Starting phenix.real_space_refine on Mon Aug 25 09:22:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yrp_39547/08_2025/8yrp_39547.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yrp_39547/08_2025/8yrp_39547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yrp_39547/08_2025/8yrp_39547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yrp_39547/08_2025/8yrp_39547.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yrp_39547/08_2025/8yrp_39547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yrp_39547/08_2025/8yrp_39547.map" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1667 atoms to isotropic. 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 114 5.16 5 C 16238 2.51 5 N 4267 2.21 5 O 4843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25462 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7906 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 51, 'TRANS': 961} Chain breaks: 8 Chain: "B" Number of atoms: 7955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 7955 Classifications: {'peptide': 1017} Link IDs: {'PTRANS': 50, 'TRANS': 966} Chain breaks: 9 Chain: "C" Number of atoms: 7934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7934 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 51, 'TRANS': 964} Chain breaks: 8 Chain: "n" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 873 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "o" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 794 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 6, 'TRANS': 98} Time building chain proxies: 5.91, per 1000 atoms: 0.23 Number of scatterers: 25462 At special positions: 0 Unit cell: (146.08, 175.96, 184.26, 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 114 16.00 O 4843 8.00 N 4267 7.00 C 16238 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.02 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.02 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.02 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.73 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.04 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.02 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.05 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.05 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.02 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.02 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.01 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.04 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.02 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=1.99 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.04 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.02 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.04 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.02 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.02 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=1.77 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS n 22 " - pdb=" SG CYS n 96 " distance=2.03 Simple disulfide: pdb=" SG CYS o 23 " - pdb=" SG CYS o 88 " distance=2.03 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: 1.56 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6104 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 50 sheets defined 21.0% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.605A pdb=" N TRP A 351 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.540A pdb=" N LEU A 385 " --> pdb=" O PRO A 382 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 382 through 386' Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 744 through 753 removed outlier: 4.126A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 814 through 824 removed outlier: 4.131A pdb=" N ASP A 818 " --> pdb=" O SER A 814 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 898 through 905 removed outlier: 4.112A pdb=" N ARG A 903 " --> pdb=" O GLN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.665A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 removed outlier: 3.633A pdb=" N PHE A 925 " --> pdb=" O ILE A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 965 Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.684A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1029 removed outlier: 4.833A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 335 through 341 removed outlier: 4.081A pdb=" N VAL B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.777A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 406 removed outlier: 3.916A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 403 through 406' Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 436 through 441 removed outlier: 3.511A pdb=" N SER B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.250A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 780 Processing helix chain 'B' and resid 814 through 824 Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.548A pdb=" N ALA B 869 " --> pdb=" O ASP B 865 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 875 " --> pdb=" O TYR B 871 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR B 881 " --> pdb=" O ALA B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 886 No H-bonds generated for 'chain 'B' and resid 884 through 886' Processing helix chain 'B' and resid 896 through 905 removed outlier: 3.505A pdb=" N ALA B 901 " --> pdb=" O ALA B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 939 removed outlier: 3.724A pdb=" N PHE B 925 " --> pdb=" O ILE B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 966 Processing helix chain 'B' and resid 974 through 982 Processing helix chain 'B' and resid 983 through 1030 removed outlier: 4.457A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER B1028 " --> pdb=" O ALA B1024 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.504A pdb=" N ILE C 408 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 753 removed outlier: 3.586A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 781 removed outlier: 3.614A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.672A pdb=" N ASP C 818 " --> pdb=" O SER C 814 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 881 removed outlier: 4.079A pdb=" N THR C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 880 " --> pdb=" O LEU C 876 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR C 881 " --> pdb=" O ALA C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 911 through 917 removed outlier: 3.601A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 removed outlier: 4.252A pdb=" N PHE C 925 " --> pdb=" O ILE C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 removed outlier: 3.665A pdb=" N GLN C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.617A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1029 removed outlier: 5.256A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN C 990 " --> pdb=" O GLU C 986 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C1027 " --> pdb=" O ALA C1023 " (cutoff:3.500A) Processing helix chain 'n' and resid 87 through 91 Processing helix chain 'o' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.683A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 8.807A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 201 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 199 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 204 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.270A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.552A pdb=" N ARG A 235 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 107 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.492A pdb=" N VAL A 126 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 10.095A pdb=" N GLU A 167 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.124A pdb=" N ILE A 128 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N THR A 165 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL A 130 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASN A 163 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU A 132 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA A 161 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLN A 134 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.731A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 609 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 356 removed outlier: 3.744A pdb=" N ASN A 392 " --> pdb=" O GLU A 514 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR A 428 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AA7, first strand: chain 'A' and resid 537 through 541 Processing sheet with id=AA8, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.399A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 710 through 711 Processing sheet with id=AB1, first strand: chain 'A' and resid 724 through 726 removed outlier: 3.885A pdb=" N LEU A 725 " --> pdb=" O VAL A1058 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A1058 " --> pdb=" O LEU A 725 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 731 through 734 removed outlier: 3.980A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1079 through 1081 removed outlier: 3.893A pdb=" N ILE A1079 " --> pdb=" O HIS A1086 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS A1086 " --> pdb=" O ILE A1079 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N PHE A1087 " --> pdb=" O PHE A1119 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A1119 " --> pdb=" O PHE A1087 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1092 through 1095 removed outlier: 3.565A pdb=" N VAL A1092 " --> pdb=" O THR A1103 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A1103 " --> pdb=" O VAL A1092 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.041A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 266 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 89 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 90 " --> pdb=" O PHE B 192 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 204 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL B 191 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR B 202 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 201 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 225 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.256A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 166 through 170 removed outlier: 4.133A pdb=" N GLY B 103 " --> pdb=" O LEU B 239 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.669A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 309 through 316 removed outlier: 5.312A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY B 591 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 324 through 326 removed outlier: 3.507A pdb=" N THR B 586 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 352 through 356 removed outlier: 3.835A pdb=" N ASN B 352 " --> pdb=" O SER B 397 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 397 " --> pdb=" O ASN B 352 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 393 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP B 396 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.579A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC5, first strand: chain 'B' and resid 651 through 658 removed outlier: 4.875A pdb=" N THR B 694 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASN B 656 " --> pdb=" O THR B 694 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS B 669 " --> pdb=" O TYR B 693 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE B 662 " --> pdb=" O ALA B 670 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 700 through 702 Processing sheet with id=AC7, first strand: chain 'B' and resid 715 through 716 removed outlier: 3.864A pdb=" N ASN B 715 " --> pdb=" O ALA B1068 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B1068 " --> pdb=" O ASN B 715 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 725 through 726 removed outlier: 3.642A pdb=" N LEU B 725 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B1052 " --> pdb=" O VAL B1059 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B1061 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B1050 " --> pdb=" O LEU B1061 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 732 through 734 Processing sheet with id=AD1, first strand: chain 'B' and resid 1074 through 1075 removed outlier: 3.530A pdb=" N VAL B1094 " --> pdb=" O PHE B1101 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B1101 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.991A pdb=" N GLY B1122 " --> pdb=" O ALA B1085 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE B1079 " --> pdb=" O HIS B1086 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.745A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY C 89 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.988A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.577A pdb=" N GLY C 103 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.718A pdb=" N VAL C 126 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE C 128 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL C 130 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU C 132 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN C 134 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA C 161 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 192 through 195 removed outlier: 4.112A pdb=" N ILE C 201 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL C 225 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AD9, first strand: chain 'C' and resid 309 through 310 removed outlier: 4.669A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 352 through 355 removed outlier: 3.986A pdb=" N ALA C 395 " --> pdb=" O LYS C 354 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN C 392 " --> pdb=" O GLU C 514 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU C 514 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP C 434 " --> pdb=" O ARG C 507 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 432 " --> pdb=" O VAL C 509 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 511 " --> pdb=" O CYS C 430 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N CYS C 430 " --> pdb=" O LEU C 511 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 450 through 452 removed outlier: 3.621A pdb=" N TYR C 451 " --> pdb=" O GLN C 491 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN C 491 " --> pdb=" O TYR C 451 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 536 through 541 Processing sheet with id=AE4, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.168A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 710 through 718 removed outlier: 3.591A pdb=" N THR C 714 " --> pdb=" O GLN C1069 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLN C1069 " --> pdb=" O THR C 714 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N PHE C 716 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ILE C 718 " --> pdb=" O TYR C1065 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N TYR C1065 " --> pdb=" O ILE C 718 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C1094 " --> pdb=" O PHE C1101 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE C1101 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 724 through 726 removed outlier: 3.665A pdb=" N LEU C 725 " --> pdb=" O VAL C1058 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1079 through 1081 removed outlier: 3.950A pdb=" N ILE C1079 " --> pdb=" O HIS C1086 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY C1122 " --> pdb=" O ALA C1085 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE C1087 " --> pdb=" O VAL C1120 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL C1120 " --> pdb=" O PHE C1087 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'n' and resid 3 through 6 removed outlier: 3.566A pdb=" N ASP n 73 " --> pdb=" O GLN n 78 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'n' and resid 58 through 60 removed outlier: 3.556A pdb=" N ASN n 59 " --> pdb=" O GLY n 51 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG n 39 " --> pdb=" O GLU n 47 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE n 49 " --> pdb=" O TRP n 37 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TRP n 37 " --> pdb=" O ILE n 49 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLY n 51 " --> pdb=" O TRP n 35 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TRP n 35 " --> pdb=" O GLY n 51 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL n 93 " --> pdb=" O GLN n 40 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TYR n 105 " --> pdb=" O ARG n 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'n' and resid 58 through 60 removed outlier: 3.556A pdb=" N ASN n 59 " --> pdb=" O GLY n 51 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG n 39 " --> pdb=" O GLU n 47 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE n 49 " --> pdb=" O TRP n 37 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N TRP n 37 " --> pdb=" O ILE n 49 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N GLY n 51 " --> pdb=" O TRP n 35 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TRP n 35 " --> pdb=" O GLY n 51 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL n 93 " --> pdb=" O GLN n 40 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'n' and resid 68 through 69 removed outlier: 3.575A pdb=" N THR n 69 " --> pdb=" O HIS n 82 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'o' and resid 4 through 6 Processing sheet with id=AF4, first strand: chain 'o' and resid 10 through 12 removed outlier: 5.637A pdb=" N LEU o 11 " --> pdb=" O GLU o 104 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA o 84 " --> pdb=" O VAL o 103 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'o' and resid 53 through 54 removed outlier: 6.644A pdb=" N TRP o 35 " --> pdb=" O LEU o 47 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS o 90 " --> pdb=" O PHE o 96 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE o 96 " --> pdb=" O HIS o 90 " (cutoff:3.500A) 866 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.65 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 7581 1.34 - 1.47: 7199 1.47 - 1.60: 11116 1.60 - 1.74: 3 1.74 - 1.87: 138 Bond restraints: 26037 Sorted by residual: bond pdb=" CA LYS A 823 " pdb=" C LYS A 823 " ideal model delta sigma weight residual 1.522 1.631 -0.109 1.72e-02 3.38e+03 4.02e+01 bond pdb=" C PRO B 984 " pdb=" N PRO B 985 " ideal model delta sigma weight residual 1.334 1.429 -0.095 2.34e-02 1.83e+03 1.64e+01 bond pdb=" C CYS A1041 " pdb=" N GLY A1042 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.48e-02 4.57e+03 1.60e+01 bond pdb=" C ALA B1054 " pdb=" N PRO B1055 " ideal model delta sigma weight residual 1.333 1.386 -0.053 1.44e-02 4.82e+03 1.33e+01 bond pdb=" N VAL C 532 " pdb=" CA VAL C 532 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.83e+00 ... (remaining 26032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 34247 3.39 - 6.78: 1009 6.78 - 10.17: 125 10.17 - 13.57: 30 13.57 - 16.96: 6 Bond angle restraints: 35417 Sorted by residual: angle pdb=" N ILE A 718 " pdb=" CA ILE A 718 " pdb=" C ILE A 718 " ideal model delta sigma weight residual 108.12 98.09 10.03 1.44e+00 4.82e-01 4.85e+01 angle pdb=" N GLY A 878 " pdb=" CA GLY A 878 " pdb=" C GLY A 878 " ideal model delta sigma weight residual 113.18 128.74 -15.56 2.37e+00 1.78e-01 4.31e+01 angle pdb=" N ILE A1079 " pdb=" CA ILE A1079 " pdb=" C ILE A1079 " ideal model delta sigma weight residual 107.24 96.50 10.74 1.68e+00 3.54e-01 4.09e+01 angle pdb=" C SER B 801 " pdb=" N GLN B 802 " pdb=" CA GLN B 802 " ideal model delta sigma weight residual 122.26 112.12 10.14 1.59e+00 3.96e-01 4.07e+01 angle pdb=" CA PHE A 821 " pdb=" CB PHE A 821 " pdb=" CG PHE A 821 " ideal model delta sigma weight residual 113.80 120.07 -6.27 1.00e+00 1.00e+00 3.94e+01 ... (remaining 35412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 13628 17.71 - 35.42: 1505 35.42 - 53.13: 307 53.13 - 70.84: 67 70.84 - 88.55: 24 Dihedral angle restraints: 15531 sinusoidal: 6047 harmonic: 9484 Sorted by residual: dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 523 " pdb=" CB CYS A 523 " ideal model delta sinusoidal sigma weight residual 93.00 5.51 87.49 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS A 660 " pdb=" SG CYS A 660 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual 93.00 177.07 -84.07 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CB CYS A 736 " pdb=" SG CYS A 736 " pdb=" SG CYS A 758 " pdb=" CB CYS A 758 " ideal model delta sinusoidal sigma weight residual -86.00 -6.32 -79.68 1 1.00e+01 1.00e-02 7.88e+01 ... (remaining 15528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 3606 0.120 - 0.239: 375 0.239 - 0.359: 35 0.359 - 0.478: 7 0.478 - 0.598: 3 Chirality restraints: 4026 Sorted by residual: chirality pdb=" CG LEU A 943 " pdb=" CB LEU A 943 " pdb=" CD1 LEU A 943 " pdb=" CD2 LEU A 943 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 8.94e+00 chirality pdb=" CG LEU C 609 " pdb=" CB LEU C 609 " pdb=" CD1 LEU C 609 " pdb=" CD2 LEU C 609 " both_signs ideal model delta sigma weight residual False -2.59 -2.07 -0.52 2.00e-01 2.50e+01 6.67e+00 chirality pdb=" CB ILE A 664 " pdb=" CA ILE A 664 " pdb=" CG1 ILE A 664 " pdb=" CG2 ILE A 664 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.49 2.00e-01 2.50e+01 5.93e+00 ... (remaining 4023 not shown) Planarity restraints: 4585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A1106 " -0.026 2.00e-02 2.50e+03 5.10e-02 2.61e+01 pdb=" C ASN A1106 " 0.088 2.00e-02 2.50e+03 pdb=" O ASN A1106 " -0.032 2.00e-02 2.50e+03 pdb=" N PHE A1107 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1067 " -0.026 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C PRO A1067 " 0.088 2.00e-02 2.50e+03 pdb=" O PRO A1067 " -0.033 2.00e-02 2.50e+03 pdb=" N ALA A1068 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1061 " 0.023 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C LEU A1061 " -0.082 2.00e-02 2.50e+03 pdb=" O LEU A1061 " 0.030 2.00e-02 2.50e+03 pdb=" N HIS A1062 " 0.029 2.00e-02 2.50e+03 ... (remaining 4582 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 9 2.03 - 2.75: 3645 2.75 - 3.47: 35560 3.47 - 4.18: 60316 4.18 - 4.90: 102187 Nonbonded interactions: 201717 Sorted by model distance: nonbonded pdb=" O SER A 671 " pdb=" CG1 ILE A 691 " model vdw 1.316 3.440 nonbonded pdb=" OG SER A 671 " pdb=" CE2 TYR A 693 " model vdw 1.515 3.340 nonbonded pdb=" CG2 VAL A 318 " pdb=" SG CYS A 588 " model vdw 1.741 3.820 nonbonded pdb=" CB SER A 671 " pdb=" CE2 TYR A 693 " model vdw 1.905 3.740 nonbonded pdb=" O LYS B1026 " pdb=" CB CYS B1030 " model vdw 1.910 2.752 ... (remaining 201712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 805 or resid 809 through 1133)) selection = (chain 'B' and (resid 14 through 619 or resid 635 through 672 or resid 689 throu \ gh 825 or resid 853 through 1133)) selection = (chain 'C' and (resid 14 through 619 or resid 635 through 672 or resid 689 throu \ gh 805 or resid 809 through 1133)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.840 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 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 : 0.010 0.702 26080 Z= 0.493 Angle : 1.424 37.265 35503 Z= 0.789 Chirality : 0.078 0.598 4026 Planarity : 0.009 0.109 4585 Dihedral : 15.382 88.551 9298 Min Nonbonded Distance : 1.316 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.53 % Allowed : 7.17 % Favored : 92.30 % Rotamer: Outliers : 1.44 % Allowed : 11.13 % Favored : 87.43 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.67 (0.13), residues: 3206 helix: -1.74 (0.17), residues: 583 sheet: -0.69 (0.22), residues: 520 loop : -2.19 (0.11), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1037 TYR 0.054 0.004 TYR B1108 PHE 0.060 0.005 PHE A1050 TRP 0.046 0.004 TRP C1100 HIS 0.016 0.003 HIS C1056 Details of bonding type rmsd covalent geometry : bond 0.00935 (26037) covalent geometry : angle 1.38970 (35417) SS BOND : bond 0.11453 ( 43) SS BOND : angle 6.42992 ( 86) hydrogen bonds : bond 0.27517 ( 853) hydrogen bonds : angle 9.64945 ( 2376) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 302 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.3980 (mmtt) cc_final: 0.3159 (mptt) REVERT: A 44 ARG cc_start: 0.7210 (mtt90) cc_final: 0.6988 (mpp80) REVERT: A 377 CYS cc_start: 0.6134 (OUTLIER) cc_final: 0.5584 (t) REVERT: A 560 PHE cc_start: 0.6816 (p90) cc_final: 0.6536 (p90) REVERT: A 943 LEU cc_start: 0.6458 (mp) cc_final: 0.6178 (mt) REVERT: A 971 ILE cc_start: 0.8339 (pt) cc_final: 0.7986 (tp) REVERT: B 167 GLU cc_start: 0.7924 (tp30) cc_final: 0.7099 (tm-30) REVERT: B 198 TYR cc_start: 0.6687 (m-80) cc_final: 0.6208 (m-10) REVERT: B 460 LYS cc_start: 0.7214 (tptp) cc_final: 0.6973 (tptp) REVERT: B 884 TRP cc_start: 0.4345 (p90) cc_final: 0.4006 (p-90) REVERT: C 198 TYR cc_start: 0.7571 (m-10) cc_final: 0.7086 (m-10) REVERT: C 349 TYR cc_start: 0.7659 (p90) cc_final: 0.7368 (p90) REVERT: C 419 TYR cc_start: 0.5213 (m-10) cc_final: 0.4694 (m-80) REVERT: C 531 LEU cc_start: 0.4316 (OUTLIER) cc_final: 0.3723 (mt) REVERT: C 583 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7450 (pt) REVERT: C 1070 GLU cc_start: 0.4182 (pm20) cc_final: 0.3851 (pt0) REVERT: n 70 MET cc_start: -0.0552 (mtp) cc_final: -0.0883 (mtm) REVERT: n 99 MET cc_start: 0.5222 (tmm) cc_final: 0.4373 (ttt) REVERT: n 110 THR cc_start: 0.4377 (p) cc_final: 0.3975 (m) outliers start: 41 outliers final: 14 residues processed: 338 average time/residue: 0.1723 time to fit residues: 89.4572 Evaluate side-chains 173 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 881 THR Chi-restraints excluded: chain A residue 1030 CYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 356 ILE Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain C residue 583 LEU Chi-restraints excluded: chain o residue 6 GLN Chi-restraints excluded: chain o residue 10 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 209 ASN A 216 GLN A 538 ASN A 753 GLN A 782 GLN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 911 GLN A1034 GLN ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 ASN A1099 HIS A1117 ASN A1123 ASN B 23 GLN B 49 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN B 386 ASN ** B 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN ** B 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 963 GLN B 990 GLN B1021 ASN B1086 HIS C 17 ASN C 49 HIS C 87 ASN C 115 GLN C 163 ASN C 186 ASN C 491 GLN C 517 HIS ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 782 GLN C 870 GLN C1000 GLN ** n 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 3 GLN o 31 ASN o 89 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.139179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.112931 restraints weight = 111396.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.115521 restraints weight = 67055.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.116901 restraints weight = 43473.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.118235 restraints weight = 29894.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.118374 restraints weight = 24423.645| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 26080 Z= 0.260 Angle : 0.821 12.139 35503 Z= 0.436 Chirality : 0.050 0.255 4026 Planarity : 0.006 0.093 4585 Dihedral : 7.280 60.819 3529 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.64 % Favored : 93.29 % Rotamer: Outliers : 3.55 % Allowed : 15.03 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.46 (0.13), residues: 3206 helix: -1.67 (0.17), residues: 615 sheet: -0.69 (0.22), residues: 525 loop : -1.97 (0.12), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 401 TYR 0.033 0.002 TYR A 311 PHE 0.041 0.003 PHE C 800 TRP 0.020 0.002 TRP B 631 HIS 0.014 0.002 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00546 (26037) covalent geometry : angle 0.81691 (35417) SS BOND : bond 0.01239 ( 43) SS BOND : angle 1.88822 ( 86) hydrogen bonds : bond 0.08341 ( 853) hydrogen bonds : angle 7.92152 ( 2376) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 195 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7317 (mtt90) cc_final: 0.7019 (mpp80) REVERT: A 503 TYR cc_start: 0.1909 (OUTLIER) cc_final: 0.1535 (m-80) REVERT: A 569 ASP cc_start: 0.7230 (t70) cc_final: 0.6880 (t0) REVERT: A 962 LYS cc_start: 0.9146 (mmmt) cc_final: 0.8939 (mmmm) REVERT: A 1015 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8020 (mp0) REVERT: B 167 GLU cc_start: 0.8275 (tp30) cc_final: 0.7517 (tm-30) REVERT: B 198 TYR cc_start: 0.6999 (m-80) cc_final: 0.6622 (m-10) REVERT: B 308 LYS cc_start: 0.5741 (OUTLIER) cc_final: 0.5475 (ttmm) REVERT: B 355 ARG cc_start: 0.8192 (ttp-170) cc_final: 0.7956 (tmm-80) REVERT: B 771 GLU cc_start: 0.8453 (tt0) cc_final: 0.8067 (tm-30) REVERT: B 1065 TYR cc_start: 0.6095 (m-80) cc_final: 0.5801 (m-80) REVERT: B 1105 ARG cc_start: 0.5263 (mtt180) cc_final: 0.4380 (tpm170) REVERT: C 312 GLN cc_start: 0.7367 (tm-30) cc_final: 0.7097 (tm-30) REVERT: C 565 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.4791 (ttm170) REVERT: C 740 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8446 (tt) REVERT: C 1070 GLU cc_start: 0.4171 (pm20) cc_final: 0.3443 (pt0) REVERT: n 70 MET cc_start: -0.0218 (mtp) cc_final: -0.0581 (mtm) REVERT: o 6 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.5643 (mp10) REVERT: o 45 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7629 (ptpp) outliers start: 101 outliers final: 55 residues processed: 279 average time/residue: 0.1648 time to fit residues: 74.8029 Evaluate side-chains 213 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 152 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 801 SER Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 914 LEU Chi-restraints excluded: chain B residue 955 GLN Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 886 PHE Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain o residue 6 GLN Chi-restraints excluded: chain o residue 45 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 100 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 125 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 39 optimal weight: 40.0000 chunk 181 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 253 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 GLN ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 GLN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 924 GLN B 951 ASN ** B1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN C1034 GLN C1046 HIS n 40 GLN o 38 GLN ** o 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.138521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.112429 restraints weight = 112491.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.115233 restraints weight = 61937.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.116201 restraints weight = 43037.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.117422 restraints weight = 30501.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.118007 restraints weight = 24541.189| |-----------------------------------------------------------------------------| r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 26080 Z= 0.226 Angle : 0.747 11.908 35503 Z= 0.395 Chirality : 0.048 0.310 4026 Planarity : 0.006 0.165 4585 Dihedral : 6.514 59.894 3511 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.46 % Allowed : 16.65 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.13), residues: 3206 helix: -1.51 (0.18), residues: 619 sheet: -0.69 (0.21), residues: 598 loop : -1.91 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 212 TYR 0.023 0.002 TYR B 378 PHE 0.035 0.002 PHE A1060 TRP 0.012 0.001 TRP B 631 HIS 0.011 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00481 (26037) covalent geometry : angle 0.74359 (35417) SS BOND : bond 0.00525 ( 43) SS BOND : angle 1.68657 ( 86) hydrogen bonds : bond 0.07011 ( 853) hydrogen bonds : angle 7.46003 ( 2376) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 179 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 TYR cc_start: 0.1563 (OUTLIER) cc_final: 0.1270 (m-80) REVERT: A 882 SER cc_start: 0.4867 (OUTLIER) cc_final: 0.4531 (p) REVERT: B 58 PHE cc_start: 0.5316 (OUTLIER) cc_final: 0.5054 (m-10) REVERT: B 167 GLU cc_start: 0.8303 (tp30) cc_final: 0.7982 (tm-30) REVERT: B 198 TYR cc_start: 0.7021 (m-80) cc_final: 0.6644 (m-10) REVERT: B 201 ILE cc_start: 0.7106 (mp) cc_final: 0.6702 (mt) REVERT: B 273 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: B 308 LYS cc_start: 0.5827 (OUTLIER) cc_final: 0.5615 (ttmm) REVERT: B 358 ASN cc_start: 0.7853 (t0) cc_final: 0.7409 (m-40) REVERT: B 725 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7531 (pp) REVERT: B 771 GLU cc_start: 0.8381 (tt0) cc_final: 0.7996 (tm-30) REVERT: B 867 MET cc_start: 0.7631 (mtm) cc_final: 0.7398 (mmp) REVERT: B 907 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6144 (mm) REVERT: B 1065 TYR cc_start: 0.6251 (m-80) cc_final: 0.5967 (m-80) REVERT: C 740 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8283 (tt) REVERT: C 867 MET cc_start: 0.7995 (mtt) cc_final: 0.7697 (ptp) REVERT: o 6 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.6676 (mp10) REVERT: o 45 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7769 (ptpp) outliers start: 127 outliers final: 64 residues processed: 282 average time/residue: 0.1552 time to fit residues: 71.0895 Evaluate side-chains 224 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 150 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 PHE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 273 PHE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 308 LYS Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1039 ASP Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1062 HIS Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain o residue 6 GLN Chi-restraints excluded: chain o residue 45 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 258 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 245 optimal weight: 50.0000 chunk 14 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 947 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 963 GLN C 312 GLN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN C 955 GLN ** C1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.137484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.111178 restraints weight = 112148.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.114424 restraints weight = 61635.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.115025 restraints weight = 41566.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.116077 restraints weight = 29962.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.116677 restraints weight = 23997.726| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6090 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 26080 Z= 0.233 Angle : 0.746 11.932 35503 Z= 0.393 Chirality : 0.048 0.304 4026 Planarity : 0.006 0.132 4585 Dihedral : 6.305 59.587 3503 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.92 % Allowed : 18.19 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.14), residues: 3206 helix: -1.38 (0.18), residues: 609 sheet: -0.83 (0.21), residues: 590 loop : -1.82 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 212 TYR 0.025 0.002 TYR B 378 PHE 0.036 0.002 PHE C 800 TRP 0.016 0.002 TRP n 34 HIS 0.012 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00508 (26037) covalent geometry : angle 0.74171 (35417) SS BOND : bond 0.00529 ( 43) SS BOND : angle 1.81862 ( 86) hydrogen bonds : bond 0.06655 ( 853) hydrogen bonds : angle 7.33701 ( 2376) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 167 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.5441 (OUTLIER) cc_final: 0.5017 (tp) REVERT: A 503 TYR cc_start: 0.1522 (OUTLIER) cc_final: 0.1257 (m-80) REVERT: A 717 THR cc_start: 0.5916 (OUTLIER) cc_final: 0.5590 (t) REVERT: A 882 SER cc_start: 0.5053 (OUTLIER) cc_final: 0.4731 (p) REVERT: B 167 GLU cc_start: 0.8271 (tp30) cc_final: 0.7943 (tm-30) REVERT: B 198 TYR cc_start: 0.6898 (m-80) cc_final: 0.6488 (m-10) REVERT: B 201 ILE cc_start: 0.7212 (mp) cc_final: 0.6780 (mt) REVERT: B 358 ASN cc_start: 0.7803 (t0) cc_final: 0.7397 (m-40) REVERT: B 617 GLU cc_start: 0.4501 (pm20) cc_final: 0.4206 (pm20) REVERT: B 725 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7657 (pp) REVERT: B 771 GLU cc_start: 0.8352 (tt0) cc_final: 0.8012 (tm-30) REVERT: B 1065 TYR cc_start: 0.6252 (m-80) cc_final: 0.6000 (m-80) REVERT: C 740 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8255 (tt) REVERT: o 6 GLN cc_start: 0.7648 (OUTLIER) cc_final: 0.6466 (mp10) outliers start: 140 outliers final: 86 residues processed: 285 average time/residue: 0.1494 time to fit residues: 70.3392 Evaluate side-chains 237 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 144 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 653 HIS Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 597 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 955 GLN Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1039 ASP Chi-restraints excluded: chain C residue 1046 HIS Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1062 HIS Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain o residue 6 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 177 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 267 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 260 optimal weight: 8.9990 chunk 32 optimal weight: 30.0000 chunk 306 optimal weight: 40.0000 chunk 85 optimal weight: 9.9990 chunk 176 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 772 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** B1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.140083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.114010 restraints weight = 107781.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.116983 restraints weight = 58944.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.117995 restraints weight = 41402.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.119015 restraints weight = 28962.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.119624 restraints weight = 23788.143| |-----------------------------------------------------------------------------| r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26080 Z= 0.170 Angle : 0.682 11.449 35503 Z= 0.355 Chirality : 0.047 0.306 4026 Planarity : 0.005 0.097 4585 Dihedral : 6.026 58.566 3503 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.50 % Allowed : 19.56 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.14), residues: 3206 helix: -1.22 (0.19), residues: 623 sheet: -0.75 (0.22), residues: 594 loop : -1.71 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 212 TYR 0.024 0.001 TYR B 378 PHE 0.027 0.002 PHE A1060 TRP 0.012 0.001 TRP n 34 HIS 0.008 0.001 HIS A1099 Details of bonding type rmsd covalent geometry : bond 0.00368 (26037) covalent geometry : angle 0.67745 (35417) SS BOND : bond 0.00435 ( 43) SS BOND : angle 1.75653 ( 86) hydrogen bonds : bond 0.05883 ( 853) hydrogen bonds : angle 6.99695 ( 2376) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 170 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 TYR cc_start: 0.1325 (OUTLIER) cc_final: 0.1083 (m-80) REVERT: A 882 SER cc_start: 0.4904 (OUTLIER) cc_final: 0.4614 (p) REVERT: B 167 GLU cc_start: 0.8289 (tp30) cc_final: 0.7997 (tm-30) REVERT: B 198 TYR cc_start: 0.6952 (m-80) cc_final: 0.6608 (m-10) REVERT: B 201 ILE cc_start: 0.7135 (mp) cc_final: 0.6719 (mt) REVERT: B 358 ASN cc_start: 0.7973 (t0) cc_final: 0.7504 (m-40) REVERT: B 634 TYR cc_start: 0.3626 (OUTLIER) cc_final: 0.3003 (m-80) REVERT: B 771 GLU cc_start: 0.8380 (tt0) cc_final: 0.8067 (tm-30) REVERT: B 1065 TYR cc_start: 0.6182 (m-80) cc_final: 0.5929 (m-80) REVERT: B 1105 ARG cc_start: 0.6496 (mtt180) cc_final: 0.4451 (tpt170) REVERT: C 740 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8143 (tt) REVERT: C 867 MET cc_start: 0.7990 (mtt) cc_final: 0.7737 (ptp) REVERT: o 6 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.6662 (mp10) outliers start: 128 outliers final: 82 residues processed: 278 average time/residue: 0.1559 time to fit residues: 71.1027 Evaluate side-chains 235 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 148 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 653 HIS Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 853 PHE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 955 GLN Chi-restraints excluded: chain B residue 966 SER Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 289 CYS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1046 HIS Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1062 HIS Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain C residue 1099 HIS Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain o residue 6 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 19 optimal weight: 6.9990 chunk 317 optimal weight: 7.9990 chunk 238 optimal weight: 30.0000 chunk 276 optimal weight: 0.7980 chunk 228 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 277 optimal weight: 0.7980 chunk 37 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 HIS ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 GLN A1021 ASN ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 870 GLN B 953 ASN B1034 GLN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN C1106 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.137119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.109796 restraints weight = 111100.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.112157 restraints weight = 68156.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.113069 restraints weight = 45691.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.114258 restraints weight = 33771.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.114618 restraints weight = 27201.621| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 26080 Z= 0.258 Angle : 0.772 11.785 35503 Z= 0.407 Chirality : 0.049 0.319 4026 Planarity : 0.006 0.082 4585 Dihedral : 6.190 52.680 3500 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 5.16 % Allowed : 20.02 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.22 (0.14), residues: 3206 helix: -1.34 (0.18), residues: 627 sheet: -0.91 (0.21), residues: 596 loop : -1.75 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1105 TYR 0.033 0.002 TYR A1065 PHE 0.039 0.003 PHE C 800 TRP 0.012 0.002 TRP B 884 HIS 0.015 0.002 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00564 (26037) covalent geometry : angle 0.76704 (35417) SS BOND : bond 0.00604 ( 43) SS BOND : angle 1.86314 ( 86) hydrogen bonds : bond 0.06486 ( 853) hydrogen bonds : angle 7.17157 ( 2376) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 151 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.4722 (tp) REVERT: A 503 TYR cc_start: 0.1367 (OUTLIER) cc_final: 0.1148 (m-80) REVERT: A 882 SER cc_start: 0.5107 (OUTLIER) cc_final: 0.4801 (p) REVERT: A 1015 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: A 1016 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8402 (tt) REVERT: B 167 GLU cc_start: 0.8291 (tp30) cc_final: 0.8008 (tm-30) REVERT: B 198 TYR cc_start: 0.7035 (m-80) cc_final: 0.6676 (m-10) REVERT: B 201 ILE cc_start: 0.7204 (mp) cc_final: 0.6779 (mt) REVERT: B 358 ASN cc_start: 0.7837 (t0) cc_final: 0.7364 (m-40) REVERT: B 634 TYR cc_start: 0.3673 (OUTLIER) cc_final: 0.2977 (m-80) REVERT: B 725 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7532 (pp) REVERT: B 771 GLU cc_start: 0.8361 (tt0) cc_final: 0.7970 (tm-30) REVERT: B 953 ASN cc_start: 0.8102 (t0) cc_final: 0.7902 (t0) REVERT: C 740 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8280 (tt) outliers start: 147 outliers final: 104 residues processed: 277 average time/residue: 0.1567 time to fit residues: 72.0834 Evaluate side-chains 259 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 147 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 271 ARG Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 963 GLN Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 725 LEU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 VAL Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 865 ASP Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 955 GLN Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1099 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 289 CYS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1039 ASP Chi-restraints excluded: chain C residue 1046 HIS Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1062 HIS Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain C residue 1106 ASN Chi-restraints excluded: chain C residue 1107 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 98 optimal weight: 7.9990 chunk 249 optimal weight: 6.9990 chunk 69 optimal weight: 0.0770 chunk 157 optimal weight: 0.4980 chunk 289 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 235 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 219 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 overall best weight: 3.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 899 GLN ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 ASN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 ASN ** o 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.137211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.110940 restraints weight = 109472.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.114109 restraints weight = 61278.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.114901 restraints weight = 42773.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.115961 restraints weight = 29836.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.116590 restraints weight = 24032.646| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 26080 Z= 0.222 Angle : 0.740 11.644 35503 Z= 0.387 Chirality : 0.048 0.247 4026 Planarity : 0.005 0.070 4585 Dihedral : 5.971 26.834 3497 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.85 % Allowed : 21.32 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.14), residues: 3206 helix: -1.27 (0.19), residues: 620 sheet: -0.96 (0.21), residues: 594 loop : -1.73 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 763 TYR 0.026 0.002 TYR A1065 PHE 0.034 0.002 PHE C 800 TRP 0.010 0.001 TRP C 884 HIS 0.012 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00486 (26037) covalent geometry : angle 0.73508 (35417) SS BOND : bond 0.00509 ( 43) SS BOND : angle 1.84446 ( 86) hydrogen bonds : bond 0.06146 ( 853) hydrogen bonds : angle 7.09915 ( 2376) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 156 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.5217 (OUTLIER) cc_final: 0.4731 (tp) REVERT: A 311 TYR cc_start: 0.7505 (m-80) cc_final: 0.7271 (m-10) REVERT: A 503 TYR cc_start: 0.1304 (OUTLIER) cc_final: 0.1053 (m-80) REVERT: A 882 SER cc_start: 0.5138 (OUTLIER) cc_final: 0.4856 (p) REVERT: B 167 GLU cc_start: 0.8183 (tp30) cc_final: 0.7798 (tm-30) REVERT: B 198 TYR cc_start: 0.6976 (m-80) cc_final: 0.6612 (m-10) REVERT: B 201 ILE cc_start: 0.7225 (mp) cc_final: 0.6775 (mt) REVERT: B 358 ASN cc_start: 0.7916 (t0) cc_final: 0.7433 (m-40) REVERT: B 634 TYR cc_start: 0.3650 (OUTLIER) cc_final: 0.2929 (m-80) REVERT: B 771 GLU cc_start: 0.8288 (tt0) cc_final: 0.7901 (tm-30) REVERT: B 1065 TYR cc_start: 0.6327 (m-80) cc_final: 0.6043 (m-80) REVERT: C 740 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8166 (tt) REVERT: C 856 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8970 (pp) REVERT: C 867 MET cc_start: 0.8011 (mtt) cc_final: 0.7734 (ptp) REVERT: C 1046 HIS cc_start: 0.1432 (OUTLIER) cc_final: 0.0188 (p90) REVERT: o 86 TYR cc_start: 0.2626 (OUTLIER) cc_final: 0.1417 (t80) outliers start: 138 outliers final: 101 residues processed: 270 average time/residue: 0.1561 time to fit residues: 69.7892 Evaluate side-chains 253 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 144 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 560 PHE Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 759 THR Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 955 GLN Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1099 HIS Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 289 CYS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1027 MET Chi-restraints excluded: chain C residue 1039 ASP Chi-restraints excluded: chain C residue 1046 HIS Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1062 HIS Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain C residue 1106 ASN Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain o residue 86 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 101 optimal weight: 50.0000 chunk 59 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 39 optimal weight: 50.0000 chunk 244 optimal weight: 10.0000 chunk 47 optimal weight: 0.0970 chunk 224 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 243 optimal weight: 0.0970 chunk 198 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 overall best weight: 1.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN B1034 GLN C 542 ASN C 955 GLN ** C1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 38 GLN ** o 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.139296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.113600 restraints weight = 110559.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.116986 restraints weight = 67028.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.118289 restraints weight = 38358.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.119656 restraints weight = 28304.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.119455 restraints weight = 25872.492| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26080 Z= 0.153 Angle : 0.688 12.722 35503 Z= 0.354 Chirality : 0.046 0.414 4026 Planarity : 0.005 0.067 4585 Dihedral : 5.652 26.746 3497 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.51 % Allowed : 22.83 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.14), residues: 3206 helix: -1.03 (0.19), residues: 616 sheet: -0.82 (0.23), residues: 554 loop : -1.68 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 763 TYR 0.034 0.001 TYR A 168 PHE 0.032 0.002 PHE B 273 TRP 0.011 0.001 TRP n 35 HIS 0.011 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00339 (26037) covalent geometry : angle 0.68498 (35417) SS BOND : bond 0.00375 ( 43) SS BOND : angle 1.55093 ( 86) hydrogen bonds : bond 0.05329 ( 853) hydrogen bonds : angle 6.76128 ( 2376) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 166 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.5276 (OUTLIER) cc_final: 0.4819 (tp) REVERT: A 503 TYR cc_start: 0.1402 (OUTLIER) cc_final: 0.1096 (m-80) REVERT: A 882 SER cc_start: 0.4911 (OUTLIER) cc_final: 0.4697 (p) REVERT: A 1016 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8337 (tt) REVERT: A 1050 PHE cc_start: 0.4295 (m-80) cc_final: 0.4041 (m-80) REVERT: B 198 TYR cc_start: 0.6893 (m-80) cc_final: 0.6520 (m-10) REVERT: B 201 ILE cc_start: 0.7077 (mp) cc_final: 0.6645 (mt) REVERT: B 358 ASN cc_start: 0.7906 (t0) cc_final: 0.7446 (m-40) REVERT: B 634 TYR cc_start: 0.3720 (OUTLIER) cc_final: 0.3008 (m-80) REVERT: B 1065 TYR cc_start: 0.6191 (m-80) cc_final: 0.5945 (m-80) REVERT: B 1105 ARG cc_start: 0.6625 (mtt180) cc_final: 0.4667 (tpt170) REVERT: C 856 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8956 (pp) REVERT: C 867 MET cc_start: 0.7999 (mtt) cc_final: 0.7751 (ptp) outliers start: 100 outliers final: 80 residues processed: 250 average time/residue: 0.1485 time to fit residues: 61.7673 Evaluate side-chains 229 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 143 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 503 TYR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 955 GLN Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1099 HIS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 289 CYS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1062 HIS Chi-restraints excluded: chain C residue 1066 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 305 optimal weight: 50.0000 chunk 62 optimal weight: 2.9990 chunk 246 optimal weight: 40.0000 chunk 234 optimal weight: 8.9990 chunk 178 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 280 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN C1009 GLN C1106 ASN ** o 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.138737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.111756 restraints weight = 111561.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.114790 restraints weight = 66068.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.115217 restraints weight = 44780.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.116460 restraints weight = 33101.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.116974 restraints weight = 27140.622| |-----------------------------------------------------------------------------| r_work (final): 0.4328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26080 Z= 0.174 Angle : 0.699 11.728 35503 Z= 0.360 Chirality : 0.046 0.279 4026 Planarity : 0.005 0.069 4585 Dihedral : 5.631 26.334 3497 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 4.18 % Allowed : 23.08 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (0.14), residues: 3206 helix: -0.98 (0.19), residues: 621 sheet: -0.84 (0.23), residues: 556 loop : -1.66 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 763 TYR 0.040 0.002 TYR A1065 PHE 0.033 0.002 PHE A1107 TRP 0.011 0.001 TRP A1100 HIS 0.009 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00384 (26037) covalent geometry : angle 0.69577 (35417) SS BOND : bond 0.00399 ( 43) SS BOND : angle 1.54079 ( 86) hydrogen bonds : bond 0.05388 ( 853) hydrogen bonds : angle 6.75581 ( 2376) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 156 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.5342 (OUTLIER) cc_final: 0.4845 (tp) REVERT: A 882 SER cc_start: 0.4874 (OUTLIER) cc_final: 0.4633 (p) REVERT: A 1016 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8394 (tt) REVERT: B 198 TYR cc_start: 0.7015 (m-80) cc_final: 0.6683 (m-10) REVERT: B 201 ILE cc_start: 0.7050 (mp) cc_final: 0.6644 (mt) REVERT: B 358 ASN cc_start: 0.7720 (t0) cc_final: 0.7290 (m-40) REVERT: B 634 TYR cc_start: 0.3674 (OUTLIER) cc_final: 0.2952 (m-80) REVERT: B 1065 TYR cc_start: 0.6237 (m-80) cc_final: 0.5970 (m-80) REVERT: C 856 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9022 (pp) REVERT: C 867 MET cc_start: 0.8075 (mtt) cc_final: 0.7734 (ptp) REVERT: C 1009 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8435 (mt0) REVERT: C 1022 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8242 (mt) outliers start: 119 outliers final: 93 residues processed: 256 average time/residue: 0.1564 time to fit residues: 66.5299 Evaluate side-chains 246 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 146 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 955 GLN Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1099 HIS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 289 CYS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 955 GLN Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1009 GLN Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1027 MET Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1062 HIS Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain C residue 1106 ASN Chi-restraints excluded: chain C residue 1107 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 202 optimal weight: 50.0000 chunk 249 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 30 optimal weight: 30.0000 chunk 250 optimal weight: 20.0000 chunk 25 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 234 optimal weight: 8.9990 chunk 189 optimal weight: 0.8980 chunk 239 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN C 955 GLN C1106 ASN ** o 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.138427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.111627 restraints weight = 111563.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.114684 restraints weight = 65197.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.114953 restraints weight = 42600.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.116091 restraints weight = 32831.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.116445 restraints weight = 26541.254| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26080 Z= 0.183 Angle : 0.716 12.904 35503 Z= 0.369 Chirality : 0.047 0.253 4026 Planarity : 0.005 0.069 4585 Dihedral : 5.647 26.517 3497 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.86 % Allowed : 23.39 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.14), residues: 3206 helix: -0.99 (0.20), residues: 616 sheet: -0.86 (0.22), residues: 583 loop : -1.68 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 763 TYR 0.054 0.002 TYR A1065 PHE 0.045 0.002 PHE A1107 TRP 0.010 0.001 TRP n 106 HIS 0.009 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00406 (26037) covalent geometry : angle 0.71249 (35417) SS BOND : bond 0.00399 ( 43) SS BOND : angle 1.58675 ( 86) hydrogen bonds : bond 0.05382 ( 853) hydrogen bonds : angle 6.75062 ( 2376) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6412 Ramachandran restraints generated. 3206 Oldfield, 0 Emsley, 3206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 149 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.5358 (OUTLIER) cc_final: 0.4859 (tp) REVERT: A 882 SER cc_start: 0.4872 (OUTLIER) cc_final: 0.4620 (p) REVERT: A 1016 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8446 (tt) REVERT: A 1050 PHE cc_start: 0.4521 (m-80) cc_final: 0.4117 (m-80) REVERT: B 198 TYR cc_start: 0.7021 (m-80) cc_final: 0.6696 (m-10) REVERT: B 201 ILE cc_start: 0.7030 (mp) cc_final: 0.6624 (mt) REVERT: B 358 ASN cc_start: 0.7854 (t0) cc_final: 0.7401 (m-40) REVERT: B 634 TYR cc_start: 0.3721 (OUTLIER) cc_final: 0.2985 (m-80) REVERT: B 771 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7030 (tm-30) REVERT: B 1065 TYR cc_start: 0.6280 (m-80) cc_final: 0.5997 (m-80) REVERT: B 1105 ARG cc_start: 0.6469 (mtt180) cc_final: 0.4513 (tpt90) REVERT: C 856 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9045 (pp) REVERT: C 867 MET cc_start: 0.8106 (mtt) cc_final: 0.7767 (ptp) REVERT: C 1022 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8247 (mt) outliers start: 110 outliers final: 96 residues processed: 239 average time/residue: 0.1631 time to fit residues: 64.8574 Evaluate side-chains 249 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 146 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 481 VAL Chi-restraints excluded: chain A residue 538 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 694 THR Chi-restraints excluded: chain A residue 702 SER Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain A residue 816 ILE Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 863 LEU Chi-restraints excluded: chain A residue 867 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 882 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1008 GLN Chi-restraints excluded: chain A residue 1015 GLU Chi-restraints excluded: chain A residue 1016 ILE Chi-restraints excluded: chain A residue 1032 LEU Chi-restraints excluded: chain A residue 1053 SER Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 38 TYR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 652 GLU Chi-restraints excluded: chain B residue 719 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 748 SER Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 771 GLU Chi-restraints excluded: chain B residue 857 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 955 GLN Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1099 HIS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 289 CYS Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 541 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 700 GLU Chi-restraints excluded: chain C residue 705 TYR Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 783 VAL Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 856 LEU Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 882 SER Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 892 LEU Chi-restraints excluded: chain C residue 949 VAL Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1027 MET Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1062 HIS Chi-restraints excluded: chain C residue 1066 VAL Chi-restraints excluded: chain C residue 1106 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 151 optimal weight: 2.9990 chunk 240 optimal weight: 50.0000 chunk 323 optimal weight: 30.0000 chunk 3 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 256 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 517 HIS C1009 GLN ** C1106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.138030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.110994 restraints weight = 110872.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.114174 restraints weight = 66480.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.114710 restraints weight = 41841.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.115809 restraints weight = 31748.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.116178 restraints weight = 26365.781| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26080 Z= 0.190 Angle : 0.720 12.256 35503 Z= 0.372 Chirality : 0.047 0.243 4026 Planarity : 0.005 0.070 4585 Dihedral : 5.677 26.058 3497 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 4.04 % Allowed : 23.39 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.14), residues: 3206 helix: -0.96 (0.19), residues: 626 sheet: -0.84 (0.22), residues: 595 loop : -1.72 (0.13), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C1105 TYR 0.048 0.002 TYR A1065 PHE 0.046 0.002 PHE A1107 TRP 0.013 0.001 TRP B 884 HIS 0.010 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00420 (26037) covalent geometry : angle 0.71662 (35417) SS BOND : bond 0.00414 ( 43) SS BOND : angle 1.57054 ( 86) hydrogen bonds : bond 0.05407 ( 853) hydrogen bonds : angle 6.76422 ( 2376) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5125.75 seconds wall clock time: 89 minutes 34.04 seconds (5374.04 seconds total)