Starting phenix.real_space_refine on Sun May 25 12:56:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yrp_39547/05_2025/8yrp_39547.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yrp_39547/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8yrp_39547/05_2025/8yrp_39547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yrp_39547/05_2025/8yrp_39547.map" model { file = "/net/cci-nas-00/data/ceres_data/8yrp_39547/05_2025/8yrp_39547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yrp_39547/05_2025/8yrp_39547.cif" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.90, per 1000 atoms: 0.55 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: 5.66 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 3.16 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: 10.05 Time building geometry restraints manager: 6.69 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: 4.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 0.900 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 53.310 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.200 ------------------------------------------------------------------------------- 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 : 13.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.046 0.004 TRP C1100 HIS 0.016 0.003 HIS C1056 PHE 0.060 0.005 PHE A1050 TYR 0.054 0.004 TYR B1108 ARG 0.011 0.001 ARG A1037 Details of bonding type rmsd hydrogen bonds : bond 0.27517 ( 853) hydrogen bonds : angle 9.64945 ( 2376) SS BOND : bond 0.11453 ( 43) SS BOND : angle 6.42992 ( 86) covalent geometry : bond 0.00935 (26037) covalent geometry : angle 1.38970 (35417) *********************** 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 : 2.614 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: A 41 LYS cc_start: 0.3980 (mmtt) cc_final: 0.3158 (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: 0.6537 (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: 0.6207 (m-10) REVERT: B 460 LYS cc_start: 0.7214 (tptp) cc_final: 0.6974 (tptp) REVERT: B 884 TRP cc_start: 0.4345 (p90) cc_final: 0.4005 (p-90) REVERT: C 198 TYR cc_start: 0.7571 (m-10) cc_final: 0.7089 (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: 0.3844 time to fit residues: 200.6895 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 : 2.954 ------------------------------------------------------------------------------- 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 273 optimal weight: 3.9990 chunk 245 optimal weight: 50.0000 chunk 136 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 131 optimal weight: 20.0000 chunk 253 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 294 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 491 GLN ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN A 753 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 237 GLN ** 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 ** B1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 C 782 GLN C 870 GLN C 953 ASN C1000 GLN C1081 HIS o 3 GLN o 31 ASN ** o 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 90 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.141490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.115966 restraints weight = 109985.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.119103 restraints weight = 60756.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.119997 restraints weight = 40874.331| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26080 Z= 0.192 Angle : 0.756 11.990 35503 Z= 0.400 Chirality : 0.048 0.218 4026 Planarity : 0.005 0.082 4585 Dihedral : 7.060 61.542 3529 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.90 % Favored : 94.04 % Rotamer: Outliers : 3.16 % Allowed : 14.72 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.13), residues: 3206 helix: -1.58 (0.18), residues: 615 sheet: -0.54 (0.22), residues: 561 loop : -1.90 (0.12), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 631 HIS 0.011 0.001 HIS C1062 PHE 0.039 0.002 PHE A 821 TYR 0.033 0.002 TYR A 311 ARG 0.007 0.001 ARG B 401 Details of bonding type rmsd hydrogen bonds : bond 0.07856 ( 853) hydrogen bonds : angle 7.75927 ( 2376) SS BOND : bond 0.00498 ( 43) SS BOND : angle 1.86219 ( 86) covalent geometry : bond 0.00393 (26037) covalent geometry : angle 0.75109 (35417) *********************** 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 299 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 209 time to evaluate : 2.591 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: A 311 TYR cc_start: 0.7380 (m-80) cc_final: 0.6884 (m-10) REVERT: A 971 ILE cc_start: 0.8041 (pt) cc_final: 0.7758 (tp) REVERT: B 167 GLU cc_start: 0.8304 (tp30) cc_final: 0.7629 (tm-30) REVERT: B 198 TYR cc_start: 0.6854 (m-80) cc_final: 0.6450 (m-10) REVERT: B 273 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: B 355 ARG cc_start: 0.8143 (ttp-170) cc_final: 0.7925 (tmm-80) REVERT: B 771 GLU cc_start: 0.8263 (tt0) cc_final: 0.7945 (tm-30) REVERT: C 312 GLN cc_start: 0.7229 (tm-30) cc_final: 0.7005 (tm-30) REVERT: C 565 ARG cc_start: 0.6221 (OUTLIER) cc_final: 0.5367 (ttm170) REVERT: C 740 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8330 (tt) REVERT: n 70 MET cc_start: -0.0017 (mtp) cc_final: -0.0381 (mtm) REVERT: o 6 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6381 (mp10) outliers start: 90 outliers final: 41 residues processed: 279 average time/residue: 0.3488 time to fit residues: 157.8716 Evaluate side-chains 205 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 2.996 ------------------------------------------------------------------------------- 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 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 738 MET 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 821 PHE Chi-restraints excluded: chain A residue 863 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 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 431 VAL Chi-restraints excluded: chain B residue 481 VAL 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 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 331 THR Chi-restraints excluded: chain C residue 334 CYS Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 608 VAL 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 263 optimal weight: 10.0000 chunk 134 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 320 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 275 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 143 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 GLN ** A 899 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 420 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 924 GLN ** B 951 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1034 GLN C1046 HIS o 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.139159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.112783 restraints weight = 110626.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.116350 restraints weight = 61239.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.116979 restraints weight = 39106.947| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 26080 Z= 0.227 Angle : 0.745 11.800 35503 Z= 0.393 Chirality : 0.048 0.329 4026 Planarity : 0.005 0.087 4585 Dihedral : 6.322 59.692 3505 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.86 % Allowed : 16.19 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.13), residues: 3206 helix: -1.49 (0.18), residues: 619 sheet: -0.56 (0.21), residues: 597 loop : -1.87 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 631 HIS 0.011 0.001 HIS A1062 PHE 0.035 0.002 PHE C 800 TYR 0.021 0.002 TYR A 311 ARG 0.004 0.001 ARG A1012 Details of bonding type rmsd hydrogen bonds : bond 0.07043 ( 853) hydrogen bonds : angle 7.42320 ( 2376) SS BOND : bond 0.00706 ( 43) SS BOND : angle 1.68099 ( 86) covalent geometry : bond 0.00484 (26037) covalent geometry : angle 0.74133 (35417) *********************** 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 284 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 174 time to evaluate : 2.619 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 166 PHE cc_start: 0.8380 (t80) cc_final: 0.8165 (t80) REVERT: A 503 TYR cc_start: 0.1552 (OUTLIER) cc_final: 0.1256 (m-80) REVERT: A 1015 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7835 (mp0) REVERT: B 58 PHE cc_start: 0.5347 (OUTLIER) cc_final: 0.5097 (m-10) REVERT: B 167 GLU cc_start: 0.8390 (tp30) cc_final: 0.8070 (tm-30) REVERT: B 198 TYR cc_start: 0.7015 (m-80) cc_final: 0.6620 (m-10) REVERT: B 201 ILE cc_start: 0.7159 (mp) cc_final: 0.6723 (mt) REVERT: B 308 LYS cc_start: 0.5972 (OUTLIER) cc_final: 0.5726 (ttmm) REVERT: B 358 ASN cc_start: 0.8008 (t0) cc_final: 0.7537 (m-40) REVERT: B 725 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7500 (pp) REVERT: B 771 GLU cc_start: 0.8398 (tt0) cc_final: 0.8097 (tm-30) REVERT: C 740 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8272 (tt) REVERT: C 867 MET cc_start: 0.7926 (mtt) cc_final: 0.7641 (ptp) REVERT: o 6 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6581 (mp10) outliers start: 110 outliers final: 64 residues processed: 264 average time/residue: 0.3379 time to fit residues: 146.2008 Evaluate side-chains 218 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 147 time to evaluate : 2.740 ------------------------------------------------------------------------------- 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 551 THR Chi-restraints excluded: chain A residue 579 THR 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 816 ILE 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 946 LEU 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 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 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 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 768 ILE Chi-restraints excluded: chain B residue 789 THR 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 955 GLN Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain C residue 227 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 331 THR Chi-restraints excluded: chain C residue 547 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 63 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 319 optimal weight: 50.0000 chunk 199 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 223 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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** ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 HIS ** B 237 GLN ** 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 951 ASN B 953 ASN ** B1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.142700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.116644 restraints weight = 106089.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.120058 restraints weight = 57752.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.120761 restraints weight = 38718.164| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26080 Z= 0.154 Angle : 0.666 11.779 35503 Z= 0.347 Chirality : 0.046 0.430 4026 Planarity : 0.005 0.061 4585 Dihedral : 5.811 59.951 3502 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.86 % Allowed : 17.28 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.14), residues: 3206 helix: -1.23 (0.19), residues: 622 sheet: -0.48 (0.22), residues: 587 loop : -1.73 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP n 34 HIS 0.009 0.001 HIS A1099 PHE 0.027 0.002 PHE A1060 TYR 0.022 0.001 TYR B 378 ARG 0.006 0.000 ARG B 355 Details of bonding type rmsd hydrogen bonds : bond 0.05965 ( 853) hydrogen bonds : angle 7.00990 ( 2376) SS BOND : bond 0.00405 ( 43) SS BOND : angle 1.67946 ( 86) covalent geometry : bond 0.00327 (26037) covalent geometry : angle 0.66194 (35417) *********************** 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 289 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 179 time to evaluate : 2.832 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: 0.1344 (OUTLIER) cc_final: 0.1096 (m-80) REVERT: A 1011 ILE cc_start: 0.8924 (mm) cc_final: 0.8552 (mm) REVERT: A 1015 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: B 129 LYS cc_start: 0.8649 (mtmm) cc_final: 0.8379 (pptt) REVERT: B 167 GLU cc_start: 0.8159 (tp30) cc_final: 0.7601 (tm-30) REVERT: B 198 TYR cc_start: 0.6834 (m-80) cc_final: 0.6419 (m-10) REVERT: B 201 ILE cc_start: 0.7169 (mp) cc_final: 0.6756 (mt) REVERT: B 358 ASN cc_start: 0.8067 (t0) cc_final: 0.7640 (m-40) REVERT: B 771 GLU cc_start: 0.8214 (tt0) cc_final: 0.7992 (tm-30) REVERT: B 907 ILE cc_start: 0.6556 (OUTLIER) cc_final: 0.5953 (mm) REVERT: B 1065 TYR cc_start: 0.6142 (m-80) cc_final: 0.5934 (m-80) REVERT: C 740 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8169 (tt) REVERT: C 867 MET cc_start: 0.7993 (mtt) cc_final: 0.7633 (ptp) REVERT: o 6 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6331 (mp10) outliers start: 110 outliers final: 64 residues processed: 268 average time/residue: 0.3260 time to fit residues: 146.1998 Evaluate side-chains 221 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 152 time to evaluate : 2.572 ------------------------------------------------------------------------------- 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 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 551 THR 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 816 ILE 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 1079 ILE 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 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 431 VAL Chi-restraints excluded: chain B residue 481 VAL 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 732 THR Chi-restraints excluded: chain B residue 789 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 907 ILE Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain C residue 227 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 331 THR Chi-restraints excluded: chain C residue 334 CYS 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 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 886 PHE Chi-restraints excluded: chain C residue 892 LEU 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 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 7 optimal weight: 6.9990 chunk 294 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 211 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 179 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 220 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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** B 115 GLN ** B 237 GLN ** 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 963 GLN ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 90 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.140154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.114380 restraints weight = 112330.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.117455 restraints weight = 65297.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.118772 restraints weight = 40487.872| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5983 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26080 Z= 0.159 Angle : 0.657 11.787 35503 Z= 0.341 Chirality : 0.046 0.401 4026 Planarity : 0.004 0.057 4585 Dihedral : 5.673 59.985 3501 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.04 % Allowed : 18.48 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 3206 helix: -1.18 (0.19), residues: 637 sheet: -0.45 (0.22), residues: 577 loop : -1.65 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP n 34 HIS 0.009 0.001 HIS A1062 PHE 0.027 0.002 PHE A1060 TYR 0.022 0.001 TYR B 378 ARG 0.011 0.000 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.05615 ( 853) hydrogen bonds : angle 6.78430 ( 2376) SS BOND : bond 0.00447 ( 43) SS BOND : angle 1.41313 ( 86) covalent geometry : bond 0.00342 (26037) covalent geometry : angle 0.65415 (35417) *********************** 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 281 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 166 time to evaluate : 2.683 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: A 503 TYR cc_start: 0.1582 (OUTLIER) cc_final: 0.1259 (m-80) REVERT: A 882 SER cc_start: 0.4709 (OUTLIER) cc_final: 0.4382 (p) REVERT: A 1011 ILE cc_start: 0.9009 (mm) cc_final: 0.8667 (mm) REVERT: A 1015 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: A 1050 PHE cc_start: 0.4153 (m-80) cc_final: 0.3619 (m-80) REVERT: B 129 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8597 (pptt) REVERT: B 167 GLU cc_start: 0.8320 (tp30) cc_final: 0.7789 (tm-30) REVERT: B 198 TYR cc_start: 0.6943 (m-80) cc_final: 0.6580 (m-10) REVERT: B 201 ILE cc_start: 0.7000 (mp) cc_final: 0.6632 (mt) REVERT: B 358 ASN cc_start: 0.8021 (t0) cc_final: 0.7592 (m-40) REVERT: B 771 GLU cc_start: 0.8431 (tt0) cc_final: 0.8109 (tm-30) REVERT: B 907 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.6084 (mm) REVERT: B 1065 TYR cc_start: 0.6021 (m-80) cc_final: 0.5747 (m-80) REVERT: C 740 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8105 (tt) REVERT: o 6 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6088 (mp10) outliers start: 115 outliers final: 73 residues processed: 260 average time/residue: 0.3163 time to fit residues: 137.8276 Evaluate side-chains 226 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 147 time to evaluate : 2.715 ------------------------------------------------------------------------------- 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 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 551 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 653 HIS 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 752 LEU 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 48 LEU 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 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 652 GLU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 789 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 862 LEU Chi-restraints excluded: chain B residue 885 THR Chi-restraints excluded: chain B residue 892 LEU Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 955 GLN Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 227 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 331 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 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 1027 MET 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 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 194 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 173 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 321 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 273 optimal weight: 0.0970 chunk 313 optimal weight: 8.9990 chunk 315 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 overall best weight: 2.5984 ------------------------------------------------------------------------------- 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** ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 GLN ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 90 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.139355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.113637 restraints weight = 111594.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.117008 restraints weight = 64216.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.117882 restraints weight = 39983.476| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6025 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26080 Z= 0.182 Angle : 0.685 11.725 35503 Z= 0.356 Chirality : 0.047 0.413 4026 Planarity : 0.005 0.120 4585 Dihedral : 5.690 59.070 3501 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.43 % Allowed : 18.62 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.14), residues: 3206 helix: -1.20 (0.19), residues: 641 sheet: -0.60 (0.22), residues: 584 loop : -1.59 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP n 106 HIS 0.011 0.001 HIS B1046 PHE 0.028 0.002 PHE C 800 TYR 0.027 0.002 TYR A 168 ARG 0.015 0.001 ARG C 763 Details of bonding type rmsd hydrogen bonds : bond 0.05636 ( 853) hydrogen bonds : angle 6.72621 ( 2376) SS BOND : bond 0.00491 ( 43) SS BOND : angle 1.76833 ( 86) covalent geometry : bond 0.00397 (26037) covalent geometry : angle 0.68039 (35417) *********************** 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 286 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 160 time to evaluate : 2.943 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: 0.5335 (OUTLIER) cc_final: 0.4821 (tp) REVERT: A 503 TYR cc_start: 0.1555 (OUTLIER) cc_final: 0.1270 (m-80) REVERT: A 882 SER cc_start: 0.4710 (OUTLIER) cc_final: 0.4386 (p) REVERT: A 1015 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7805 (mp0) REVERT: B 167 GLU cc_start: 0.8298 (tp30) cc_final: 0.8091 (tm-30) REVERT: B 198 TYR cc_start: 0.6952 (m-80) cc_final: 0.6599 (m-10) REVERT: B 201 ILE cc_start: 0.7064 (mp) cc_final: 0.6691 (mt) REVERT: B 291 LEU cc_start: 0.8487 (tp) cc_final: 0.8159 (tp) REVERT: B 358 ASN cc_start: 0.7982 (t0) cc_final: 0.7530 (m-40) REVERT: B 771 GLU cc_start: 0.8354 (tt0) cc_final: 0.8022 (tm-30) REVERT: B 1065 TYR cc_start: 0.6205 (m-80) cc_final: 0.5941 (m-80) REVERT: C 198 TYR cc_start: 0.7302 (m-10) cc_final: 0.6987 (m-80) REVERT: C 740 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8090 (tt) REVERT: o 6 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.5968 (mp10) outliers start: 126 outliers final: 89 residues processed: 262 average time/residue: 0.3186 time to fit residues: 140.1745 Evaluate side-chains 233 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 138 time to evaluate : 2.864 ------------------------------------------------------------------------------- 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 551 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 597 THR 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 752 LEU 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 946 LEU 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 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 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 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 652 GLU Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 768 ILE Chi-restraints excluded: chain B residue 789 THR 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 972 SER Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 227 LEU 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 300 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 331 THR 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 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 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 974 VAL Chi-restraints excluded: chain C residue 1027 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 72 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 65 optimal weight: 0.4980 chunk 154 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 216 optimal weight: 8.9990 chunk 269 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 189 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 GLN ** B 870 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1052 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.142326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.116356 restraints weight = 112143.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.119337 restraints weight = 66475.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.119813 restraints weight = 40384.003| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26080 Z= 0.124 Angle : 0.632 11.501 35503 Z= 0.323 Chirality : 0.045 0.328 4026 Planarity : 0.004 0.056 4585 Dihedral : 5.446 59.226 3501 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.30 % Allowed : 20.27 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.14), residues: 3206 helix: -0.99 (0.19), residues: 637 sheet: -0.52 (0.22), residues: 577 loop : -1.52 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP n 35 HIS 0.009 0.001 HIS B1046 PHE 0.029 0.002 PHE A1107 TYR 0.027 0.001 TYR A1065 ARG 0.010 0.000 ARG C 763 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 853) hydrogen bonds : angle 6.39871 ( 2376) SS BOND : bond 0.00305 ( 43) SS BOND : angle 1.55716 ( 86) covalent geometry : bond 0.00267 (26037) covalent geometry : angle 0.62859 (35417) *********************** 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 265 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 171 time to evaluate : 2.772 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: 0.5348 (OUTLIER) cc_final: 0.4848 (tp) REVERT: A 882 SER cc_start: 0.4605 (OUTLIER) cc_final: 0.4309 (p) REVERT: A 1015 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: A 1016 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8473 (tt) REVERT: A 1050 PHE cc_start: 0.4147 (m-80) cc_final: 0.3912 (m-80) REVERT: B 167 GLU cc_start: 0.8295 (tp30) cc_final: 0.8058 (tm-30) REVERT: B 198 TYR cc_start: 0.6870 (m-80) cc_final: 0.6502 (m-10) REVERT: B 201 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6678 (mt) REVERT: B 358 ASN cc_start: 0.7734 (t0) cc_final: 0.7335 (m-40) REVERT: B 634 TYR cc_start: 0.3781 (OUTLIER) cc_final: 0.3112 (m-80) REVERT: B 962 LYS cc_start: 0.9388 (mttm) cc_final: 0.9182 (mttm) REVERT: B 1065 TYR cc_start: 0.5982 (m-80) cc_final: 0.5739 (m-80) REVERT: C 898 MET cc_start: 0.4559 (mmm) cc_final: 0.4301 (mmt) REVERT: C 985 PRO cc_start: 0.8873 (Cg_exo) cc_final: 0.8510 (Cg_endo) REVERT: C 986 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7508 (pm20) outliers start: 94 outliers final: 70 residues processed: 249 average time/residue: 0.3338 time to fit residues: 137.3992 Evaluate side-chains 225 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 149 time to evaluate : 2.767 ------------------------------------------------------------------------------- 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 551 THR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 597 THR 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 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 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 201 ILE Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 225 VAL 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 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 789 THR 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 886 PHE 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 62 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 272 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 757 PHE Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 885 THR Chi-restraints excluded: chain C residue 886 PHE Chi-restraints excluded: chain C residue 892 LEU 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 Chi-restraints excluded: chain C residue 1107 PHE Chi-restraints excluded: chain o residue 6 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 322 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 247 optimal weight: 40.0000 chunk 243 optimal weight: 9.9990 chunk 299 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 171 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 188 optimal weight: 0.6980 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 653 HIS ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1021 ASN ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1069 GLN A1104 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 578 GLN B 707 ASN ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 870 GLN ** B 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN C1099 HIS C1106 ASN o 31 ASN ** o 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.136172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.109433 restraints weight = 111075.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.110970 restraints weight = 72401.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.112579 restraints weight = 48914.543| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6261 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 26080 Z= 0.340 Angle : 0.870 11.947 35503 Z= 0.458 Chirality : 0.053 0.712 4026 Planarity : 0.006 0.108 4585 Dihedral : 6.259 55.710 3501 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 23.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 4.00 % Allowed : 20.76 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.14), residues: 3206 helix: -1.44 (0.18), residues: 629 sheet: -0.81 (0.23), residues: 549 loop : -1.70 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 884 HIS 0.017 0.002 HIS A1062 PHE 0.047 0.003 PHE C 800 TYR 0.040 0.003 TYR A1065 ARG 0.010 0.001 ARG A1105 Details of bonding type rmsd hydrogen bonds : bond 0.06749 ( 853) hydrogen bonds : angle 7.17503 ( 2376) SS BOND : bond 0.00697 ( 43) SS BOND : angle 2.11469 ( 86) covalent geometry : bond 0.00748 (26037) covalent geometry : angle 0.86479 (35417) *********************** 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 260 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 146 time to evaluate : 2.769 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: 0.5238 (OUTLIER) cc_final: 0.4758 (tp) REVERT: A 882 SER cc_start: 0.5097 (OUTLIER) cc_final: 0.4751 (p) REVERT: B 167 GLU cc_start: 0.8304 (tp30) cc_final: 0.8085 (tm-30) REVERT: B 198 TYR cc_start: 0.7085 (m-80) cc_final: 0.6721 (m-10) REVERT: B 201 ILE cc_start: 0.7314 (mp) cc_final: 0.6879 (mt) REVERT: B 358 ASN cc_start: 0.8038 (t0) cc_final: 0.7492 (m-40) REVERT: B 634 TYR cc_start: 0.3758 (OUTLIER) cc_final: 0.2992 (m-80) REVERT: B 771 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: C 740 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8235 (tt) REVERT: C 985 PRO cc_start: 0.8912 (Cg_exo) cc_final: 0.8553 (Cg_endo) REVERT: C 986 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7478 (pm20) REVERT: o 89 GLN cc_start: 0.5483 (tp40) cc_final: 0.5234 (tp40) outliers start: 114 outliers final: 80 residues processed: 245 average time/residue: 0.3431 time to fit residues: 143.2320 Evaluate side-chains 221 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 136 time to evaluate : 2.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 166 PHE 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 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 597 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 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 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 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 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 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 972 SER Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1099 HIS Chi-restraints excluded: chain C residue 133 PHE Chi-restraints excluded: chain C residue 144 TYR Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 313 THR 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 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 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 955 GLN Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 975 LEU 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 6 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 140 optimal weight: 8.9990 chunk 200 optimal weight: 0.9990 chunk 160 optimal weight: 0.0570 chunk 179 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 296 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 272 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.9702 ------------------------------------------------------------------------------- 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 933 GLN ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 ASN B 760 GLN ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1052 GLN 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 = 0.4721 r_free = 0.4721 target = 0.140678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.114499 restraints weight = 112057.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.117342 restraints weight = 64245.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.117501 restraints weight = 41722.909| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26080 Z= 0.138 Angle : 0.674 12.006 35503 Z= 0.346 Chirality : 0.046 0.413 4026 Planarity : 0.005 0.059 4585 Dihedral : 5.675 53.199 3500 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.09 % Allowed : 21.99 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.14), residues: 3206 helix: -1.01 (0.19), residues: 627 sheet: -0.66 (0.23), residues: 554 loop : -1.58 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP n 35 HIS 0.012 0.001 HIS B1046 PHE 0.037 0.002 PHE A1107 TYR 0.051 0.001 TYR A1065 ARG 0.009 0.000 ARG C1105 Details of bonding type rmsd hydrogen bonds : bond 0.05073 ( 853) hydrogen bonds : angle 6.59769 ( 2376) SS BOND : bond 0.00315 ( 43) SS BOND : angle 1.58217 ( 86) covalent geometry : bond 0.00302 (26037) covalent geometry : angle 0.67004 (35417) *********************** 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 246 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 158 time to evaluate : 2.583 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 311 TYR cc_start: 0.7120 (m-80) cc_final: 0.6916 (m-80) REVERT: A 882 SER cc_start: 0.4481 (OUTLIER) cc_final: 0.4266 (p) REVERT: A 1015 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: A 1016 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8436 (tt) REVERT: A 1050 PHE cc_start: 0.3934 (m-80) cc_final: 0.3624 (m-80) REVERT: B 198 TYR cc_start: 0.7045 (m-80) cc_final: 0.6704 (m-10) REVERT: B 201 ILE cc_start: 0.7081 (mp) cc_final: 0.6693 (mt) REVERT: B 358 ASN cc_start: 0.7933 (t0) cc_final: 0.7446 (m-40) REVERT: B 634 TYR cc_start: 0.3745 (OUTLIER) cc_final: 0.3054 (m-80) REVERT: B 771 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: B 1065 TYR cc_start: 0.6074 (m-80) cc_final: 0.5827 (m-80) REVERT: C 985 PRO cc_start: 0.8894 (Cg_exo) cc_final: 0.8428 (Cg_endo) REVERT: C 986 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7451 (pm20) outliers start: 88 outliers final: 67 residues processed: 233 average time/residue: 0.3267 time to fit residues: 125.5219 Evaluate side-chains 221 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 149 time to evaluate : 2.610 ------------------------------------------------------------------------------- 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 316 PHE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 481 VAL 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 694 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 738 MET 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 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 310 ILE 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 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 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 972 SER Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1099 HIS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 565 ARG Chi-restraints excluded: chain C residue 583 LEU 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 757 PHE Chi-restraints excluded: chain C residue 783 VAL 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 974 VAL Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1062 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 192 optimal weight: 5.9990 chunk 59 optimal weight: 0.0060 chunk 159 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 322 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 254 optimal weight: 7.9990 chunk 321 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.3402 ------------------------------------------------------------------------------- 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 933 GLN ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN n 40 GLN ** 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 = 0.4700 r_free = 0.4700 target = 0.139343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.112838 restraints weight = 111108.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.115422 restraints weight = 68330.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.116038 restraints weight = 46207.240| |-----------------------------------------------------------------------------| r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 26080 Z= 0.172 Angle : 0.689 13.365 35503 Z= 0.355 Chirality : 0.046 0.267 4026 Planarity : 0.005 0.069 4585 Dihedral : 5.475 25.942 3497 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 2.92 % Allowed : 22.02 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.14), residues: 3206 helix: -1.05 (0.19), residues: 635 sheet: -0.71 (0.22), residues: 563 loop : -1.59 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 884 HIS 0.010 0.001 HIS B1046 PHE 0.044 0.002 PHE A1107 TYR 0.055 0.002 TYR A1065 ARG 0.011 0.000 ARG C 763 Details of bonding type rmsd hydrogen bonds : bond 0.05212 ( 853) hydrogen bonds : angle 6.59304 ( 2376) SS BOND : bond 0.00386 ( 43) SS BOND : angle 1.63930 ( 86) covalent geometry : bond 0.00379 (26037) covalent geometry : angle 0.68527 (35417) ********************** 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 233 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 150 time to evaluate : 2.645 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 311 TYR cc_start: 0.7245 (m-80) cc_final: 0.6997 (m-80) REVERT: A 882 SER cc_start: 0.4822 (OUTLIER) cc_final: 0.4484 (p) REVERT: A 1015 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: A 1016 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8457 (tt) REVERT: A 1050 PHE cc_start: 0.4440 (m-80) cc_final: 0.4103 (m-80) REVERT: B 167 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7359 (tp30) REVERT: B 198 TYR cc_start: 0.6999 (m-80) cc_final: 0.6630 (m-10) REVERT: B 201 ILE cc_start: 0.7076 (mp) cc_final: 0.6684 (mt) REVERT: B 358 ASN cc_start: 0.8057 (t0) cc_final: 0.7559 (m-40) REVERT: B 634 TYR cc_start: 0.3765 (OUTLIER) cc_final: 0.3069 (m-80) REVERT: B 1065 TYR cc_start: 0.6123 (m-80) cc_final: 0.5869 (m-80) REVERT: C 985 PRO cc_start: 0.8878 (Cg_exo) cc_final: 0.8431 (Cg_endo) REVERT: o 86 TYR cc_start: 0.2970 (OUTLIER) cc_final: 0.1727 (t80) outliers start: 83 outliers final: 68 residues processed: 217 average time/residue: 0.3413 time to fit residues: 122.5936 Evaluate side-chains 216 residues out of total 2847 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 143 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 166 PHE 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 316 PHE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 481 VAL 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 725 LEU Chi-restraints excluded: chain A residue 738 MET 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 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 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 164 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 225 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 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 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 975 LEU Chi-restraints excluded: chain B residue 1099 HIS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 300 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 757 PHE 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 974 VAL Chi-restraints excluded: chain C residue 1053 SER 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 86 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 316 optimal weight: 40.0000 chunk 252 optimal weight: 8.9990 chunk 260 optimal weight: 8.9990 chunk 244 optimal weight: 0.0670 chunk 193 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 314 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 99 optimal weight: 0.0980 chunk 54 optimal weight: 0.9990 overall best weight: 0.8324 ------------------------------------------------------------------------------- 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** ** A 899 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 GLN ** A1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 446 ASN ** B 918 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 GLN o 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.141740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.115729 restraints weight = 111915.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.118646 restraints weight = 64680.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.119137 restraints weight = 42489.889| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6026 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26080 Z= 0.126 Angle : 0.654 12.088 35503 Z= 0.331 Chirality : 0.045 0.338 4026 Planarity : 0.004 0.062 4585 Dihedral : 5.170 30.299 3497 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.49 % Allowed : 22.55 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3206 helix: -0.72 (0.20), residues: 626 sheet: -0.72 (0.22), residues: 579 loop : -1.50 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP n 35 HIS 0.010 0.001 HIS B1046 PHE 0.023 0.001 PHE B 55 TYR 0.021 0.001 TYR B 378 ARG 0.008 0.000 ARG B 317 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 853) hydrogen bonds : angle 6.26722 ( 2376) SS BOND : bond 0.00336 ( 43) SS BOND : angle 1.37670 ( 86) covalent geometry : bond 0.00276 (26037) covalent geometry : angle 0.65147 (35417) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8872.82 seconds wall clock time: 156 minutes 28.08 seconds (9388.08 seconds total)