Starting phenix.real_space_refine on Sat Jun 21 07:12:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk3_32557/06_2025/7wk3_32557.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk3_32557/06_2025/7wk3_32557.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wk3_32557/06_2025/7wk3_32557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk3_32557/06_2025/7wk3_32557.map" model { file = "/net/cci-nas-00/data/ceres_data/7wk3_32557/06_2025/7wk3_32557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk3_32557/06_2025/7wk3_32557.cif" } resolution = 3.4 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15874 2.51 5 N 4133 2.21 5 O 4684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24805 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8219 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 54, 'TRANS': 993} Chain breaks: 7 Chain: "B" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 2, 'PTRANS': 54, 'TRANS': 1000} Chain breaks: 7 Chain: "C" Number of atoms: 8293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1057, 8293 Classifications: {'peptide': 1057} Link IDs: {'CIS': 2, 'PTRANS': 54, 'TRANS': 1000} Chain breaks: 7 Time building chain proxies: 14.99, per 1000 atoms: 0.60 Number of scatterers: 24805 At special positions: 0 Unit cell: (147.555, 144.276, 196.74, 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 4684 8.00 N 4133 7.00 C 15874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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: 5.37 Conformation dependent library (CDL) restraints added in 3.0 seconds 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5936 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 47 sheets defined 23.3% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.767A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 341' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.772A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 removed outlier: 3.685A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.932A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.685A pdb=" N ALA A 876 " --> pdb=" O GLN A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.078A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.768A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.229A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.912A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.783A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 removed outlier: 3.983A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.861A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 634 through 639 removed outlier: 3.536A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 4.187A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.734A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.693A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 883 removed outlier: 3.704A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.849A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.621A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 5.722A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.683A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.785A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.095A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 4.147A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.385A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.827A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.960A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY C 639 " --> pdb=" O TYR C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 4.055A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.587A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 removed outlier: 3.717A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.707A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.502A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 941 removed outlier: 5.659A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.765A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.757A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.257A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.968A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.045A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.951A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.538A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.170A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.994A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.926A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 6.675A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.648A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.181A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.415A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.912A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.517A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.066A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.682A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ILE B 210 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.653A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.625A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 317 removed outlier: 3.500A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.648A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.478A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.478A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.656A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.246A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.948A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 728 removed outlier: 3.642A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.315A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.960A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.760A pdb=" N PHE C 186 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN C 188 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR C 208 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.688A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.540A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.019A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD9, first strand: chain 'C' and resid 244 through 245 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.527A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.108A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 359 Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.868A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.235A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 712 through 728 removed outlier: 3.814A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 712 through 728 removed outlier: 3.814A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.402A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 968 hydrogen bonds defined for protein. 2616 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: 12.10 Time building geometry restraints manager: 6.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7967 1.35 - 1.46: 6235 1.46 - 1.58: 11038 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 25384 Sorted by residual: bond pdb=" C CYS A 336 " pdb=" N PRO A 337 " ideal model delta sigma weight residual 1.334 1.550 -0.216 2.34e-02 1.83e+03 8.53e+01 bond pdb=" C PRO A 25 " pdb=" N PRO A 26 " ideal model delta sigma weight residual 1.334 1.505 -0.171 2.34e-02 1.83e+03 5.35e+01 bond pdb=" C PRO B 25 " pdb=" N PRO B 26 " ideal model delta sigma weight residual 1.334 1.497 -0.163 2.34e-02 1.83e+03 4.83e+01 bond pdb=" C CYS C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.334 1.495 -0.161 2.34e-02 1.83e+03 4.76e+01 bond pdb=" C LEU C 229 " pdb=" N PRO C 230 " ideal model delta sigma weight residual 1.334 1.482 -0.148 2.34e-02 1.83e+03 4.01e+01 ... (remaining 25379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 33566 1.48 - 2.96: 801 2.96 - 4.44: 140 4.44 - 5.92: 4 5.92 - 7.40: 4 Bond angle restraints: 34515 Sorted by residual: angle pdb=" C ASN B 122 " pdb=" N ALA B 123 " pdb=" CA ALA B 123 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 112.83 109.98 2.85 9.90e-01 1.02e+00 8.29e+00 angle pdb=" C ASN A 122 " pdb=" N ALA A 123 " pdb=" CA ALA A 123 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 8.01e+00 angle pdb=" N ILE A 468 " pdb=" CA ILE A 468 " pdb=" C ILE A 468 " ideal model delta sigma weight residual 112.83 110.08 2.75 9.90e-01 1.02e+00 7.70e+00 angle pdb=" N GLY C 103 " pdb=" CA GLY C 103 " pdb=" C GLY C 103 " ideal model delta sigma weight residual 110.45 113.82 -3.37 1.30e+00 5.92e-01 6.71e+00 ... (remaining 34510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 14828 15.83 - 31.66: 234 31.66 - 47.49: 81 47.49 - 63.32: 14 63.32 - 79.15: 1 Dihedral angle restraints: 15158 sinusoidal: 5944 harmonic: 9214 Sorted by residual: dihedral pdb=" CA LYS C 795 " pdb=" C LYS C 795 " pdb=" N TYR C 796 " pdb=" CA TYR C 796 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA PHE C 157 " pdb=" C PHE C 157 " pdb=" N ARG C 158 " pdb=" CA ARG C 158 " ideal model delta harmonic sigma weight residual 0.00 21.91 -21.91 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LYS A 795 " pdb=" C LYS A 795 " pdb=" N TYR A 796 " pdb=" CA TYR A 796 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 15155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2416 0.030 - 0.061: 991 0.061 - 0.091: 191 0.091 - 0.121: 270 0.121 - 0.152: 36 Chirality restraints: 3904 Sorted by residual: chirality pdb=" CA ILE C 410 " pdb=" N ILE C 410 " pdb=" C ILE C 410 " pdb=" CB ILE C 410 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA ILE A 95 " pdb=" N ILE A 95 " pdb=" C ILE A 95 " pdb=" CB ILE A 95 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA ILE B 714 " pdb=" N ILE B 714 " pdb=" C ILE B 714 " pdb=" CB ILE B 714 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 ... (remaining 3901 not shown) Planarity restraints: 4462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.80e+00 pdb=" N PRO A 295 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 216 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO B 217 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 217 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 217 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 216 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO C 217 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 217 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 217 " -0.023 5.00e-02 4.00e+02 ... (remaining 4459 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 184 2.58 - 3.16: 20884 3.16 - 3.74: 35661 3.74 - 4.32: 52838 4.32 - 4.90: 86686 Nonbonded interactions: 196253 Sorted by model distance: nonbonded pdb=" OG1 THR A 33 " pdb=" O GLY A 219 " model vdw 1.998 3.040 nonbonded pdb=" O ASN A 978 " pdb=" OG SER A 982 " model vdw 2.013 3.040 nonbonded pdb=" OG SER B 813 " pdb=" OE2 GLU B 868 " model vdw 2.023 3.040 nonbonded pdb=" OH TYR A 674 " pdb=" OE1 GLN A 690 " model vdw 2.046 3.040 nonbonded pdb=" OG SER C 813 " pdb=" OE2 GLU C 868 " model vdw 2.061 3.040 ... (remaining 196248 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' selection = (chain 'B' and (resid 14 through 631 or resid 641 through 1147)) selection = (chain 'C' and (resid 14 through 631 or resid 641 through 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.190 Set scattering table: 0.210 Process input model: 58.030 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.110 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5453 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.216 25423 Z= 0.187 Angle : 0.565 7.403 34593 Z= 0.352 Chirality : 0.043 0.152 3904 Planarity : 0.003 0.049 4462 Dihedral : 7.179 79.153 9105 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % 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: -2.17 (0.12), residues: 3114 helix: -2.17 (0.16), residues: 646 sheet: -0.80 (0.16), residues: 670 loop : -1.39 (0.12), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 633 HIS 0.003 0.001 HIS C1048 PHE 0.018 0.001 PHE B 718 TYR 0.016 0.001 TYR C 707 ARG 0.005 0.000 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.25453 ( 924) hydrogen bonds : angle 9.89997 ( 2616) SS BOND : bond 0.00228 ( 39) SS BOND : angle 0.82304 ( 78) covalent geometry : bond 0.00382 (25384) covalent geometry : angle 0.56406 (34515) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 791 time to evaluate : 2.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6932 (mtt-85) cc_final: 0.6374 (ttp80) REVERT: A 578 ASP cc_start: 0.2983 (t70) cc_final: 0.1219 (t0) REVERT: A 756 TYR cc_start: 0.6677 (m-80) cc_final: 0.6253 (m-80) REVERT: B 315 THR cc_start: 0.7102 (m) cc_final: 0.6523 (m) REVERT: B 535 LYS cc_start: 0.7362 (mttt) cc_final: 0.7151 (mttp) REVERT: B 537 LYS cc_start: 0.6839 (ttmt) cc_final: 0.6628 (mtpp) REVERT: B 581 THR cc_start: 0.4450 (p) cc_final: 0.2476 (m) REVERT: B 737 ASP cc_start: 0.6361 (t0) cc_final: 0.5845 (t0) REVERT: C 553 THR cc_start: 0.4797 (p) cc_final: 0.4313 (m) REVERT: C 737 ASP cc_start: 0.6897 (t0) cc_final: 0.6565 (t70) REVERT: C 800 PHE cc_start: 0.6037 (m-10) cc_final: 0.5823 (m-80) outliers start: 0 outliers final: 0 residues processed: 791 average time/residue: 0.4863 time to fit residues: 577.3184 Evaluate side-chains 529 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 529 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 265 optimal weight: 0.1980 chunk 237 optimal weight: 0.0980 chunk 132 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A1071 GLN B 188 ASN B 505 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN B 913 GLN B 949 GLN B 954 HIS B 965 GLN B1083 HIS B1101 HIS C 30 ASN C 409 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 613 GLN C 895 GLN C 901 GLN C 954 HIS C1071 GLN C1088 HIS C1113 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.173166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.138651 restraints weight = 49759.088| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.20 r_work: 0.3648 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25423 Z= 0.200 Angle : 0.664 9.663 34593 Z= 0.351 Chirality : 0.047 0.236 3904 Planarity : 0.004 0.045 4462 Dihedral : 4.475 23.403 3391 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.77 % Allowed : 9.57 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 3114 helix: 0.41 (0.19), residues: 659 sheet: -0.41 (0.17), residues: 675 loop : -1.06 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 104 HIS 0.012 0.002 HIS B 954 PHE 0.043 0.002 PHE A 92 TYR 0.035 0.002 TYR A 265 ARG 0.011 0.001 ARG B1107 Details of bonding type rmsd hydrogen bonds : bond 0.05276 ( 924) hydrogen bonds : angle 6.21612 ( 2616) SS BOND : bond 0.00858 ( 39) SS BOND : angle 1.34968 ( 78) covalent geometry : bond 0.00456 (25384) covalent geometry : angle 0.66155 (34515) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 579 time to evaluate : 2.586 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 34 ARG cc_start: 0.8317 (mtt-85) cc_final: 0.5858 (ttp80) REVERT: A 190 ARG cc_start: 0.7825 (ttm110) cc_final: 0.7399 (ttm110) REVERT: A 207 HIS cc_start: 0.7255 (m170) cc_final: 0.6768 (m170) REVERT: A 304 LYS cc_start: 0.8934 (mttt) cc_final: 0.8718 (mmmm) REVERT: A 307 THR cc_start: 0.8650 (m) cc_final: 0.8301 (p) REVERT: A 558 LYS cc_start: 0.6904 (tmtt) cc_final: 0.6571 (tmtt) REVERT: A 567 ARG cc_start: 0.7511 (ptp-110) cc_final: 0.7184 (ptp-110) REVERT: A 585 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6734 (pp) REVERT: A 737 ASP cc_start: 0.7584 (t0) cc_final: 0.7364 (t0) REVERT: A 819 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7140 (mt-10) REVERT: A 1038 LYS cc_start: 0.8936 (mttt) cc_final: 0.8725 (mtpp) REVERT: B 87 ASN cc_start: 0.7666 (p0) cc_final: 0.7440 (p0) REVERT: B 104 TRP cc_start: 0.8668 (m-90) cc_final: 0.8403 (m-90) REVERT: B 191 GLU cc_start: 0.7656 (pt0) cc_final: 0.7453 (mt-10) REVERT: B 278 LYS cc_start: 0.8960 (tttt) cc_final: 0.8506 (ttpt) REVERT: B 326 ILE cc_start: 0.8594 (mm) cc_final: 0.8385 (mm) REVERT: B 329 PHE cc_start: 0.6465 (t80) cc_final: 0.6254 (t80) REVERT: B 351 TYR cc_start: 0.7370 (p90) cc_final: 0.6643 (p90) REVERT: B 395 VAL cc_start: 0.7717 (t) cc_final: 0.7435 (m) REVERT: B 528 LYS cc_start: 0.6866 (ttpt) cc_final: 0.5111 (tttp) REVERT: B 763 LEU cc_start: 0.8314 (mt) cc_final: 0.7857 (mp) REVERT: B 765 ARG cc_start: 0.7786 (tmm-80) cc_final: 0.7545 (ttp80) REVERT: B 797 PHE cc_start: 0.7999 (m-80) cc_final: 0.7724 (m-80) REVERT: B 882 ILE cc_start: 0.8728 (mt) cc_final: 0.8516 (mt) REVERT: C 170 TYR cc_start: 0.7559 (t80) cc_final: 0.7271 (t80) REVERT: C 197 ILE cc_start: 0.7720 (pt) cc_final: 0.7401 (pt) REVERT: C 202 LYS cc_start: 0.7550 (mttt) cc_final: 0.7318 (mtmm) REVERT: C 304 LYS cc_start: 0.8851 (mttt) cc_final: 0.8647 (mmmm) REVERT: C 607 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8198 (mm-40) REVERT: C 710 ASN cc_start: 0.8412 (p0) cc_final: 0.8118 (p0) REVERT: C 748 GLU cc_start: 0.7581 (tp30) cc_final: 0.7362 (tp30) REVERT: C 776 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8506 (tppp) REVERT: C 947 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7653 (mttm) REVERT: C 950 ASP cc_start: 0.7882 (t70) cc_final: 0.7640 (t0) REVERT: C 1081 ILE cc_start: 0.8424 (pt) cc_final: 0.8204 (mm) REVERT: C 1144 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8204 (mm-30) outliers start: 49 outliers final: 32 residues processed: 602 average time/residue: 0.5293 time to fit residues: 485.2586 Evaluate side-chains 520 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 484 time to evaluate : 5.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1144 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 105 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 247 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 239 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 310 optimal weight: 0.9980 chunk 233 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 245 HIS B 519 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN B 901 GLN B 913 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.165133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.129721 restraints weight = 48334.900| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.22 r_work: 0.3549 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 25423 Z= 0.185 Angle : 0.607 9.082 34593 Z= 0.320 Chirality : 0.046 0.216 3904 Planarity : 0.004 0.056 4462 Dihedral : 4.372 21.918 3391 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.53 % Allowed : 11.30 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.14), residues: 3114 helix: 1.03 (0.20), residues: 651 sheet: 0.12 (0.18), residues: 645 loop : -0.96 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 886 HIS 0.006 0.001 HIS C1064 PHE 0.029 0.002 PHE B 718 TYR 0.026 0.002 TYR A 91 ARG 0.010 0.001 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.05072 ( 924) hydrogen bonds : angle 5.76852 ( 2616) SS BOND : bond 0.00737 ( 39) SS BOND : angle 1.34757 ( 78) covalent geometry : bond 0.00425 (25384) covalent geometry : angle 0.60419 (34515) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 540 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8136 (mtt-85) cc_final: 0.6380 (ttp80) REVERT: A 190 ARG cc_start: 0.7792 (ttm110) cc_final: 0.7396 (ttm110) REVERT: A 207 HIS cc_start: 0.7206 (m170) cc_final: 0.6818 (m-70) REVERT: A 239 GLN cc_start: 0.7901 (tt0) cc_final: 0.7566 (tp40) REVERT: A 304 LYS cc_start: 0.8980 (mttt) cc_final: 0.8774 (mmtp) REVERT: A 307 THR cc_start: 0.8735 (m) cc_final: 0.8374 (p) REVERT: A 591 SER cc_start: 0.9147 (t) cc_final: 0.8871 (p) REVERT: A 884 SER cc_start: 0.9057 (m) cc_final: 0.8693 (t) REVERT: A 933 LYS cc_start: 0.8645 (ttmm) cc_final: 0.8345 (mttp) REVERT: A 1002 GLN cc_start: 0.8359 (tp40) cc_final: 0.7702 (tp40) REVERT: A 1038 LYS cc_start: 0.9081 (mttt) cc_final: 0.8803 (mtpp) REVERT: B 45 SER cc_start: 0.8768 (p) cc_final: 0.8502 (t) REVERT: B 104 TRP cc_start: 0.8842 (m-90) cc_final: 0.8407 (m-90) REVERT: B 160 TYR cc_start: 0.7585 (p90) cc_final: 0.7380 (p90) REVERT: B 190 ARG cc_start: 0.7835 (mtm180) cc_final: 0.7557 (mtt90) REVERT: B 191 GLU cc_start: 0.7777 (pt0) cc_final: 0.7432 (mt-10) REVERT: B 195 LYS cc_start: 0.7632 (tppt) cc_final: 0.7388 (tppt) REVERT: B 237 ARG cc_start: 0.8505 (mtm-85) cc_final: 0.7563 (ptt90) REVERT: B 278 LYS cc_start: 0.8919 (tttt) cc_final: 0.8493 (ttpt) REVERT: B 329 PHE cc_start: 0.6624 (t80) cc_final: 0.6407 (t80) REVERT: B 346 ARG cc_start: 0.7746 (ttt-90) cc_final: 0.7527 (ttp80) REVERT: B 395 VAL cc_start: 0.8011 (t) cc_final: 0.7738 (m) REVERT: B 528 LYS cc_start: 0.7070 (ttpt) cc_final: 0.5333 (mmtp) REVERT: B 643 PHE cc_start: 0.8304 (t80) cc_final: 0.8074 (t80) REVERT: B 790 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8514 (mtpp) REVERT: B 882 ILE cc_start: 0.8859 (mt) cc_final: 0.8646 (mt) REVERT: B 1072 GLU cc_start: 0.8606 (pm20) cc_final: 0.8345 (pm20) REVERT: C 170 TYR cc_start: 0.7719 (t80) cc_final: 0.7346 (t80) REVERT: C 202 LYS cc_start: 0.7748 (mttt) cc_final: 0.7363 (mtpp) REVERT: C 319 ARG cc_start: 0.7859 (mmm160) cc_final: 0.7469 (mmt90) REVERT: C 607 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8269 (mm-40) REVERT: C 643 PHE cc_start: 0.8213 (t80) cc_final: 0.8013 (t80) REVERT: C 710 ASN cc_start: 0.8699 (p0) cc_final: 0.8361 (p0) REVERT: C 725 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7419 (mt-10) REVERT: C 739 THR cc_start: 0.8238 (m) cc_final: 0.7982 (p) REVERT: C 776 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8362 (tppp) REVERT: C 795 LYS cc_start: 0.8394 (mmtp) cc_final: 0.8124 (mmtp) REVERT: C 947 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7654 (mttm) REVERT: C 965 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8428 (mm-40) REVERT: C 988 GLU cc_start: 0.7815 (pm20) cc_final: 0.7495 (pm20) REVERT: C 1002 GLN cc_start: 0.8515 (tp40) cc_final: 0.8189 (tp40) REVERT: C 1081 ILE cc_start: 0.8459 (pt) cc_final: 0.8183 (pt) outliers start: 70 outliers final: 44 residues processed: 569 average time/residue: 0.4003 time to fit residues: 345.6326 Evaluate side-chains 527 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 482 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 287 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 202 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 303 optimal weight: 0.5980 chunk 213 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 298 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 251 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 188 ASN B 207 HIS B 563 GLN B 658 ASN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 955 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.163491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128211 restraints weight = 48405.199| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 3.13 r_work: 0.3527 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25423 Z= 0.149 Angle : 0.573 8.437 34593 Z= 0.300 Chirality : 0.044 0.174 3904 Planarity : 0.004 0.045 4462 Dihedral : 4.286 20.325 3391 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.74 % Allowed : 12.78 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.14), residues: 3114 helix: 1.29 (0.21), residues: 655 sheet: 0.22 (0.18), residues: 680 loop : -0.86 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 64 HIS 0.005 0.001 HIS B1088 PHE 0.038 0.002 PHE B 342 TYR 0.027 0.001 TYR A 91 ARG 0.007 0.000 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 924) hydrogen bonds : angle 5.43363 ( 2616) SS BOND : bond 0.00351 ( 39) SS BOND : angle 1.18765 ( 78) covalent geometry : bond 0.00338 (25384) covalent geometry : angle 0.57075 (34515) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 497 time to evaluate : 3.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.7973 (mtt-85) cc_final: 0.6354 (ttp80) REVERT: A 190 ARG cc_start: 0.7871 (ttm110) cc_final: 0.7434 (ttm110) REVERT: A 207 HIS cc_start: 0.7139 (m170) cc_final: 0.6631 (m-70) REVERT: A 239 GLN cc_start: 0.8127 (tt0) cc_final: 0.7540 (tp-100) REVERT: A 307 THR cc_start: 0.8768 (m) cc_final: 0.8385 (p) REVERT: A 567 ARG cc_start: 0.7595 (ptp-110) cc_final: 0.7347 (ptp90) REVERT: A 588 THR cc_start: 0.8382 (m) cc_final: 0.7842 (p) REVERT: A 591 SER cc_start: 0.9209 (t) cc_final: 0.8706 (p) REVERT: A 918 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8090 (mp0) REVERT: A 933 LYS cc_start: 0.8640 (ttmm) cc_final: 0.8311 (mttp) REVERT: A 1002 GLN cc_start: 0.8318 (tp40) cc_final: 0.7631 (tp40) REVERT: A 1038 LYS cc_start: 0.9123 (mttt) cc_final: 0.8856 (mtpp) REVERT: B 45 SER cc_start: 0.8765 (p) cc_final: 0.8557 (t) REVERT: B 100 ILE cc_start: 0.8684 (mm) cc_final: 0.8467 (mm) REVERT: B 191 GLU cc_start: 0.7822 (pt0) cc_final: 0.7483 (mt-10) REVERT: B 237 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.7542 (ptt90) REVERT: B 278 LYS cc_start: 0.8848 (tttt) cc_final: 0.8550 (ttpt) REVERT: B 329 PHE cc_start: 0.6661 (t80) cc_final: 0.6455 (t80) REVERT: B 346 ARG cc_start: 0.7783 (ttt-90) cc_final: 0.7567 (ttp80) REVERT: B 386 LYS cc_start: 0.8274 (mmmt) cc_final: 0.7708 (mptt) REVERT: B 395 VAL cc_start: 0.8267 (t) cc_final: 0.8008 (m) REVERT: B 454 ARG cc_start: 0.7641 (ttp-110) cc_final: 0.7317 (mtm-85) REVERT: B 528 LYS cc_start: 0.7072 (ttpt) cc_final: 0.5078 (ttmm) REVERT: B 537 LYS cc_start: 0.8650 (tttt) cc_final: 0.8360 (tttp) REVERT: B 547 LYS cc_start: 0.8144 (mttt) cc_final: 0.7857 (mttp) REVERT: B 583 GLU cc_start: 0.7570 (pm20) cc_final: 0.7182 (pm20) REVERT: B 737 ASP cc_start: 0.7836 (t0) cc_final: 0.7529 (t0) REVERT: B 790 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8542 (mtpp) REVERT: B 882 ILE cc_start: 0.8855 (mt) cc_final: 0.8648 (mt) REVERT: B 888 PHE cc_start: 0.8672 (p90) cc_final: 0.8261 (p90) REVERT: B 935 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8063 (tt0) REVERT: B 1050 MET cc_start: 0.8581 (mtm) cc_final: 0.8319 (mtp) REVERT: C 170 TYR cc_start: 0.7761 (t80) cc_final: 0.7372 (t80) REVERT: C 195 LYS cc_start: 0.8156 (pttt) cc_final: 0.7905 (pttt) REVERT: C 202 LYS cc_start: 0.7885 (mttt) cc_final: 0.7527 (mttm) REVERT: C 238 PHE cc_start: 0.7398 (p90) cc_final: 0.7007 (p90) REVERT: C 280 ASN cc_start: 0.8022 (p0) cc_final: 0.7767 (p0) REVERT: C 281 GLU cc_start: 0.6807 (pm20) cc_final: 0.6489 (pp20) REVERT: C 319 ARG cc_start: 0.7779 (mmm160) cc_final: 0.7459 (mpt180) REVERT: C 643 PHE cc_start: 0.8250 (t80) cc_final: 0.8026 (t80) REVERT: C 710 ASN cc_start: 0.8738 (p0) cc_final: 0.8395 (p0) REVERT: C 725 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7416 (mt-10) REVERT: C 739 THR cc_start: 0.8433 (m) cc_final: 0.8147 (p) REVERT: C 745 ASP cc_start: 0.6576 (m-30) cc_final: 0.6303 (p0) REVERT: C 776 LYS cc_start: 0.8591 (mmmm) cc_final: 0.8317 (tppp) REVERT: C 787 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7587 (mm-40) REVERT: C 821 LEU cc_start: 0.8618 (tp) cc_final: 0.8267 (tt) REVERT: C 822 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8465 (mm) REVERT: C 936 ASP cc_start: 0.8153 (t70) cc_final: 0.7921 (m-30) REVERT: C 947 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7611 (mttm) REVERT: C 965 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8447 (mm-40) REVERT: C 1002 GLN cc_start: 0.8495 (tp40) cc_final: 0.8200 (tp40) REVERT: C 1081 ILE cc_start: 0.8522 (pt) cc_final: 0.8270 (mm) outliers start: 76 outliers final: 54 residues processed: 536 average time/residue: 0.4058 time to fit residues: 328.3434 Evaluate side-chains 526 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 470 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 922 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 140 optimal weight: 4.9990 chunk 213 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 221 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 422 ASN A 450 ASN A 564 GLN ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN A 965 GLN B 271 GLN B 563 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS B1074 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN C 658 ASN C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.156401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121248 restraints weight = 47981.763| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.03 r_work: 0.3426 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 25423 Z= 0.254 Angle : 0.670 9.828 34593 Z= 0.355 Chirality : 0.047 0.197 3904 Planarity : 0.004 0.048 4462 Dihedral : 4.820 23.395 3391 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.47 % Allowed : 12.53 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.14), residues: 3114 helix: 1.06 (0.21), residues: 658 sheet: 0.07 (0.18), residues: 706 loop : -0.93 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 64 HIS 0.009 0.002 HIS C 207 PHE 0.042 0.003 PHE B 342 TYR 0.033 0.002 TYR C 707 ARG 0.005 0.001 ARG A 995 Details of bonding type rmsd hydrogen bonds : bond 0.05488 ( 924) hydrogen bonds : angle 5.48468 ( 2616) SS BOND : bond 0.00422 ( 39) SS BOND : angle 1.69752 ( 78) covalent geometry : bond 0.00587 (25384) covalent geometry : angle 0.66548 (34515) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 508 time to evaluate : 2.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 THR cc_start: 0.8864 (m) cc_final: 0.8501 (p) REVERT: A 588 THR cc_start: 0.8340 (m) cc_final: 0.7814 (p) REVERT: A 646 ARG cc_start: 0.8356 (ttp-170) cc_final: 0.8135 (mtm-85) REVERT: A 869 MET cc_start: 0.8702 (mtp) cc_final: 0.8186 (mtm) REVERT: A 918 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8062 (mp0) REVERT: A 1002 GLN cc_start: 0.8473 (tp40) cc_final: 0.7961 (tp40) REVERT: A 1017 GLU cc_start: 0.8114 (mm-30) cc_final: 0.6689 (mm-30) REVERT: A 1038 LYS cc_start: 0.9278 (mttt) cc_final: 0.8974 (mtpp) REVERT: B 100 ILE cc_start: 0.8797 (mm) cc_final: 0.8560 (mm) REVERT: B 133 PHE cc_start: 0.7355 (m-80) cc_final: 0.7127 (m-80) REVERT: B 191 GLU cc_start: 0.7876 (pt0) cc_final: 0.7497 (mt-10) REVERT: B 237 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.8304 (mtm180) REVERT: B 278 LYS cc_start: 0.8832 (tttt) cc_final: 0.8474 (ttmm) REVERT: B 346 ARG cc_start: 0.8131 (ttt-90) cc_final: 0.7892 (ttp80) REVERT: B 386 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8173 (mttt) REVERT: B 387 LEU cc_start: 0.8648 (mt) cc_final: 0.8424 (mt) REVERT: B 395 VAL cc_start: 0.8450 (t) cc_final: 0.8209 (m) REVERT: B 537 LYS cc_start: 0.8634 (tttt) cc_final: 0.8369 (tttp) REVERT: B 547 LYS cc_start: 0.8490 (mttt) cc_final: 0.8100 (mttm) REVERT: B 935 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8408 (tm-30) REVERT: B 1002 GLN cc_start: 0.8370 (tp40) cc_final: 0.7902 (tp40) REVERT: B 1038 LYS cc_start: 0.8944 (mmmm) cc_final: 0.8671 (mmtp) REVERT: B 1106 GLN cc_start: 0.6878 (mm-40) cc_final: 0.6651 (mm-40) REVERT: C 48 LEU cc_start: 0.8984 (mm) cc_final: 0.8777 (mp) REVERT: C 170 TYR cc_start: 0.7964 (t80) cc_final: 0.7528 (t80) REVERT: C 202 LYS cc_start: 0.8135 (mttt) cc_final: 0.7864 (mttp) REVERT: C 298 GLU cc_start: 0.8679 (tp30) cc_final: 0.8280 (tp30) REVERT: C 704 SER cc_start: 0.8444 (t) cc_final: 0.8053 (t) REVERT: C 725 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7514 (mt-10) REVERT: C 739 THR cc_start: 0.8723 (m) cc_final: 0.8462 (p) REVERT: C 745 ASP cc_start: 0.6876 (m-30) cc_final: 0.6612 (p0) REVERT: C 776 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8326 (tppp) REVERT: C 787 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7710 (mm-40) REVERT: C 795 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8425 (mmtp) REVERT: C 804 GLN cc_start: 0.8309 (mm-40) cc_final: 0.7863 (mm-40) REVERT: C 821 LEU cc_start: 0.8540 (tp) cc_final: 0.8200 (tt) REVERT: C 947 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7785 (mttm) REVERT: C 955 ASN cc_start: 0.8306 (t0) cc_final: 0.7981 (t0) REVERT: C 965 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8505 (mm-40) REVERT: C 1002 GLN cc_start: 0.8661 (tp40) cc_final: 0.8277 (tp40) outliers start: 96 outliers final: 57 residues processed: 561 average time/residue: 0.4490 time to fit residues: 384.2922 Evaluate side-chains 522 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 464 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 659 SER Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1086 LYS Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 271 optimal weight: 0.4980 chunk 202 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 279 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 787 GLN A 901 GLN A 914 ASN A 955 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.157834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.122631 restraints weight = 47599.944| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.03 r_work: 0.3446 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25423 Z= 0.154 Angle : 0.611 10.390 34593 Z= 0.319 Chirality : 0.045 0.248 3904 Planarity : 0.004 0.047 4462 Dihedral : 4.587 29.416 3391 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.71 % Allowed : 14.84 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3114 helix: 1.21 (0.21), residues: 683 sheet: 0.25 (0.19), residues: 654 loop : -0.94 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 64 HIS 0.003 0.001 HIS C1058 PHE 0.054 0.002 PHE B 342 TYR 0.021 0.001 TYR C 707 ARG 0.005 0.000 ARG C1019 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 924) hydrogen bonds : angle 5.27056 ( 2616) SS BOND : bond 0.00330 ( 39) SS BOND : angle 1.81429 ( 78) covalent geometry : bond 0.00355 (25384) covalent geometry : angle 0.60590 (34515) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 478 time to evaluate : 2.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7275 (tp30) REVERT: A 239 GLN cc_start: 0.8129 (tt0) cc_final: 0.7620 (tp40) REVERT: A 307 THR cc_start: 0.8890 (m) cc_final: 0.8527 (p) REVERT: A 577 ARG cc_start: 0.7259 (ptm160) cc_final: 0.6843 (ttm-80) REVERT: A 646 ARG cc_start: 0.8374 (ttp-170) cc_final: 0.8143 (mtm-85) REVERT: A 918 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8139 (mp0) REVERT: A 933 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8436 (mttp) REVERT: A 1002 GLN cc_start: 0.8246 (tp40) cc_final: 0.7875 (tp40) REVERT: A 1017 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7325 (mm-30) REVERT: A 1030 SER cc_start: 0.8943 (m) cc_final: 0.8567 (p) REVERT: A 1038 LYS cc_start: 0.9275 (mttt) cc_final: 0.8948 (mmmm) REVERT: B 41 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7194 (mmtt) REVERT: B 100 ILE cc_start: 0.8747 (mm) cc_final: 0.8527 (mm) REVERT: B 191 GLU cc_start: 0.7851 (pt0) cc_final: 0.7550 (mt-10) REVERT: B 237 ARG cc_start: 0.8594 (mtm-85) cc_final: 0.8218 (mtm180) REVERT: B 278 LYS cc_start: 0.8875 (tttt) cc_final: 0.8539 (ttpt) REVERT: B 346 ARG cc_start: 0.7958 (ttt-90) cc_final: 0.7715 (ttp80) REVERT: B 386 LYS cc_start: 0.8503 (mmmt) cc_final: 0.8204 (mttt) REVERT: B 387 LEU cc_start: 0.8695 (mt) cc_final: 0.8409 (mt) REVERT: B 395 VAL cc_start: 0.8371 (t) cc_final: 0.8092 (m) REVERT: B 537 LYS cc_start: 0.8617 (tttt) cc_final: 0.8353 (tttp) REVERT: B 547 LYS cc_start: 0.8491 (mttt) cc_final: 0.8196 (mttm) REVERT: B 583 GLU cc_start: 0.7609 (pm20) cc_final: 0.7104 (pm20) REVERT: B 737 ASP cc_start: 0.7831 (t0) cc_final: 0.7529 (t0) REVERT: B 935 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8381 (tm-30) REVERT: B 964 LYS cc_start: 0.8854 (tppp) cc_final: 0.8499 (tppp) REVERT: B 995 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.8084 (ttm-80) REVERT: B 1002 GLN cc_start: 0.8224 (tp40) cc_final: 0.7690 (tp40) REVERT: B 1123 SER cc_start: 0.8845 (t) cc_final: 0.8333 (m) REVERT: C 48 LEU cc_start: 0.8974 (mm) cc_final: 0.8770 (mp) REVERT: C 170 TYR cc_start: 0.7962 (t80) cc_final: 0.7570 (t80) REVERT: C 201 PHE cc_start: 0.8038 (t80) cc_final: 0.7728 (t80) REVERT: C 202 LYS cc_start: 0.8230 (mttt) cc_final: 0.7863 (mttp) REVERT: C 298 GLU cc_start: 0.8635 (tp30) cc_final: 0.8230 (tp30) REVERT: C 578 ASP cc_start: 0.7555 (t0) cc_final: 0.7328 (t70) REVERT: C 710 ASN cc_start: 0.8888 (p0) cc_final: 0.8546 (p0) REVERT: C 725 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7487 (mt-10) REVERT: C 739 THR cc_start: 0.8758 (m) cc_final: 0.8527 (p) REVERT: C 776 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8295 (tppp) REVERT: C 787 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7661 (mm-40) REVERT: C 795 LYS cc_start: 0.8595 (mmtp) cc_final: 0.8368 (mmtp) REVERT: C 804 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7647 (mm-40) REVERT: C 821 LEU cc_start: 0.8576 (tp) cc_final: 0.8202 (tt) REVERT: C 935 GLN cc_start: 0.8306 (tt0) cc_final: 0.7269 (tt0) REVERT: C 947 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7727 (mttm) REVERT: C 955 ASN cc_start: 0.8310 (t0) cc_final: 0.7926 (t0) REVERT: C 965 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8478 (mm-40) REVERT: C 1002 GLN cc_start: 0.8504 (tp40) cc_final: 0.7782 (tp40) REVERT: C 1019 ARG cc_start: 0.7513 (ttp80) cc_final: 0.7268 (ttp80) REVERT: C 1097 SER cc_start: 0.8719 (t) cc_final: 0.8336 (p) REVERT: C 1127 ASP cc_start: 0.8497 (p0) cc_final: 0.8268 (p0) outliers start: 75 outliers final: 53 residues processed: 524 average time/residue: 0.4398 time to fit residues: 351.8739 Evaluate side-chains 513 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 458 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1086 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 208 optimal weight: 0.8980 chunk 286 optimal weight: 0.0370 chunk 307 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 0.0050 chunk 254 optimal weight: 10.0000 chunk 295 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 overall best weight: 0.4472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN B 544 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.158516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.123297 restraints weight = 47857.458| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.04 r_work: 0.3460 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.6815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25423 Z= 0.130 Angle : 0.592 9.017 34593 Z= 0.310 Chirality : 0.044 0.182 3904 Planarity : 0.004 0.044 4462 Dihedral : 4.412 25.750 3391 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.53 % Allowed : 15.23 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3114 helix: 1.37 (0.21), residues: 671 sheet: 0.29 (0.19), residues: 659 loop : -0.87 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 64 HIS 0.003 0.001 HIS B1088 PHE 0.054 0.002 PHE B 342 TYR 0.020 0.001 TYR A 265 ARG 0.004 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 924) hydrogen bonds : angle 5.10430 ( 2616) SS BOND : bond 0.00362 ( 39) SS BOND : angle 1.68570 ( 78) covalent geometry : bond 0.00296 (25384) covalent geometry : angle 0.58713 (34515) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 485 time to evaluate : 2.507 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: A 96 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7325 (tp30) REVERT: A 192 PHE cc_start: 0.8679 (m-80) cc_final: 0.8458 (m-80) REVERT: A 239 GLN cc_start: 0.8087 (tt0) cc_final: 0.7591 (tp40) REVERT: A 307 THR cc_start: 0.8877 (m) cc_final: 0.8498 (p) REVERT: A 577 ARG cc_start: 0.7373 (ptm160) cc_final: 0.6836 (mtp85) REVERT: A 646 ARG cc_start: 0.8338 (ttp-170) cc_final: 0.8103 (mtm-85) REVERT: A 933 LYS cc_start: 0.8678 (ttmm) cc_final: 0.8427 (mttp) REVERT: A 955 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.8058 (t0) REVERT: A 990 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7022 (tm-30) REVERT: A 1002 GLN cc_start: 0.8167 (tp40) cc_final: 0.7770 (tp40) REVERT: A 1030 SER cc_start: 0.8959 (m) cc_final: 0.8621 (t) REVERT: A 1038 LYS cc_start: 0.9256 (mttt) cc_final: 0.8939 (mmmm) REVERT: B 41 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7615 (mmmm) REVERT: B 100 ILE cc_start: 0.8754 (mm) cc_final: 0.8529 (mm) REVERT: B 191 GLU cc_start: 0.7865 (pt0) cc_final: 0.7624 (mt-10) REVERT: B 278 LYS cc_start: 0.8875 (tttt) cc_final: 0.8568 (ttpt) REVERT: B 346 ARG cc_start: 0.7920 (ttt-90) cc_final: 0.7647 (ttp80) REVERT: B 386 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8153 (mttt) REVERT: B 387 LEU cc_start: 0.8741 (mt) cc_final: 0.8437 (mt) REVERT: B 395 VAL cc_start: 0.8362 (t) cc_final: 0.8072 (m) REVERT: B 537 LYS cc_start: 0.8581 (tttt) cc_final: 0.8357 (tttp) REVERT: B 547 LYS cc_start: 0.8478 (mttt) cc_final: 0.8124 (mttm) REVERT: B 583 GLU cc_start: 0.7585 (pm20) cc_final: 0.7090 (pm20) REVERT: B 737 ASP cc_start: 0.7727 (t0) cc_final: 0.7438 (t70) REVERT: B 752 LEU cc_start: 0.9115 (mm) cc_final: 0.8853 (mt) REVERT: B 755 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8807 (mp10) REVERT: B 765 ARG cc_start: 0.7886 (tmm-80) cc_final: 0.7463 (tmm-80) REVERT: B 935 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8294 (tm-30) REVERT: B 964 LYS cc_start: 0.8849 (tppp) cc_final: 0.8501 (tppp) REVERT: B 1002 GLN cc_start: 0.8183 (tp40) cc_final: 0.7594 (tp40) REVERT: B 1123 SER cc_start: 0.8685 (t) cc_final: 0.8116 (m) REVERT: C 170 TYR cc_start: 0.7929 (t80) cc_final: 0.7525 (t80) REVERT: C 202 LYS cc_start: 0.8173 (mttt) cc_final: 0.7833 (mttp) REVERT: C 298 GLU cc_start: 0.8647 (tp30) cc_final: 0.8382 (tp30) REVERT: C 578 ASP cc_start: 0.7586 (t0) cc_final: 0.7356 (t70) REVERT: C 710 ASN cc_start: 0.8863 (p0) cc_final: 0.8515 (p0) REVERT: C 725 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7453 (mt-10) REVERT: C 739 THR cc_start: 0.8745 (m) cc_final: 0.8513 (p) REVERT: C 776 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8290 (tppp) REVERT: C 787 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7605 (mm-40) REVERT: C 804 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7855 (mm-40) REVERT: C 821 LEU cc_start: 0.8554 (tp) cc_final: 0.8156 (tt) REVERT: C 947 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7700 (mttm) REVERT: C 955 ASN cc_start: 0.8241 (t0) cc_final: 0.7901 (t0) REVERT: C 957 GLN cc_start: 0.8404 (tt0) cc_final: 0.7946 (tt0) REVERT: C 1002 GLN cc_start: 0.8414 (tp40) cc_final: 0.7884 (tp40) REVERT: C 1127 ASP cc_start: 0.8433 (p0) cc_final: 0.8190 (p0) outliers start: 70 outliers final: 56 residues processed: 523 average time/residue: 0.4142 time to fit residues: 328.1663 Evaluate side-chains 523 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 464 time to evaluate : 2.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1086 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 213 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 71 optimal weight: 0.0870 chunk 270 optimal weight: 0.5980 chunk 226 optimal weight: 1.9990 chunk 300 optimal weight: 0.5980 chunk 279 optimal weight: 2.9990 chunk 252 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.157609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122275 restraints weight = 47632.534| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.03 r_work: 0.3450 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.6995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25423 Z= 0.147 Angle : 0.600 8.365 34593 Z= 0.315 Chirality : 0.044 0.176 3904 Planarity : 0.004 0.047 4462 Dihedral : 4.394 21.615 3391 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.45 % Allowed : 16.03 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3114 helix: 1.38 (0.21), residues: 671 sheet: 0.24 (0.19), residues: 675 loop : -0.86 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 353 HIS 0.004 0.001 HIS C1064 PHE 0.056 0.002 PHE B 342 TYR 0.022 0.001 TYR B 660 ARG 0.005 0.000 ARG B 328 Details of bonding type rmsd hydrogen bonds : bond 0.04307 ( 924) hydrogen bonds : angle 5.06673 ( 2616) SS BOND : bond 0.00348 ( 39) SS BOND : angle 1.72931 ( 78) covalent geometry : bond 0.00340 (25384) covalent geometry : angle 0.59540 (34515) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 478 time to evaluate : 2.666 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: A 96 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7163 (tp30) REVERT: A 192 PHE cc_start: 0.8659 (m-80) cc_final: 0.8446 (m-80) REVERT: A 239 GLN cc_start: 0.8107 (tt0) cc_final: 0.7576 (tp40) REVERT: A 307 THR cc_start: 0.8872 (m) cc_final: 0.8410 (p) REVERT: A 577 ARG cc_start: 0.7440 (ptm160) cc_final: 0.6924 (ttm-80) REVERT: A 646 ARG cc_start: 0.8375 (ttp-170) cc_final: 0.8130 (mtm-85) REVERT: A 773 GLU cc_start: 0.8196 (tt0) cc_final: 0.7945 (tt0) REVERT: A 933 LYS cc_start: 0.8694 (ttmm) cc_final: 0.8424 (mttp) REVERT: A 953 ASN cc_start: 0.8580 (m-40) cc_final: 0.8364 (m-40) REVERT: A 955 ASN cc_start: 0.8169 (m-40) cc_final: 0.7948 (t0) REVERT: A 1002 GLN cc_start: 0.8193 (tp40) cc_final: 0.7767 (tp40) REVERT: A 1030 SER cc_start: 0.8950 (m) cc_final: 0.8666 (t) REVERT: A 1038 LYS cc_start: 0.9276 (mttt) cc_final: 0.8985 (mtpp) REVERT: B 41 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7861 (mmmm) REVERT: B 100 ILE cc_start: 0.8773 (mm) cc_final: 0.8544 (mm) REVERT: B 237 ARG cc_start: 0.8534 (mtm-85) cc_final: 0.8333 (mtp180) REVERT: B 240 THR cc_start: 0.6989 (OUTLIER) cc_final: 0.6546 (t) REVERT: B 278 LYS cc_start: 0.8856 (tttt) cc_final: 0.8554 (ttpt) REVERT: B 386 LYS cc_start: 0.8478 (mmmt) cc_final: 0.8177 (mttt) REVERT: B 387 LEU cc_start: 0.8835 (mt) cc_final: 0.8523 (mt) REVERT: B 395 VAL cc_start: 0.8366 (t) cc_final: 0.8102 (m) REVERT: B 400 PHE cc_start: 0.6800 (p90) cc_final: 0.6347 (p90) REVERT: B 425 LEU cc_start: 0.8138 (mt) cc_final: 0.7910 (mm) REVERT: B 454 ARG cc_start: 0.7889 (mtm180) cc_final: 0.7646 (mtm180) REVERT: B 537 LYS cc_start: 0.8636 (tttt) cc_final: 0.8346 (tttp) REVERT: B 547 LYS cc_start: 0.8511 (mttt) cc_final: 0.8216 (mttm) REVERT: B 583 GLU cc_start: 0.7613 (pm20) cc_final: 0.7010 (pm20) REVERT: B 737 ASP cc_start: 0.7867 (t0) cc_final: 0.7535 (t70) REVERT: B 787 GLN cc_start: 0.7759 (mp10) cc_final: 0.7423 (mp10) REVERT: B 935 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8230 (tm-30) REVERT: B 964 LYS cc_start: 0.8859 (tppp) cc_final: 0.8636 (ttmm) REVERT: B 1002 GLN cc_start: 0.8205 (tp40) cc_final: 0.7614 (tp40) REVERT: B 1038 LYS cc_start: 0.9015 (mmmm) cc_final: 0.8769 (mmtp) REVERT: B 1123 SER cc_start: 0.8625 (t) cc_final: 0.8419 (t) REVERT: C 170 TYR cc_start: 0.7894 (t80) cc_final: 0.7504 (t80) REVERT: C 202 LYS cc_start: 0.8138 (mttt) cc_final: 0.7816 (mttp) REVERT: C 298 GLU cc_start: 0.8581 (tp30) cc_final: 0.8303 (tp30) REVERT: C 578 ASP cc_start: 0.7585 (t0) cc_final: 0.7349 (t70) REVERT: C 710 ASN cc_start: 0.8898 (p0) cc_final: 0.8582 (p0) REVERT: C 725 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7582 (mt-10) REVERT: C 776 LYS cc_start: 0.8553 (mmmm) cc_final: 0.8291 (tppp) REVERT: C 787 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7636 (mm-40) REVERT: C 804 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7876 (mm-40) REVERT: C 821 LEU cc_start: 0.8554 (tp) cc_final: 0.8165 (tt) REVERT: C 947 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7767 (mttm) REVERT: C 955 ASN cc_start: 0.8305 (t0) cc_final: 0.7946 (t0) REVERT: C 1002 GLN cc_start: 0.8430 (tp40) cc_final: 0.7873 (tp40) REVERT: C 1097 SER cc_start: 0.8709 (t) cc_final: 0.8301 (p) REVERT: C 1127 ASP cc_start: 0.8402 (p0) cc_final: 0.8157 (p0) outliers start: 68 outliers final: 52 residues processed: 518 average time/residue: 0.4056 time to fit residues: 318.2503 Evaluate side-chains 515 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 461 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1086 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 284 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 76 optimal weight: 0.0170 chunk 267 optimal weight: 0.0670 chunk 210 optimal weight: 0.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 657 ASN B 755 GLN C 52 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.158172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.122786 restraints weight = 47690.938| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 3.06 r_work: 0.3457 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.7117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 25423 Z= 0.135 Angle : 0.602 11.197 34593 Z= 0.316 Chirality : 0.044 0.196 3904 Planarity : 0.004 0.054 4462 Dihedral : 4.346 20.193 3391 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.38 % Allowed : 16.53 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.15), residues: 3114 helix: 1.45 (0.21), residues: 671 sheet: 0.26 (0.19), residues: 673 loop : -0.82 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 353 HIS 0.003 0.001 HIS C1064 PHE 0.055 0.002 PHE B 342 TYR 0.025 0.001 TYR C 707 ARG 0.007 0.000 ARG C 355 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 924) hydrogen bonds : angle 5.03411 ( 2616) SS BOND : bond 0.00284 ( 39) SS BOND : angle 1.77192 ( 78) covalent geometry : bond 0.00315 (25384) covalent geometry : angle 0.59697 (34515) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 474 time to evaluate : 2.721 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: A 96 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7395 (tp30) REVERT: A 239 GLN cc_start: 0.8068 (tt0) cc_final: 0.7590 (tp40) REVERT: A 307 THR cc_start: 0.8858 (m) cc_final: 0.8408 (p) REVERT: A 577 ARG cc_start: 0.7427 (ptm160) cc_final: 0.6908 (ttm-80) REVERT: A 646 ARG cc_start: 0.8389 (ttp-170) cc_final: 0.8174 (mtm-85) REVERT: A 763 LEU cc_start: 0.8267 (mt) cc_final: 0.7865 (mp) REVERT: A 773 GLU cc_start: 0.8179 (tt0) cc_final: 0.7922 (tt0) REVERT: A 933 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8431 (mttp) REVERT: A 953 ASN cc_start: 0.8545 (m-40) cc_final: 0.8108 (m-40) REVERT: A 1002 GLN cc_start: 0.8175 (tp40) cc_final: 0.7805 (tp40) REVERT: A 1030 SER cc_start: 0.8944 (m) cc_final: 0.8672 (t) REVERT: A 1038 LYS cc_start: 0.9261 (mttt) cc_final: 0.8953 (mmmm) REVERT: B 100 ILE cc_start: 0.8807 (mm) cc_final: 0.8584 (mm) REVERT: B 278 LYS cc_start: 0.8847 (tttt) cc_final: 0.8529 (ttpt) REVERT: B 386 LYS cc_start: 0.8506 (mmmt) cc_final: 0.8223 (mttt) REVERT: B 387 LEU cc_start: 0.8879 (mt) cc_final: 0.8568 (mt) REVERT: B 395 VAL cc_start: 0.8303 (t) cc_final: 0.8034 (m) REVERT: B 425 LEU cc_start: 0.8104 (mt) cc_final: 0.7889 (mm) REVERT: B 454 ARG cc_start: 0.7832 (mtm180) cc_final: 0.7608 (mtm180) REVERT: B 547 LYS cc_start: 0.8508 (mttt) cc_final: 0.8204 (mttm) REVERT: B 558 LYS cc_start: 0.8670 (mptt) cc_final: 0.8455 (mttt) REVERT: B 583 GLU cc_start: 0.7626 (pm20) cc_final: 0.7013 (pm20) REVERT: B 737 ASP cc_start: 0.7786 (t0) cc_final: 0.7557 (t0) REVERT: B 765 ARG cc_start: 0.7944 (tmm-80) cc_final: 0.7302 (tmm-80) REVERT: B 787 GLN cc_start: 0.7791 (mp10) cc_final: 0.7451 (mp10) REVERT: B 790 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8485 (mtmm) REVERT: B 935 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8270 (tm-30) REVERT: B 964 LYS cc_start: 0.8867 (tppp) cc_final: 0.8614 (ttmm) REVERT: B 1002 GLN cc_start: 0.8182 (tp40) cc_final: 0.7802 (tp40) REVERT: B 1019 ARG cc_start: 0.8278 (tpp-160) cc_final: 0.7978 (tpm170) REVERT: B 1038 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8761 (mmtp) REVERT: B 1072 GLU cc_start: 0.8614 (pm20) cc_final: 0.8367 (pm20) REVERT: C 153 MET cc_start: 0.3623 (pmm) cc_final: 0.3369 (pmm) REVERT: C 170 TYR cc_start: 0.7888 (t80) cc_final: 0.7488 (t80) REVERT: C 202 LYS cc_start: 0.8117 (mttt) cc_final: 0.7793 (mttp) REVERT: C 237 ARG cc_start: 0.7708 (mmm-85) cc_final: 0.7458 (mmm-85) REVERT: C 298 GLU cc_start: 0.8618 (tp30) cc_final: 0.8340 (tp30) REVERT: C 355 ARG cc_start: 0.7082 (ptt-90) cc_final: 0.6848 (ptt-90) REVERT: C 578 ASP cc_start: 0.7718 (t0) cc_final: 0.7494 (t70) REVERT: C 710 ASN cc_start: 0.8906 (p0) cc_final: 0.8569 (p0) REVERT: C 725 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7593 (mt-10) REVERT: C 787 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7640 (mm-40) REVERT: C 804 GLN cc_start: 0.8454 (mm-40) cc_final: 0.7870 (mm-40) REVERT: C 821 LEU cc_start: 0.8554 (tp) cc_final: 0.8158 (tt) REVERT: C 902 MET cc_start: 0.8251 (mmm) cc_final: 0.7711 (mmt) REVERT: C 947 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7757 (mttm) REVERT: C 955 ASN cc_start: 0.8213 (t0) cc_final: 0.7960 (t0) REVERT: C 957 GLN cc_start: 0.8431 (tt0) cc_final: 0.7954 (tt0) REVERT: C 1002 GLN cc_start: 0.8412 (tp40) cc_final: 0.8089 (tp-100) REVERT: C 1127 ASP cc_start: 0.8411 (p0) cc_final: 0.8166 (p0) outliers start: 66 outliers final: 55 residues processed: 512 average time/residue: 0.4445 time to fit residues: 345.5396 Evaluate side-chains 518 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 462 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 541 PHE Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 61 optimal weight: 0.6980 chunk 165 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 307 optimal weight: 0.0060 chunk 143 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 ASN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.157220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122034 restraints weight = 47696.293| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 3.05 r_work: 0.3438 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.7292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 25423 Z= 0.163 Angle : 0.628 8.745 34593 Z= 0.329 Chirality : 0.044 0.214 3904 Planarity : 0.004 0.051 4462 Dihedral : 4.407 22.298 3391 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.20 % Allowed : 17.15 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.15), residues: 3114 helix: 1.43 (0.21), residues: 671 sheet: 0.22 (0.19), residues: 669 loop : -0.87 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 353 HIS 0.004 0.001 HIS C 49 PHE 0.056 0.002 PHE B 342 TYR 0.024 0.001 TYR C 707 ARG 0.011 0.001 ARG B 346 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 924) hydrogen bonds : angle 5.05813 ( 2616) SS BOND : bond 0.00330 ( 39) SS BOND : angle 1.92434 ( 78) covalent geometry : bond 0.00382 (25384) covalent geometry : angle 0.62157 (34515) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6228 Ramachandran restraints generated. 3114 Oldfield, 0 Emsley, 3114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 470 time to evaluate : 3.916 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: A 96 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7345 (tp30) REVERT: A 307 THR cc_start: 0.8867 (m) cc_final: 0.8415 (p) REVERT: A 532 ASN cc_start: 0.8367 (t0) cc_final: 0.8126 (t0) REVERT: A 577 ARG cc_start: 0.7448 (ptm160) cc_final: 0.6965 (ttm-80) REVERT: A 646 ARG cc_start: 0.8418 (ttp-170) cc_final: 0.8168 (mtm-85) REVERT: A 675 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7344 (mm-40) REVERT: A 953 ASN cc_start: 0.8556 (m-40) cc_final: 0.8133 (m-40) REVERT: A 1002 GLN cc_start: 0.8225 (tp40) cc_final: 0.7814 (tp40) REVERT: A 1017 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7412 (tp30) REVERT: A 1030 SER cc_start: 0.8905 (m) cc_final: 0.8686 (t) REVERT: A 1038 LYS cc_start: 0.9266 (mttt) cc_final: 0.8952 (mmmm) REVERT: B 41 LYS cc_start: 0.7689 (mmmt) cc_final: 0.7426 (mmmt) REVERT: B 100 ILE cc_start: 0.8814 (mm) cc_final: 0.8590 (mm) REVERT: B 278 LYS cc_start: 0.8857 (tttt) cc_final: 0.8532 (ttpt) REVERT: B 386 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8345 (mttt) REVERT: B 387 LEU cc_start: 0.8939 (mt) cc_final: 0.8643 (mt) REVERT: B 395 VAL cc_start: 0.8290 (t) cc_final: 0.8005 (m) REVERT: B 425 LEU cc_start: 0.7978 (mt) cc_final: 0.7761 (mm) REVERT: B 454 ARG cc_start: 0.7821 (mtm180) cc_final: 0.7539 (mtm-85) REVERT: B 547 LYS cc_start: 0.8535 (mttt) cc_final: 0.8226 (mttm) REVERT: B 558 LYS cc_start: 0.8716 (mptt) cc_final: 0.8501 (mttt) REVERT: B 583 GLU cc_start: 0.7656 (pm20) cc_final: 0.7050 (pm20) REVERT: B 737 ASP cc_start: 0.7844 (t0) cc_final: 0.7594 (t0) REVERT: B 787 GLN cc_start: 0.7819 (mp10) cc_final: 0.7481 (mp10) REVERT: B 790 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8467 (mtmm) REVERT: B 935 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8267 (tm-30) REVERT: B 964 LYS cc_start: 0.8880 (tppp) cc_final: 0.8647 (ttmm) REVERT: B 1002 GLN cc_start: 0.8231 (tp40) cc_final: 0.7678 (tp40) REVERT: B 1019 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7963 (tpm170) REVERT: B 1038 LYS cc_start: 0.9027 (mmmm) cc_final: 0.8767 (mmtp) REVERT: B 1072 GLU cc_start: 0.8637 (pm20) cc_final: 0.8397 (pm20) REVERT: C 170 TYR cc_start: 0.7921 (t80) cc_final: 0.7522 (t80) REVERT: C 202 LYS cc_start: 0.8121 (mttt) cc_final: 0.7873 (mptt) REVERT: C 237 ARG cc_start: 0.7726 (mmm-85) cc_final: 0.7487 (mmm-85) REVERT: C 298 GLU cc_start: 0.8582 (tp30) cc_final: 0.8159 (tp30) REVERT: C 355 ARG cc_start: 0.7090 (ptt-90) cc_final: 0.6834 (ptt-90) REVERT: C 578 ASP cc_start: 0.7665 (t0) cc_final: 0.7432 (t70) REVERT: C 710 ASN cc_start: 0.8927 (p0) cc_final: 0.8604 (p0) REVERT: C 725 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7565 (mt-10) REVERT: C 787 GLN cc_start: 0.7983 (mm-40) cc_final: 0.7647 (mm-40) REVERT: C 804 GLN cc_start: 0.8488 (mm-40) cc_final: 0.7894 (mm-40) REVERT: C 821 LEU cc_start: 0.8562 (tp) cc_final: 0.8161 (tt) REVERT: C 947 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7829 (mttm) REVERT: C 955 ASN cc_start: 0.8260 (t0) cc_final: 0.7995 (t0) REVERT: C 957 GLN cc_start: 0.8360 (tt0) cc_final: 0.8082 (tt0) REVERT: C 1002 GLN cc_start: 0.8442 (tp40) cc_final: 0.7874 (tp40) REVERT: C 1127 ASP cc_start: 0.8400 (p0) cc_final: 0.8149 (p0) outliers start: 61 outliers final: 56 residues processed: 505 average time/residue: 0.5540 time to fit residues: 437.0913 Evaluate side-chains 521 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 463 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 947 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 287 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 chunk 105 optimal weight: 0.0030 chunk 293 optimal weight: 0.9980 chunk 234 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 296 optimal weight: 0.0020 chunk 281 optimal weight: 0.0970 chunk 140 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 0.2154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 965 GLN B1101 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.159439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.124304 restraints weight = 47646.706| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.07 r_work: 0.3478 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.7311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25423 Z= 0.117 Angle : 0.601 12.504 34593 Z= 0.313 Chirality : 0.044 0.203 3904 Planarity : 0.004 0.052 4462 Dihedral : 4.239 21.340 3391 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.88 % Allowed : 17.58 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 3114 helix: 1.55 (0.21), residues: 671 sheet: 0.29 (0.19), residues: 665 loop : -0.83 (0.14), residues: 1778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 353 HIS 0.003 0.001 HIS B1101 PHE 0.054 0.001 PHE B 342 TYR 0.019 0.001 TYR C 707 ARG 0.010 0.000 ARG B 346 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 924) hydrogen bonds : angle 4.94485 ( 2616) SS BOND : bond 0.00270 ( 39) SS BOND : angle 1.44326 ( 78) covalent geometry : bond 0.00263 (25384) covalent geometry : angle 0.59739 (34515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14481.23 seconds wall clock time: 253 minutes 26.09 seconds (15206.09 seconds total)