 ASN 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 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 960 SER Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 985 ASN Chi-restraints excluded: chain D residue 991 MET Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 315 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 354 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 237 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 GLN A 604 ASN A 713 HIS A 949 HIS A 990 HIS B 604 ASN B 713 HIS B 949 HIS B 990 HIS C 370 GLN C 604 ASN C 713 HIS C 840 HIS C 949 HIS C 990 HIS D 370 GLN D 604 ASN D 713 HIS D 949 HIS D 990 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.133421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.117127 restraints weight = 47254.066| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.56 r_work: 0.3068 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 33468 Z= 0.311 Angle : 0.675 6.938 45660 Z= 0.357 Chirality : 0.049 0.172 4752 Planarity : 0.006 0.076 6036 Dihedral : 6.168 48.811 4468 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 6.63 % Allowed : 21.93 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 4036 helix: -0.59 (0.22), residues: 488 sheet: 0.64 (0.14), residues: 1384 loop : -0.81 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 553 HIS 0.009 0.002 HIS D 151 PHE 0.016 0.002 PHE C 384 TYR 0.027 0.003 TYR B 100 ARG 0.007 0.001 ARG D 473 Details of bonding type rmsd hydrogen bonds : bond 0.04654 ( 1164) hydrogen bonds : angle 5.51708 ( 3228) covalent geometry : bond 0.00721 (33468) covalent geometry : angle 0.67486 (45660) *********************** 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 927 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 698 time to evaluate : 3.924 Fit side-chains REVERT: A 131 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7333 (mm-30) REVERT: A 177 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.8009 (tp) REVERT: A 202 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8152 (pmm) REVERT: A 250 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6611 (tt) REVERT: A 388 ARG cc_start: 0.8926 (ttt180) cc_final: 0.8699 (ttt180) REVERT: A 395 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.6361 (t70) REVERT: A 423 MET cc_start: 0.8551 (ttm) cc_final: 0.8160 (ttm) REVERT: A 502 MET cc_start: 0.8601 (mtp) cc_final: 0.8351 (mtt) REVERT: A 781 ARG cc_start: 0.8322 (ptm160) cc_final: 0.7488 (ptp90) REVERT: A 852 SER cc_start: 0.8970 (p) cc_final: 0.8762 (p) REVERT: A 969 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: A 980 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7110 (mm-30) REVERT: A 1022 GLN cc_start: 0.7402 (mm-40) cc_final: 0.6559 (tm-30) REVERT: B 202 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8193 (pmm) REVERT: B 250 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6467 (tt) REVERT: B 336 ARG cc_start: 0.8130 (ptt-90) cc_final: 0.7794 (ptt-90) REVERT: B 388 ARG cc_start: 0.8907 (ttt180) cc_final: 0.8692 (ttt180) REVERT: B 395 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.6395 (t70) REVERT: B 423 MET cc_start: 0.8547 (ttm) cc_final: 0.8164 (ttm) REVERT: B 502 MET cc_start: 0.8594 (mtp) cc_final: 0.8291 (mtt) REVERT: B 781 ARG cc_start: 0.8313 (ptm160) cc_final: 0.7478 (ptp90) REVERT: B 852 SER cc_start: 0.8954 (p) cc_final: 0.8750 (p) REVERT: B 969 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: B 980 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7098 (mm-30) REVERT: B 1022 GLN cc_start: 0.7445 (mm-40) cc_final: 0.6587 (tm-30) REVERT: C 202 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8109 (pmm) REVERT: C 250 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6473 (tt) REVERT: C 336 ARG cc_start: 0.8134 (ptt-90) cc_final: 0.7808 (ptt-90) REVERT: C 395 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.6358 (t70) REVERT: C 423 MET cc_start: 0.8533 (ttm) cc_final: 0.8147 (ttm) REVERT: C 502 MET cc_start: 0.8645 (mtp) cc_final: 0.8383 (mtt) REVERT: C 781 ARG cc_start: 0.8288 (ptm160) cc_final: 0.7412 (ptp90) REVERT: C 832 ASP cc_start: 0.5253 (t0) cc_final: 0.4994 (t0) REVERT: C 852 SER cc_start: 0.8966 (p) cc_final: 0.8759 (p) REVERT: C 969 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: C 980 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7114 (mm-30) REVERT: C 1022 GLN cc_start: 0.7451 (mm-40) cc_final: 0.6591 (tm-30) REVERT: D 131 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7247 (mm-30) REVERT: D 177 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8031 (tp) REVERT: D 202 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8121 (pmm) REVERT: D 250 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6646 (tt) REVERT: D 395 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.6397 (t70) REVERT: D 423 MET cc_start: 0.8538 (ttm) cc_final: 0.8157 (ttm) REVERT: D 502 MET cc_start: 0.8638 (mtp) cc_final: 0.8331 (mtt) REVERT: D 781 ARG cc_start: 0.8310 (ptm160) cc_final: 0.7445 (ptp90) REVERT: D 852 SER cc_start: 0.8956 (p) cc_final: 0.8745 (p) REVERT: D 969 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: D 980 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7099 (mm-30) REVERT: D 1022 GLN cc_start: 0.7450 (mm-40) cc_final: 0.6565 (tm-30) outliers start: 229 outliers final: 165 residues processed: 834 average time/residue: 0.4659 time to fit residues: 612.2026 Evaluate side-chains 831 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 648 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR 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 206 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 220 THR 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 379 MET Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 478 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 595 THR Chi-restraints excluded: chain A residue 639 THR Chi-restraints excluded: chain A residue 659 ASP 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 801 ILE 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 888 LEU Chi-restraints excluded: chain A residue 895 VAL 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 1006 GLU Chi-restraints excluded: chain B residue 44 THR 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 202 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR 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 395 HIS Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 478 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 595 THR Chi-restraints excluded: chain B residue 639 THR 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 729 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 793 ILE 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 838 THR Chi-restraints excluded: chain B residue 858 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 952 ARG 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 1006 GLU Chi-restraints excluded: chain C residue 44 THR 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 206 SER Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 220 THR 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 372 MET Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 395 HIS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 478 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 595 THR Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 659 ASP 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 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 888 LEU Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 904 GLU 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 985 ASN 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 177 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 220 THR 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 379 MET Chi-restraints excluded: chain D residue 395 HIS Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 478 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 595 THR Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain D residue 659 ASP 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 801 ILE 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 861 SER Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 904 GLU 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 985 ASN 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 324 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 228 optimal weight: 4.9990 chunk 387 optimal weight: 0.7980 chunk 216 optimal weight: 8.9990 chunk 341 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 177 optimal weight: 0.7980 chunk 283 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 370 GLN A 573 GLN A 604 ASN B 147 ASN B 163 GLN B 573 GLN B 604 ASN C 147 ASN C 163 GLN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 573 GLN C 604 ASN ** C 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN D 163 GLN D 370 GLN D 573 GLN D 604 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.136153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.119860 restraints weight = 46729.443| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.61 r_work: 0.3106 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33468 Z= 0.150 Angle : 0.553 6.537 45660 Z= 0.291 Chirality : 0.045 0.172 4752 Planarity : 0.005 0.065 6036 Dihedral : 5.756 48.806 4468 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.50 % Allowed : 23.21 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.13), residues: 4036 helix: -0.26 (0.23), residues: 488 sheet: 0.67 (0.14), residues: 1364 loop : -0.77 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 553 HIS 0.004 0.001 HIS C 151 PHE 0.009 0.001 PHE A 384 TYR 0.016 0.002 TYR B 100 ARG 0.006 0.001 ARG A 288 Details of bonding type rmsd hydrogen bonds : bond 0.03674 ( 1164) hydrogen bonds : angle 5.18628 ( 3228) covalent geometry : bond 0.00345 (33468) covalent geometry : angle 0.55317 (45660) *********************** 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 897 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 707 time to evaluate : 3.726 Fit side-chains REVERT: A 131 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7342 (mm-30) REVERT: A 135 GLN cc_start: 0.6805 (mt0) cc_final: 0.6523 (mt0) REVERT: A 177 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7925 (tp) REVERT: A 202 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8148 (pmm) REVERT: A 250 LEU cc_start: 0.7074 (OUTLIER) cc_final: 0.6538 (tt) REVERT: A 264 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: A 287 ASP cc_start: 0.8353 (p0) cc_final: 0.7820 (p0) REVERT: A 326 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7956 (mm-30) REVERT: A 336 ARG cc_start: 0.8073 (ptt-90) cc_final: 0.7773 (ptt-90) REVERT: A 423 MET cc_start: 0.8489 (ttm) cc_final: 0.7997 (ttm) REVERT: A 502 MET cc_start: 0.8440 (mtp) cc_final: 0.8104 (mtm) REVERT: A 781 ARG cc_start: 0.8148 (ptm160) cc_final: 0.7329 (ptp90) REVERT: A 852 SER cc_start: 0.8945 (p) cc_final: 0.8740 (p) REVERT: A 969 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: A 980 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6889 (mm-30) REVERT: A 1013 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6710 (mtm110) REVERT: A 1022 GLN cc_start: 0.7369 (mm-40) cc_final: 0.6602 (tm-30) REVERT: B 135 GLN cc_start: 0.7101 (mt0) cc_final: 0.6780 (mt0) REVERT: B 202 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8216 (pmm) REVERT: B 264 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: B 287 ASP cc_start: 0.8403 (p0) cc_final: 0.7895 (p0) REVERT: B 326 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7934 (mm-30) REVERT: B 336 ARG cc_start: 0.8151 (ptt-90) cc_final: 0.7840 (ptt-90) REVERT: B 423 MET cc_start: 0.8493 (ttm) cc_final: 0.8081 (ttm) REVERT: B 487 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7611 (tm-30) REVERT: B 502 MET cc_start: 0.8367 (mtp) cc_final: 0.8039 (mtm) REVERT: B 781 ARG cc_start: 0.8179 (ptm160) cc_final: 0.7352 (ptp90) REVERT: B 852 SER cc_start: 0.8929 (p) cc_final: 0.8712 (p) REVERT: B 965 GLN cc_start: 0.7290 (tp40) cc_final: 0.6478 (tp40) REVERT: B 969 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: B 980 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6970 (mm-30) REVERT: B 1022 GLN cc_start: 0.7386 (mm-40) cc_final: 0.6612 (tm-30) REVERT: C 135 GLN cc_start: 0.7092 (mt0) cc_final: 0.6768 (mt0) REVERT: C 202 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8113 (pmm) REVERT: C 250 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6370 (tt) REVERT: C 264 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7928 (pm20) REVERT: C 287 ASP cc_start: 0.8375 (p0) cc_final: 0.7839 (p0) REVERT: C 336 ARG cc_start: 0.8144 (ptt-90) cc_final: 0.7847 (ptt-90) REVERT: C 423 MET cc_start: 0.8467 (ttm) cc_final: 0.8053 (ttm) REVERT: C 502 MET cc_start: 0.8393 (mtp) cc_final: 0.8049 (mtm) REVERT: C 781 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7320 (ptp90) REVERT: C 828 ASP cc_start: 0.6637 (t0) cc_final: 0.6406 (t0) REVERT: C 852 SER cc_start: 0.8935 (p) cc_final: 0.8733 (p) REVERT: C 863 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.7070 (mt0) REVERT: C 969 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: C 980 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6865 (mm-30) REVERT: C 1013 ARG cc_start: 0.7146 (OUTLIER) cc_final: 0.6719 (mtm110) REVERT: C 1022 GLN cc_start: 0.7400 (mm-40) cc_final: 0.6622 (tm-30) REVERT: D 131 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7516 (mm-30) REVERT: D 177 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7933 (tp) REVERT: D 202 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8138 (pmm) REVERT: D 250 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6596 (tt) REVERT: D 264 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7931 (pm20) REVERT: D 287 ASP cc_start: 0.8358 (p0) cc_final: 0.7827 (p0) REVERT: D 326 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7982 (mm-30) REVERT: D 336 ARG cc_start: 0.8142 (ptt-90) cc_final: 0.7847 (ptt-90) REVERT: D 423 MET cc_start: 0.8497 (ttm) cc_final: 0.8010 (ttm) REVERT: D 502 MET cc_start: 0.8372 (mtp) cc_final: 0.7963 (mtm) REVERT: D 781 ARG cc_start: 0.8196 (ptm160) cc_final: 0.7379 (ptp90) REVERT: D 852 SER cc_start: 0.8937 (p) cc_final: 0.8727 (p) REVERT: D 969 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: D 980 GLU cc_start: 0.7356 (mm-30) cc_final: 0.6880 (mm-30) REVERT: D 1013 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6689 (mtm110) REVERT: D 1022 GLN cc_start: 0.7492 (mm-40) cc_final: 0.6650 (tm-30) outliers start: 190 outliers final: 119 residues processed: 826 average time/residue: 0.5400 time to fit residues: 709.4332 Evaluate side-chains 813 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 673 time to evaluate : 4.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE 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 219 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 250 LEU 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 436 MET Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 659 ASP Chi-restraints excluded: chain A residue 672 VAL 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 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 888 LEU 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 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 250 LEU 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 436 MET Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 530 THR 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 744 GLU Chi-restraints excluded: chain B residue 750 GLU 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 888 LEU 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 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 147 ASN Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 250 LEU 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 379 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 706 THR Chi-restraints excluded: chain C residue 724 GLU 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 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 74 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 215 LEU 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 379 MET Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 672 VAL 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 388 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 chunk 160 optimal weight: 8.9990 chunk 348 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 344 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 241 optimal weight: 5.9990 chunk 251 optimal weight: 0.3980 chunk 279 optimal weight: 5.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN A 395 HIS A 653 HIS A 719 GLN ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 GLN B 147 ASN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS B 653 HIS B 719 GLN ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 GLN C 102 ASN C 147 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 395 HIS C 719 GLN ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 964 GLN D 102 ASN D 147 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN D 395 HIS D 653 HIS D 719 GLN ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 HIS D 964 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.137458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.121431 restraints weight = 46624.912| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.58 r_work: 0.3125 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33468 Z= 0.118 Angle : 0.527 8.594 45660 Z= 0.276 Chirality : 0.044 0.172 4752 Planarity : 0.004 0.059 6036 Dihedral : 5.496 51.745 4460 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.15 % Allowed : 21.41 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 4036 helix: -0.07 (0.24), residues: 488 sheet: 0.70 (0.14), residues: 1364 loop : -0.66 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 553 HIS 0.003 0.001 HIS D 840 PHE 0.008 0.001 PHE C 150 TYR 0.025 0.001 TYR B 100 ARG 0.005 0.000 ARG D 288 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 1164) hydrogen bonds : angle 5.03775 ( 3228) covalent geometry : bond 0.00270 (33468) covalent geometry : angle 0.52706 (45660) *********************** 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 888 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 710 time to evaluate : 3.765 Fit side-chains REVERT: A 131 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7372 (mm-30) REVERT: A 135 GLN cc_start: 0.7148 (mt0) cc_final: 0.6890 (mt0) REVERT: A 177 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7972 (tp) REVERT: A 202 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8061 (pmm) REVERT: A 250 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6285 (tt) REVERT: A 264 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7623 (pm20) REVERT: A 287 ASP cc_start: 0.8330 (p0) cc_final: 0.7786 (p0) REVERT: A 336 ARG cc_start: 0.8155 (ptt-90) cc_final: 0.7865 (ptt-90) REVERT: A 438 GLU cc_start: 0.7677 (pp20) cc_final: 0.7346 (pp20) REVERT: A 502 MET cc_start: 0.8559 (mtp) cc_final: 0.8128 (mtm) REVERT: A 781 ARG cc_start: 0.8099 (ptm160) cc_final: 0.7270 (ptp90) REVERT: A 852 SER cc_start: 0.8924 (p) cc_final: 0.8723 (p) REVERT: A 969 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: A 980 GLU cc_start: 0.7354 (mm-30) cc_final: 0.6928 (mm-30) REVERT: A 987 ASP cc_start: 0.8449 (m-30) cc_final: 0.8226 (m-30) REVERT: A 1013 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6662 (mtm110) REVERT: A 1022 GLN cc_start: 0.7273 (mm-40) cc_final: 0.6622 (tm-30) REVERT: B 135 GLN cc_start: 0.7141 (mt0) cc_final: 0.6881 (mt0) REVERT: B 202 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8125 (pmm) REVERT: B 264 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: B 287 ASP cc_start: 0.8383 (p0) cc_final: 0.7862 (p0) REVERT: B 326 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7938 (mm-30) REVERT: B 423 MET cc_start: 0.8426 (ttm) cc_final: 0.8021 (ttm) REVERT: B 438 GLU cc_start: 0.7653 (pp20) cc_final: 0.7317 (pp20) REVERT: B 502 MET cc_start: 0.8432 (mtp) cc_final: 0.7967 (mtm) REVERT: B 781 ARG cc_start: 0.8129 (ptm160) cc_final: 0.7299 (ptp90) REVERT: B 852 SER cc_start: 0.8914 (p) cc_final: 0.8701 (p) REVERT: B 969 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: B 980 GLU cc_start: 0.7382 (mm-30) cc_final: 0.6947 (mm-30) REVERT: B 987 ASP cc_start: 0.8439 (m-30) cc_final: 0.8215 (m-30) REVERT: B 1013 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6641 (mtm110) REVERT: B 1022 GLN cc_start: 0.7292 (mm-40) cc_final: 0.6624 (tm-30) REVERT: C 135 GLN cc_start: 0.7122 (mt0) cc_final: 0.6861 (mt0) REVERT: C 202 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8030 (pmm) REVERT: C 264 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: C 287 ASP cc_start: 0.8367 (p0) cc_final: 0.7839 (p0) REVERT: C 323 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7099 (mp) REVERT: C 388 ARG cc_start: 0.8842 (ttt180) cc_final: 0.8594 (ttt180) REVERT: C 423 MET cc_start: 0.8397 (ttm) cc_final: 0.8000 (ttm) REVERT: C 438 GLU cc_start: 0.7637 (pp20) cc_final: 0.7327 (pp20) REVERT: C 502 MET cc_start: 0.8520 (mtp) cc_final: 0.8082 (mtm) REVERT: C 781 ARG cc_start: 0.8109 (ptm160) cc_final: 0.7270 (ptp90) REVERT: C 828 ASP cc_start: 0.6613 (t0) cc_final: 0.6388 (t0) REVERT: C 852 SER cc_start: 0.8924 (p) cc_final: 0.8711 (p) REVERT: C 969 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: C 980 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6935 (mm-30) REVERT: C 987 ASP cc_start: 0.8443 (m-30) cc_final: 0.8221 (m-30) REVERT: C 1013 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6680 (mtm110) REVERT: C 1022 GLN cc_start: 0.7365 (mm-40) cc_final: 0.6641 (tm-30) REVERT: D 131 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7555 (mm-30) REVERT: D 177 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7981 (tp) REVERT: D 202 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8058 (pmm) REVERT: D 250 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6360 (tt) REVERT: D 264 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: D 287 ASP cc_start: 0.8344 (p0) cc_final: 0.7807 (p0) REVERT: D 336 ARG cc_start: 0.8146 (ptt-90) cc_final: 0.7858 (ptt-90) REVERT: D 423 MET cc_start: 0.8406 (ttm) cc_final: 0.8093 (ttm) REVERT: D 438 GLU cc_start: 0.7622 (pp20) cc_final: 0.7312 (pp20) REVERT: D 502 MET cc_start: 0.8549 (mtp) cc_final: 0.8041 (mtm) REVERT: D 781 ARG cc_start: 0.8104 (ptm160) cc_final: 0.7293 (ptp90) REVERT: D 852 SER cc_start: 0.8927 (p) cc_final: 0.8716 (p) REVERT: D 969 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7720 (mp0) REVERT: D 980 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6943 (mm-30) REVERT: D 987 ASP cc_start: 0.8426 (m-30) cc_final: 0.8193 (m-30) REVERT: D 1013 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.6671 (mtm110) REVERT: D 1022 GLN cc_start: 0.7382 (mm-40) cc_final: 0.6657 (tm-30) outliers start: 178 outliers final: 116 residues processed: 822 average time/residue: 0.4783 time to fit residues: 614.5200 Evaluate side-chains 819 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 682 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLN Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 148 SER 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 250 LEU Chi-restraints excluded: chain A residue 264 GLU 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 436 MET Chi-restraints excluded: chain A residue 478 VAL 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 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 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 922 LEU Chi-restraints excluded: chain A residue 964 GLN Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 985 ASN Chi-restraints excluded: chain A residue 1013 ARG Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 148 SER Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 GLU 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 436 MET Chi-restraints excluded: chain B residue 478 VAL 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 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 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 964 GLN Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 985 ASN Chi-restraints excluded: chain B residue 1013 ARG Chi-restraints excluded: chain C residue 91 GLN Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 250 LEU 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 372 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 478 VAL 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 706 THR Chi-restraints excluded: chain C residue 724 GLU 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 964 GLN 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 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 177 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 264 GLU 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 436 MET Chi-restraints excluded: chain D residue 478 VAL 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 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 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 934 GLU Chi-restraints excluded: chain D residue 964 GLN Chi-restraints excluded: chain D residue 969 GLU 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 6 optimal weight: 10.0000 chunk 184 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 chunk 280 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 289 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 226 HIS A 370 GLN A 395 HIS A 604 ASN A 634 GLN A 719 GLN A 949 HIS B 102 ASN B 226 HIS B 395 HIS B 604 ASN B 634 GLN B 949 HIS C 226 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 395 HIS C 604 ASN C 719 GLN C 863 GLN C 949 HIS D 226 HIS D 370 GLN D 395 HIS D 604 ASN D 949 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.132209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.115729 restraints weight = 47405.407| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.63 r_work: 0.3047 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 33468 Z= 0.360 Angle : 0.711 7.385 45660 Z= 0.373 Chirality : 0.050 0.175 4752 Planarity : 0.006 0.062 6036 Dihedral : 6.065 50.634 4456 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 6.51 % Allowed : 21.09 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 4036 helix: -0.65 (0.22), residues: 488 sheet: 0.41 (0.13), residues: 1384 loop : -0.89 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 720 HIS 0.009 0.002 HIS D 151 PHE 0.013 0.002 PHE D 150 TYR 0.030 0.003 TYR B 100 ARG 0.010 0.001 ARG C 288 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 1164) hydrogen bonds : angle 5.38453 ( 3228) covalent geometry : bond 0.00841 (33468) covalent geometry : angle 0.71109 (45660) *********************** 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 929 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 704 time to evaluate : 4.136 Fit side-chains REVERT: A 131 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7507 (mm-30) REVERT: A 135 GLN cc_start: 0.7146 (mt0) cc_final: 0.6909 (mt0) REVERT: A 177 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8023 (tp) REVERT: A 202 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8131 (pmm) REVERT: A 250 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6617 (tt) REVERT: A 420 MET cc_start: 0.8765 (mmm) cc_final: 0.8542 (mmt) REVERT: A 588 TYR cc_start: 0.8194 (p90) cc_final: 0.7972 (p90) REVERT: A 654 TRP cc_start: 0.7589 (p90) cc_final: 0.7326 (p90) REVERT: A 781 ARG cc_start: 0.8251 (ptm160) cc_final: 0.7415 (ptp90) REVERT: A 969 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: A 987 ASP cc_start: 0.8455 (m-30) cc_final: 0.8199 (m-30) REVERT: A 1013 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6952 (mtm110) REVERT: A 1022 GLN cc_start: 0.7443 (mm-40) cc_final: 0.6588 (tm-30) REVERT: B 135 GLN cc_start: 0.7157 (mt0) cc_final: 0.6908 (mt0) REVERT: B 202 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8147 (pmm) REVERT: B 250 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6576 (tt) REVERT: B 336 ARG cc_start: 0.8092 (ptt-90) cc_final: 0.7556 (ptt-90) REVERT: B 338 GLU cc_start: 0.8420 (pt0) cc_final: 0.7661 (pt0) REVERT: B 484 VAL cc_start: 0.9443 (OUTLIER) cc_final: 0.9176 (t) REVERT: B 502 MET cc_start: 0.8629 (mtp) cc_final: 0.8339 (mtt) REVERT: B 654 TRP cc_start: 0.7579 (p90) cc_final: 0.7322 (p90) REVERT: B 781 ARG cc_start: 0.8249 (ptm160) cc_final: 0.7407 (ptp90) REVERT: B 969 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: B 1013 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6929 (mtm110) REVERT: B 1022 GLN cc_start: 0.7475 (mm-40) cc_final: 0.6615 (tm-30) REVERT: C 26 ARG cc_start: 0.8498 (ttp-170) cc_final: 0.8095 (ttm170) REVERT: C 135 GLN cc_start: 0.7143 (mt0) cc_final: 0.6894 (mt0) REVERT: C 202 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8085 (pmm) REVERT: C 250 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6589 (tt) REVERT: C 336 ARG cc_start: 0.8104 (ptt-90) cc_final: 0.7553 (ptt-90) REVERT: C 338 GLU cc_start: 0.8408 (pt0) cc_final: 0.7639 (pt0) REVERT: C 420 MET cc_start: 0.8769 (mmm) cc_final: 0.8556 (mmt) REVERT: C 588 TYR cc_start: 0.8214 (p90) cc_final: 0.7993 (p90) REVERT: C 654 TRP cc_start: 0.7565 (p90) cc_final: 0.7311 (p90) REVERT: C 781 ARG cc_start: 0.8236 (ptm160) cc_final: 0.7349 (ptp90) REVERT: C 969 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: C 987 ASP cc_start: 0.8476 (m-30) cc_final: 0.8229 (m-30) REVERT: C 1013 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6960 (mtm110) REVERT: C 1022 GLN cc_start: 0.7479 (mm-40) cc_final: 0.6614 (tm-30) REVERT: D 26 ARG cc_start: 0.8505 (ttp-170) cc_final: 0.8118 (ttm170) REVERT: D 46 ARG cc_start: 0.7128 (mtt90) cc_final: 0.6878 (mtt90) REVERT: D 131 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7456 (mm-30) REVERT: D 177 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8027 (tp) REVERT: D 202 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8113 (pmm) REVERT: D 250 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6594 (tt) REVERT: D 420 MET cc_start: 0.8765 (mmm) cc_final: 0.8545 (mmt) REVERT: D 484 VAL cc_start: 0.9433 (OUTLIER) cc_final: 0.9152 (t) REVERT: D 502 MET cc_start: 0.8631 (mtp) cc_final: 0.8326 (mtt) REVERT: D 588 TYR cc_start: 0.8186 (p90) cc_final: 0.7950 (p90) REVERT: D 654 TRP cc_start: 0.7571 (p90) cc_final: 0.7310 (p90) REVERT: D 781 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7359 (ptp90) REVERT: D 969 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7821 (mp0) REVERT: D 1013 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.6949 (mtm110) REVERT: D 1022 GLN cc_start: 0.7559 (mm-40) cc_final: 0.6655 (tm-30) outliers start: 225 outliers final: 158 residues processed: 847 average time/residue: 0.6131 time to fit residues: 830.8120 Evaluate side-chains 845 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 667 time to evaluate : 4.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 223 SER 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 279 ILE 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 436 MET 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 632 SER 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 690 SER 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 895 VAL Chi-restraints excluded: chain A residue 898 LEU 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 1013 ARG Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 148 SER 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 220 THR Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 264 GLU Chi-restraints excluded: chain B residue 279 ILE 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 436 MET 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 658 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 690 SER 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 895 VAL Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 991 MET Chi-restraints excluded: chain B residue 1013 ARG 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 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 279 ILE 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 436 MET 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 658 LEU Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 690 SER Chi-restraints excluded: chain C residue 706 THR 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 895 VAL Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 904 GLU 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 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 165 SER Chi-restraints excluded: chain D residue 177 LEU 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 223 SER 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 279 ILE 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 436 MET 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 583 ASN 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 690 SER 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 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 861 SER Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 898 LEU Chi-restraints excluded: chain D residue 904 GLU 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 1013 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 139 optimal weight: 3.9990 chunk 306 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 chunk 224 optimal weight: 7.9990 chunk 380 optimal weight: 8.9990 chunk 253 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 330 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 147 ASN A 226 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN A 395 HIS ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 ASN ** A 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN B 147 ASN B 226 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS ** B 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN C 147 ASN C 226 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 395 HIS ** C 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN D 147 ASN D 226 HIS D 370 GLN D 395 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.133988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.118015 restraints weight = 46967.122| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 1.58 r_work: 0.3079 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2968 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= 0.224 Angle : 0.609 7.202 45660 Z= 0.319 Chirality : 0.046 0.177 4752 Planarity : 0.005 0.061 6036 Dihedral : 5.852 46.380 4456 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.58 % Allowed : 22.22 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.13), residues: 4036 helix: -0.44 (0.23), residues: 488 sheet: 0.42 (0.13), residues: 1372 loop : -0.88 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 553 HIS 0.005 0.001 HIS B 151 PHE 0.009 0.002 PHE A 150 TYR 0.024 0.002 TYR B 100 ARG 0.008 0.001 ARG C 288 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 1164) hydrogen bonds : angle 5.23766 ( 3228) covalent geometry : bond 0.00523 (33468) covalent geometry : angle 0.60886 (45660) *********************** 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 913 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 720 time to evaluate : 3.788 Fit side-chains REVERT: A 26 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.8058 (ttm170) REVERT: A 131 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7500 (mm-30) REVERT: A 135 GLN cc_start: 0.7244 (mt0) cc_final: 0.6946 (mt0) REVERT: A 177 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7955 (tp) REVERT: A 202 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8157 (pmm) REVERT: A 250 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.6766 (tt) REVERT: A 287 ASP cc_start: 0.8435 (p0) cc_final: 0.7744 (p0) REVERT: A 484 VAL cc_start: 0.9399 (OUTLIER) cc_final: 0.9140 (t) REVERT: A 654 TRP cc_start: 0.7421 (p90) cc_final: 0.7201 (p90) REVERT: A 781 ARG cc_start: 0.8215 (ptm160) cc_final: 0.7366 (ptp90) REVERT: A 808 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 969 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: A 980 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6679 (mm-30) REVERT: A 987 ASP cc_start: 0.8443 (m-30) cc_final: 0.8189 (m-30) REVERT: A 1013 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6936 (mtm110) REVERT: A 1022 GLN cc_start: 0.7541 (mm-40) cc_final: 0.6653 (tm-30) REVERT: B 26 ARG cc_start: 0.8484 (ttp-170) cc_final: 0.8105 (ttm170) REVERT: B 135 GLN cc_start: 0.7246 (mt0) cc_final: 0.6935 (mt0) REVERT: B 202 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8171 (pmm) REVERT: B 250 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6531 (tt) REVERT: B 287 ASP cc_start: 0.8428 (p0) cc_final: 0.7756 (p0) REVERT: B 336 ARG cc_start: 0.8072 (ptt-90) cc_final: 0.7537 (ptt-90) REVERT: B 338 GLU cc_start: 0.8346 (pt0) cc_final: 0.7599 (pt0) REVERT: B 484 VAL cc_start: 0.9409 (OUTLIER) cc_final: 0.9141 (t) REVERT: B 502 MET cc_start: 0.8704 (mtp) cc_final: 0.8362 (mtt) REVERT: B 654 TRP cc_start: 0.7416 (p90) cc_final: 0.7201 (p90) REVERT: B 781 ARG cc_start: 0.8207 (ptm160) cc_final: 0.7354 (ptp90) REVERT: B 808 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 965 GLN cc_start: 0.7321 (tp40) cc_final: 0.6567 (tp40) REVERT: B 969 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: B 1013 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6943 (mtm110) REVERT: B 1022 GLN cc_start: 0.7547 (mm-40) cc_final: 0.6655 (tm-30) REVERT: C 26 ARG cc_start: 0.8459 (ttp-170) cc_final: 0.8058 (ttm170) REVERT: C 135 GLN cc_start: 0.7235 (mt0) cc_final: 0.6917 (mt0) REVERT: C 202 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8099 (pmm) REVERT: C 250 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6557 (tt) REVERT: C 287 ASP cc_start: 0.8421 (p0) cc_final: 0.7807 (p0) REVERT: C 336 ARG cc_start: 0.8074 (ptt-90) cc_final: 0.7531 (ptt-90) REVERT: C 338 GLU cc_start: 0.8343 (pt0) cc_final: 0.7592 (pt0) REVERT: C 484 VAL cc_start: 0.9399 (OUTLIER) cc_final: 0.9141 (t) REVERT: C 502 MET cc_start: 0.8481 (mtp) cc_final: 0.8278 (mtt) REVERT: C 654 TRP cc_start: 0.7413 (p90) cc_final: 0.7194 (p90) REVERT: C 781 ARG cc_start: 0.8175 (ptm160) cc_final: 0.7343 (ptp90) REVERT: C 808 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7619 (mm-30) REVERT: C 969 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: C 987 ASP cc_start: 0.8461 (m-30) cc_final: 0.8216 (m-30) REVERT: C 1013 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6955 (mtm110) REVERT: C 1022 GLN cc_start: 0.7539 (mm-40) cc_final: 0.6667 (tm-30) REVERT: D 26 ARG cc_start: 0.8448 (ttp-170) cc_final: 0.8055 (ttm170) REVERT: D 46 ARG cc_start: 0.7114 (mtt90) cc_final: 0.6856 (mtt90) REVERT: D 131 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7489 (mm-30) REVERT: D 177 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7975 (tp) REVERT: D 202 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8117 (pmm) REVERT: D 250 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6735 (tt) REVERT: D 287 ASP cc_start: 0.8444 (p0) cc_final: 0.7780 (p0) REVERT: D 484 VAL cc_start: 0.9387 (OUTLIER) cc_final: 0.9121 (t) REVERT: D 502 MET cc_start: 0.8697 (mtp) cc_final: 0.8364 (mtt) REVERT: D 654 TRP cc_start: 0.7432 (p90) cc_final: 0.7217 (p90) REVERT: D 781 ARG cc_start: 0.8202 (ptm160) cc_final: 0.7344 (ptp90) REVERT: D 808 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7593 (mm-30) REVERT: D 969 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: D 980 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6700 (mm-30) REVERT: D 987 ASP cc_start: 0.8434 (m-30) cc_final: 0.8178 (m-30) REVERT: D 1013 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6947 (mtm110) REVERT: D 1022 GLN cc_start: 0.7565 (mm-40) cc_final: 0.6664 (tm-30) outliers start: 193 outliers final: 140 residues processed: 842 average time/residue: 0.5126 time to fit residues: 674.9929 Evaluate side-chains 855 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 693 time to evaluate : 3.749 ------------------------------------------------------------------------------- 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 147 ASN Chi-restraints excluded: chain A residue 148 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 223 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU 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 436 MET 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 632 SER 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 690 SER Chi-restraints excluded: chain A residue 744 GLU Chi-restraints excluded: chain A residue 750 GLU 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 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 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 147 ASN Chi-restraints excluded: chain B residue 148 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 223 SER Chi-restraints excluded: chain B residue 250 LEU 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 436 MET 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 658 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU 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 895 VAL 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 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 147 ASN 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 223 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU Chi-restraints excluded: chain C residue 279 ILE 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 423 MET Chi-restraints excluded: chain C residue 436 MET 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 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 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 861 SER Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 922 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 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 147 ASN Chi-restraints excluded: chain D residue 148 SER Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 223 SER 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 478 VAL Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 583 ASN 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 744 GLU Chi-restraints excluded: chain D residue 750 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 861 SER 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 982 THR Chi-restraints excluded: chain D residue 991 MET 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 44 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 190 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 342 optimal weight: 8.9990 chunk 295 optimal weight: 5.9990 chunk 192 optimal weight: 0.6980 chunk 177 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 265 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 147 ASN A 226 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN A 395 HIS A 949 HIS B 102 ASN B 147 ASN B 226 HIS B 395 HIS B 604 ASN ** B 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 395 HIS C 604 ASN ** C 949 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN D 226 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN D 395 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3381 r_free = 0.3381 target = 0.134750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.118533 restraints weight = 46788.158| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.60 r_work: 0.3091 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2995 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 : 0.596 9.392 45660 Z= 0.311 Chirality : 0.046 0.179 4752 Planarity : 0.005 0.059 6036 Dihedral : 5.724 45.301 4452 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 5.79 % Allowed : 21.47 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 4036 helix: -0.35 (0.23), residues: 488 sheet: 0.38 (0.13), residues: 1384 loop : -0.83 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 720 HIS 0.005 0.001 HIS B 151 PHE 0.010 0.001 PHE C 150 TYR 0.031 0.002 TYR B 100 ARG 0.007 0.001 ARG A 952 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 1164) hydrogen bonds : angle 5.15659 ( 3228) covalent geometry : bond 0.00452 (33468) covalent geometry : angle 0.59644 (45660) *********************** 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 917 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 717 time to evaluate : 5.640 Fit side-chains REVERT: A 26 ARG cc_start: 0.8478 (ttp-170) cc_final: 0.8066 (ttm170) REVERT: A 131 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7511 (mm-30) REVERT: A 135 GLN cc_start: 0.7208 (mt0) cc_final: 0.6965 (mt0) REVERT: A 177 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7925 (tp) REVERT: A 202 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8130 (pmm) REVERT: A 250 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.6732 (tt) REVERT: A 287 ASP cc_start: 0.8440 (p0) cc_final: 0.7791 (p0) REVERT: A 438 GLU cc_start: 0.8094 (pp20) cc_final: 0.7661 (pp20) REVERT: A 484 VAL cc_start: 0.9360 (OUTLIER) cc_final: 0.9117 (t) REVERT: A 654 TRP cc_start: 0.7427 (p90) cc_final: 0.7212 (p90) REVERT: A 781 ARG cc_start: 0.8168 (ptm160) cc_final: 0.7351 (ptp90) REVERT: A 969 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: A 987 ASP cc_start: 0.8432 (m-30) cc_final: 0.8184 (m-30) REVERT: A 1013 ARG cc_start: 0.7420 (OUTLIER) cc_final: 0.6947 (mtm110) REVERT: A 1022 GLN cc_start: 0.7520 (mm-40) cc_final: 0.6644 (tm-30) REVERT: B 26 ARG cc_start: 0.8480 (ttp-170) cc_final: 0.8078 (ttm170) REVERT: B 135 GLN cc_start: 0.7228 (mt0) cc_final: 0.6976 (mt0) REVERT: B 202 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8165 (pmm) REVERT: B 250 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6494 (tt) REVERT: B 287 ASP cc_start: 0.8406 (p0) cc_final: 0.7768 (p0) REVERT: B 336 ARG cc_start: 0.8067 (ptt-90) cc_final: 0.7564 (ptt-90) REVERT: B 338 GLU cc_start: 0.8294 (pt0) cc_final: 0.7573 (pt0) REVERT: B 438 GLU cc_start: 0.8108 (pp20) cc_final: 0.7684 (pp20) REVERT: B 484 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.9128 (t) REVERT: B 487 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7633 (tm-30) REVERT: B 502 MET cc_start: 0.8682 (mtp) cc_final: 0.8361 (mtm) REVERT: B 781 ARG cc_start: 0.8173 (ptm160) cc_final: 0.7350 (ptp90) REVERT: B 965 GLN cc_start: 0.7293 (tp40) cc_final: 0.6495 (tp40) REVERT: B 969 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: B 1013 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6807 (mtm110) REVERT: B 1022 GLN cc_start: 0.7537 (mm-40) cc_final: 0.6645 (tm-30) REVERT: C 26 ARG cc_start: 0.8485 (ttp-170) cc_final: 0.8069 (ttm170) REVERT: C 135 GLN cc_start: 0.7214 (mt0) cc_final: 0.6957 (mt0) REVERT: C 202 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8079 (pmm) REVERT: C 250 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6733 (tt) REVERT: C 287 ASP cc_start: 0.8442 (p0) cc_final: 0.7835 (p0) REVERT: C 336 ARG cc_start: 0.8023 (ptt-90) cc_final: 0.7508 (ptt-90) REVERT: C 338 GLU cc_start: 0.8299 (pt0) cc_final: 0.7574 (pt0) REVERT: C 438 GLU cc_start: 0.8090 (pp20) cc_final: 0.7663 (pp20) REVERT: C 484 VAL cc_start: 0.9363 (OUTLIER) cc_final: 0.9116 (t) REVERT: C 502 MET cc_start: 0.8562 (mtp) cc_final: 0.8278 (mtt) REVERT: C 781 ARG cc_start: 0.8154 (ptm160) cc_final: 0.7322 (ptp90) REVERT: C 969 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: C 987 ASP cc_start: 0.8435 (m-30) cc_final: 0.8161 (m-30) REVERT: C 1013 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6820 (mtm110) REVERT: C 1022 GLN cc_start: 0.7543 (mm-40) cc_final: 0.6666 (tm-30) REVERT: D 26 ARG cc_start: 0.8471 (ttp-170) cc_final: 0.8079 (ttm170) REVERT: D 46 ARG cc_start: 0.7075 (mtt90) cc_final: 0.6836 (mtt90) REVERT: D 131 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7481 (mm-30) REVERT: D 177 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7952 (tp) REVERT: D 202 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8098 (pmm) REVERT: D 250 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6743 (tt) REVERT: D 287 ASP cc_start: 0.8430 (p0) cc_final: 0.7806 (p0) REVERT: D 487 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7608 (tm-30) REVERT: D 502 MET cc_start: 0.8658 (mtp) cc_final: 0.8313 (mtm) REVERT: D 654 TRP cc_start: 0.7433 (p90) cc_final: 0.7221 (p90) REVERT: D 781 ARG cc_start: 0.8171 (ptm160) cc_final: 0.7351 (ptp90) REVERT: D 969 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: D 987 ASP cc_start: 0.8424 (m-30) cc_final: 0.8174 (m-30) REVERT: D 1013 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6819 (mtm110) REVERT: D 1022 GLN cc_start: 0.7544 (mm-40) cc_final: 0.6656 (tm-30) outliers start: 200 outliers final: 155 residues processed: 841 average time/residue: 0.6450 time to fit residues: 866.9411 Evaluate side-chains 871 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 695 time to evaluate : 10.881 ------------------------------------------------------------------------------- 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 223 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU 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 436 MET 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 632 SER 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 729 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 858 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 898 LEU 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 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 202 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 250 LEU 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 379 MET Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 436 MET 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 658 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 690 SER 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 795 VAL 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 895 VAL Chi-restraints excluded: chain B residue 898 LEU Chi-restraints excluded: chain B residue 922 LEU 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 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 148 SER 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 223 SER Chi-restraints excluded: chain C residue 250 LEU 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 423 MET Chi-restraints excluded: chain C residue 436 MET 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 583 ASN Chi-restraints excluded: chain C residue 632 SER 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 690 SER Chi-restraints excluded: chain C residue 706 THR 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 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 895 VAL Chi-restraints excluded: chain C residue 898 LEU Chi-restraints excluded: chain C residue 904 GLU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 952 ARG 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 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 177 LEU 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 223 SER 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 478 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 583 ASN 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 690 SER 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 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 861 SER Chi-restraints excluded: chain D residue 863 GLN Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 898 LEU Chi-restraints excluded: chain D residue 904 GLU Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 982 THR Chi-restraints excluded: chain D residue 1013 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 65 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 266 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 104 optimal weight: 0.5980 chunk 23 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 357 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 147 ASN A 226 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN A 395 HIS A 949 HIS B 102 ASN B 147 ASN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS B 885 ASN B 949 HIS B 964 GLN C 102 ASN C 226 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 395 HIS C 885 ASN C 949 HIS C 964 GLN D 102 ASN D 147 ASN D 226 HIS ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN D 395 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.136426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.120266 restraints weight = 46629.879| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.61 r_work: 0.3110 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33468 Z= 0.142 Angle : 0.559 9.177 45660 Z= 0.290 Chirality : 0.045 0.177 4752 Planarity : 0.004 0.057 6036 Dihedral : 5.521 45.418 4452 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.15 % Allowed : 22.37 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 4036 helix: -0.16 (0.24), residues: 488 sheet: 0.46 (0.14), residues: 1352 loop : -0.74 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 654 HIS 0.004 0.001 HIS C 151 PHE 0.007 0.001 PHE D 629 TYR 0.026 0.002 TYR B 100 ARG 0.005 0.001 ARG A 952 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 1164) hydrogen bonds : angle 5.03668 ( 3228) covalent geometry : bond 0.00330 (33468) covalent geometry : angle 0.55927 (45660) *********************** 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 905 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 727 time to evaluate : 3.571 Fit side-chains REVERT: A 131 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7534 (mm-30) REVERT: A 135 GLN cc_start: 0.7113 (mt0) cc_final: 0.6871 (mt0) REVERT: A 202 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8040 (pmm) REVERT: A 250 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6617 (tt) REVERT: A 264 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: A 287 ASP cc_start: 0.8400 (p0) cc_final: 0.7823 (p0) REVERT: A 438 GLU cc_start: 0.8099 (pp20) cc_final: 0.7704 (pp20) REVERT: A 473 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7904 (tpm-80) REVERT: A 781 ARG cc_start: 0.8119 (ptm160) cc_final: 0.7302 (ptp90) REVERT: A 969 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: A 987 ASP cc_start: 0.8395 (m-30) cc_final: 0.8172 (m-30) REVERT: A 1013 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.6820 (mtm110) REVERT: A 1022 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6579 (tm-30) REVERT: B 135 GLN cc_start: 0.7092 (mt0) cc_final: 0.6863 (mt0) REVERT: B 202 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8078 (pmm) REVERT: B 250 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6536 (tt) REVERT: B 264 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: B 287 ASP cc_start: 0.8431 (p0) cc_final: 0.7846 (p0) REVERT: B 336 ARG cc_start: 0.8082 (ptt-90) cc_final: 0.7572 (ptt-90) REVERT: B 338 GLU cc_start: 0.8257 (pt0) cc_final: 0.7526 (pt0) REVERT: B 438 GLU cc_start: 0.8090 (pp20) cc_final: 0.7685 (pp20) REVERT: B 502 MET cc_start: 0.8520 (mtp) cc_final: 0.8148 (mtm) REVERT: B 781 ARG cc_start: 0.8145 (ptm160) cc_final: 0.7326 (ptp90) REVERT: B 969 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: B 1013 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6814 (mtm110) REVERT: B 1022 GLN cc_start: 0.7366 (mm-40) cc_final: 0.6567 (tm-30) REVERT: C 135 GLN cc_start: 0.7099 (mt0) cc_final: 0.6849 (mt0) REVERT: C 202 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8004 (pmm) REVERT: C 250 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6533 (tt) REVERT: C 264 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: C 287 ASP cc_start: 0.8465 (p0) cc_final: 0.7832 (p0) REVERT: C 336 ARG cc_start: 0.8096 (ptt-90) cc_final: 0.7559 (ptt-90) REVERT: C 338 GLU cc_start: 0.8277 (pt0) cc_final: 0.7527 (pt0) REVERT: C 438 GLU cc_start: 0.8082 (pp20) cc_final: 0.7691 (pp20) REVERT: C 473 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7884 (tpm-80) REVERT: C 502 MET cc_start: 0.8613 (mtp) cc_final: 0.8332 (mtt) REVERT: C 781 ARG cc_start: 0.8120 (ptm160) cc_final: 0.7300 (ptp90) REVERT: C 969 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: C 987 ASP cc_start: 0.8377 (m-30) cc_final: 0.8156 (m-30) REVERT: C 1013 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6853 (mtm110) REVERT: C 1022 GLN cc_start: 0.7349 (mm-40) cc_final: 0.6585 (tm-30) REVERT: D 131 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7430 (mm-30) REVERT: D 135 GLN cc_start: 0.6802 (mm110) cc_final: 0.6392 (mm-40) REVERT: D 177 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7934 (tp) REVERT: D 202 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8040 (pmm) REVERT: D 250 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6695 (tt) REVERT: D 264 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7685 (pm20) REVERT: D 287 ASP cc_start: 0.8425 (p0) cc_final: 0.7815 (p0) REVERT: D 438 GLU cc_start: 0.8070 (pp20) cc_final: 0.7669 (pp20) REVERT: D 502 MET cc_start: 0.8475 (mtp) cc_final: 0.8112 (mtm) REVERT: D 654 TRP cc_start: 0.7328 (p90) cc_final: 0.7127 (p90) REVERT: D 781 ARG cc_start: 0.8145 (ptm160) cc_final: 0.7325 (ptp90) REVERT: D 969 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: D 987 ASP cc_start: 0.8360 (m-30) cc_final: 0.8139 (m-30) REVERT: D 1013 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6829 (mtm110) REVERT: D 1022 GLN cc_start: 0.7414 (mm-40) cc_final: 0.6548 (tm-30) outliers start: 178 outliers final: 131 residues processed: 837 average time/residue: 0.4807 time to fit residues: 629.1365 Evaluate side-chains 852 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 698 time to evaluate : 3.656 ------------------------------------------------------------------------------- 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 147 ASN 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 223 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU 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 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 632 SER 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 744 GLU Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 795 VAL 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 922 LEU Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1006 GLU 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 147 ASN 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 223 SER Chi-restraints excluded: chain B residue 250 LEU 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 478 VAL 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 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 922 LEU Chi-restraints excluded: chain B residue 964 GLN Chi-restraints excluded: chain B residue 969 GLU 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 148 SER Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU 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 423 MET Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 632 SER 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 729 THR Chi-restraints excluded: chain C residue 744 GLU Chi-restraints excluded: chain C residue 750 GLU Chi-restraints excluded: chain C residue 795 VAL 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 904 GLU Chi-restraints excluded: chain C residue 922 LEU Chi-restraints excluded: chain C residue 964 GLN Chi-restraints excluded: chain C residue 969 GLU 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 147 ASN Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 177 LEU 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 223 SER 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 478 VAL 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 744 GLU Chi-restraints excluded: chain D residue 750 GLU Chi-restraints excluded: chain D residue 795 VAL 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 861 SER 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 904 GLU Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 1013 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 130 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 346 optimal weight: 0.8980 chunk 236 optimal weight: 8.9990 chunk 287 optimal weight: 9.9990 chunk 392 optimal weight: 3.9990 chunk 288 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN A 395 HIS B 102 ASN B 226 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS B 719 GLN B 885 ASN B 949 HIS ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 395 HIS C 885 ASN D 147 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN D 395 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 ASN D 719 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.135139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.118878 restraints weight = 46892.045| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.60 r_work: 0.3093 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 33468 Z= 0.207 Angle : 0.605 8.739 45660 Z= 0.314 Chirality : 0.046 0.182 4752 Planarity : 0.005 0.069 6036 Dihedral : 5.621 44.901 4452 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.98 % Allowed : 22.77 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 4036 helix: -0.25 (0.23), residues: 488 sheet: 0.43 (0.14), residues: 1372 loop : -0.76 (0.14), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 654 HIS 0.006 0.001 HIS D 151 PHE 0.011 0.002 PHE A 127 TYR 0.030 0.002 TYR B 100 ARG 0.015 0.001 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 1164) hydrogen bonds : angle 5.08594 ( 3228) covalent geometry : bond 0.00484 (33468) covalent geometry : angle 0.60468 (45660) ********************** 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 885 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 713 time to evaluate : 3.782 Fit side-chains REVERT: A 131 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7514 (mm-30) REVERT: A 135 GLN cc_start: 0.7203 (mt0) cc_final: 0.6948 (mt0) REVERT: A 202 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8049 (pmm) REVERT: A 250 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6677 (tt) REVERT: A 438 GLU cc_start: 0.8118 (pp20) cc_final: 0.7681 (pp20) REVERT: A 473 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7934 (tpm-80) REVERT: A 781 ARG cc_start: 0.8140 (ptm160) cc_final: 0.7317 (ptp90) REVERT: A 969 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: A 987 ASP cc_start: 0.8370 (m-30) cc_final: 0.8154 (m-30) REVERT: A 1013 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6815 (mtm110) REVERT: A 1022 GLN cc_start: 0.7351 (mm-40) cc_final: 0.6542 (tm-30) REVERT: B 26 ARG cc_start: 0.8473 (ttp-170) cc_final: 0.7934 (ttm170) REVERT: B 135 GLN cc_start: 0.7216 (mt0) cc_final: 0.6947 (mt0) REVERT: B 202 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8092 (pmm) REVERT: B 250 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6592 (tt) REVERT: B 336 ARG cc_start: 0.8098 (ptt-90) cc_final: 0.7612 (ptt-90) REVERT: B 338 GLU cc_start: 0.8322 (pt0) cc_final: 0.7628 (pt0) REVERT: B 438 GLU cc_start: 0.8132 (pp20) cc_final: 0.7739 (pp20) REVERT: B 484 VAL cc_start: 0.9359 (p) cc_final: 0.9104 (t) REVERT: B 487 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 502 MET cc_start: 0.8674 (mtp) cc_final: 0.8344 (mtm) REVERT: B 781 ARG cc_start: 0.8137 (ptm160) cc_final: 0.7306 (ptp90) REVERT: B 969 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: B 1013 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6816 (mtm110) REVERT: B 1022 GLN cc_start: 0.7349 (mm-40) cc_final: 0.6570 (tm-30) REVERT: C 135 GLN cc_start: 0.7195 (mt0) cc_final: 0.6915 (mt0) REVERT: C 202 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8014 (pmm) REVERT: C 250 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6593 (tt) REVERT: C 287 ASP cc_start: 0.8503 (p0) cc_final: 0.7824 (p0) REVERT: C 336 ARG cc_start: 0.8108 (ptt-90) cc_final: 0.7614 (ptt-90) REVERT: C 338 GLU cc_start: 0.8307 (pt0) cc_final: 0.7594 (pt0) REVERT: C 438 GLU cc_start: 0.8119 (pp20) cc_final: 0.7682 (pp20) REVERT: C 502 MET cc_start: 0.8572 (mtp) cc_final: 0.8256 (mtt) REVERT: C 687 GLN cc_start: 0.6261 (mp10) cc_final: 0.6055 (mp10) REVERT: C 781 ARG cc_start: 0.8119 (ptm160) cc_final: 0.7298 (ptp90) REVERT: C 969 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: C 987 ASP cc_start: 0.8433 (m-30) cc_final: 0.8160 (m-30) REVERT: C 1013 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6818 (mtm110) REVERT: C 1022 GLN cc_start: 0.7382 (mm-40) cc_final: 0.6595 (tm-30) REVERT: D 26 ARG cc_start: 0.8539 (ttp-170) cc_final: 0.8023 (ttm170) REVERT: D 131 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7484 (mm-30) REVERT: D 177 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7955 (tp) REVERT: D 202 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8038 (pmm) REVERT: D 250 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6716 (tt) REVERT: D 438 GLU cc_start: 0.8125 (pp20) cc_final: 0.7691 (pp20) REVERT: D 502 MET cc_start: 0.8668 (mtp) cc_final: 0.8334 (mtt) REVERT: D 654 TRP cc_start: 0.7335 (p90) cc_final: 0.7115 (p90) REVERT: D 781 ARG cc_start: 0.8134 (ptm160) cc_final: 0.7302 (ptp90) REVERT: D 791 ASN cc_start: 0.7415 (m-40) cc_final: 0.6972 (m-40) REVERT: D 969 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: D 987 ASP cc_start: 0.8370 (m-30) cc_final: 0.8152 (m-30) REVERT: D 1013 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6826 (mtm110) REVERT: D 1022 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6588 (tm-30) outliers start: 172 outliers final: 145 residues processed: 821 average time/residue: 0.4795 time to fit residues: 623.0139 Evaluate side-chains 864 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 701 time to evaluate : 3.516 ------------------------------------------------------------------------------- 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 223 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 250 LEU 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 473 ARG Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 632 SER 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 690 SER 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 795 VAL 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 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 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 223 SER Chi-restraints excluded: chain B residue 250 LEU 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 478 VAL 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 729 THR Chi-restraints excluded: chain B residue 744 GLU Chi-restraints excluded: chain B residue 750 GLU Chi-restraints excluded: chain B residue 795 VAL 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 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 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 148 SER 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 223 SER Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 264 GLU 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 478 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 632 SER 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 690 SER 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 795 VAL 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 904 GLU 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 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 177 LEU 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 223 SER 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 478 VAL 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 679 LEU Chi-restraints excluded: chain D residue 690 SER 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 795 VAL 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 861 SER 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 904 GLU 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 1013 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 57 optimal weight: 0.9990 chunk 365 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 289 optimal weight: 9.9990 chunk 254 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 331 optimal weight: 3.9990 chunk 204 optimal weight: 0.6980 chunk 337 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 147 ASN ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN A 395 HIS ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 GLN B 102 ASN B 147 ASN B 226 HIS ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 964 GLN C 102 ASN ** C 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 GLN C 395 HIS ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 964 GLN D 102 ASN ** D 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN D 395 HIS ** D 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 604 ASN ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 949 HIS D 964 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.137816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.121732 restraints weight = 46416.841| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.60 r_work: 0.3131 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33468 Z= 0.115 Angle : 0.552 8.483 45660 Z= 0.286 Chirality : 0.044 0.183 4752 Planarity : 0.004 0.057 6036 Dihedral : 5.379 45.813 4452 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.40 % Allowed : 23.58 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 4036 helix: -0.03 (0.24), residues: 488 sheet: 0.55 (0.14), residues: 1368 loop : -0.63 (0.14), residues: 2180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 654 HIS 0.003 0.001 HIS A 653 PHE 0.009 0.001 PHE A 127 TYR 0.023 0.002 TYR B 100 ARG 0.010 0.001 ARG C 46 Details of bonding type rmsd hydrogen bonds : bond 0.03280 ( 1164) hydrogen bonds : angle 4.99338 ( 3228) covalent geometry : bond 0.00265 (33468) covalent geometry : angle 0.55207 (45660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19466.93 seconds wall clock time: 342 minutes 48.56 seconds (20568.56 seconds total)