Starting phenix.real_space_refine on Thu Mar 5 18:43:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wk3_32557/03_2026/7wk3_32557.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wk3_32557/03_2026/7wk3_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wk3_32557/03_2026/7wk3_32557.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wk3_32557/03_2026/7wk3_32557.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wk3_32557/03_2026/7wk3_32557.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wk3_32557/03_2026/7wk3_32557.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.029 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 5.68, per 1000 atoms: 0.23 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: 1.94 Conformation dependent library (CDL) restraints added in 1.1 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: 1.02 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: 6.52 Time building geometry restraints manager: 2.65 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.020 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.260 ------------------------------------------------------------------------------- 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 : 3.77 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG A 102 TYR 0.016 0.001 TYR C 707 PHE 0.018 0.001 PHE B 718 TRP 0.010 0.001 TRP B 633 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00382 (25384) covalent geometry : angle 0.56406 (34515) SS BOND : bond 0.00228 ( 39) SS BOND : angle 0.82304 ( 78) hydrogen bonds : bond 0.25453 ( 924) hydrogen bonds : angle 9.89997 ( 2616) *********************** 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 : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6931 (mtt-85) cc_final: 0.6372 (ttp80) REVERT: A 578 ASP cc_start: 0.2983 (t70) cc_final: 0.1232 (t0) REVERT: A 756 TYR cc_start: 0.6677 (m-80) cc_final: 0.6255 (m-80) REVERT: B 315 THR cc_start: 0.7102 (m) cc_final: 0.6518 (m) REVERT: B 535 LYS cc_start: 0.7362 (mttt) cc_final: 0.7093 (mttp) REVERT: B 537 LYS cc_start: 0.6840 (ttmt) cc_final: 0.6614 (mtpp) REVERT: B 581 THR cc_start: 0.4450 (p) cc_final: 0.2440 (m) REVERT: B 737 ASP cc_start: 0.6361 (t0) cc_final: 0.5854 (t0) REVERT: C 737 ASP cc_start: 0.6896 (t0) cc_final: 0.6562 (t70) REVERT: C 800 PHE cc_start: 0.6037 (m-10) cc_final: 0.5831 (m-80) outliers start: 0 outliers final: 0 residues processed: 791 average time/residue: 0.1782 time to fit residues: 212.2903 Evaluate side-chains 530 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 A 901 GLN A1071 GLN B 188 ASN B 505 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN 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 901 GLN C 954 HIS C1071 GLN C1113 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.174190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.139872 restraints weight = 50148.474| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 3.23 r_work: 0.3665 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25423 Z= 0.188 Angle : 0.654 9.636 34593 Z= 0.346 Chirality : 0.047 0.212 3904 Planarity : 0.004 0.041 4462 Dihedral : 4.420 23.054 3391 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.88 % Allowed : 9.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 3114 helix: 0.39 (0.20), residues: 658 sheet: -0.33 (0.17), residues: 637 loop : -1.07 (0.13), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1107 TYR 0.035 0.002 TYR A 265 PHE 0.044 0.002 PHE A 92 TRP 0.019 0.002 TRP A 104 HIS 0.012 0.002 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00432 (25384) covalent geometry : angle 0.65212 (34515) SS BOND : bond 0.00527 ( 39) SS BOND : angle 1.25738 ( 78) hydrogen bonds : bond 0.05268 ( 924) hydrogen bonds : angle 6.28685 ( 2616) *********************** 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 613 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 561 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7855 (ttm110) cc_final: 0.7456 (ttm110) REVERT: A 207 HIS cc_start: 0.7280 (m170) cc_final: 0.6848 (m170) REVERT: A 290 ASP cc_start: 0.7609 (t0) cc_final: 0.7301 (t0) REVERT: A 304 LYS cc_start: 0.8922 (mttt) cc_final: 0.8709 (mmmm) REVERT: A 307 THR cc_start: 0.8631 (m) cc_final: 0.8288 (p) REVERT: A 558 LYS cc_start: 0.6876 (tmtt) cc_final: 0.6547 (tmtt) REVERT: A 567 ARG cc_start: 0.7489 (ptp-110) cc_final: 0.7151 (ptp-110) REVERT: A 578 ASP cc_start: 0.7489 (t70) cc_final: 0.7238 (t0) REVERT: A 585 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6843 (pp) REVERT: A 737 ASP cc_start: 0.7521 (t0) cc_final: 0.7291 (t0) REVERT: A 780 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8163 (mt-10) REVERT: A 819 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7114 (mt-10) REVERT: A 953 ASN cc_start: 0.8289 (m-40) cc_final: 0.7991 (m-40) REVERT: A 1038 LYS cc_start: 0.8836 (mttt) cc_final: 0.8622 (mtpp) REVERT: A 1107 ARG cc_start: 0.7489 (mmm160) cc_final: 0.7220 (mmm160) REVERT: B 87 ASN cc_start: 0.7671 (p0) cc_final: 0.7389 (p0) REVERT: B 104 TRP cc_start: 0.8660 (m-90) cc_final: 0.8392 (m-90) REVERT: B 191 GLU cc_start: 0.7647 (pt0) cc_final: 0.7446 (mt-10) REVERT: B 195 LYS cc_start: 0.7277 (tptt) cc_final: 0.7067 (ptpt) REVERT: B 326 ILE cc_start: 0.8581 (mm) cc_final: 0.8355 (mm) REVERT: B 329 PHE cc_start: 0.6439 (t80) cc_final: 0.6218 (t80) REVERT: B 351 TYR cc_start: 0.7336 (p90) cc_final: 0.6511 (p90) REVERT: B 454 ARG cc_start: 0.7597 (ttp-110) cc_final: 0.7205 (mtt180) REVERT: B 528 LYS cc_start: 0.6826 (ttpt) cc_final: 0.5099 (tttt) REVERT: B 763 LEU cc_start: 0.8303 (mt) cc_final: 0.7815 (mp) REVERT: B 765 ARG cc_start: 0.7771 (tmm-80) cc_final: 0.7534 (ttp80) REVERT: B 797 PHE cc_start: 0.7972 (m-80) cc_final: 0.7706 (m-80) REVERT: B 882 ILE cc_start: 0.8711 (mt) cc_final: 0.8498 (mt) REVERT: C 170 TYR cc_start: 0.7565 (t80) cc_final: 0.7283 (t80) REVERT: C 197 ILE cc_start: 0.7684 (pt) cc_final: 0.7356 (pt) REVERT: C 202 LYS cc_start: 0.7506 (mttt) cc_final: 0.7261 (mtmm) REVERT: C 224 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6817 (tp30) REVERT: C 607 GLN cc_start: 0.8412 (mm-40) cc_final: 0.8194 (mm-40) REVERT: C 748 GLU cc_start: 0.7592 (tp30) cc_final: 0.7385 (tp30) REVERT: C 776 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8525 (tppp) REVERT: C 947 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7605 (mttm) REVERT: C 1144 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8183 (mm-30) outliers start: 52 outliers final: 32 residues processed: 587 average time/residue: 0.1659 time to fit residues: 149.1469 Evaluate side-chains 518 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 482 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 585 LEU 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 973 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 36 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 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 199 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 242 optimal weight: 0.1980 chunk 259 optimal weight: 0.6980 chunk 197 optimal weight: 0.9980 chunk 295 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 519 HIS B 563 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 717 ASN B 901 GLN B 913 GLN B 955 ASN C 52 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 895 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.164538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.128961 restraints weight = 48602.773| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.16 r_work: 0.3539 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25423 Z= 0.192 Angle : 0.624 9.660 34593 Z= 0.328 Chirality : 0.046 0.215 3904 Planarity : 0.004 0.042 4462 Dihedral : 4.442 21.604 3391 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.96 % Allowed : 10.43 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.14), residues: 3114 helix: 1.02 (0.20), residues: 652 sheet: 0.13 (0.18), residues: 668 loop : -0.97 (0.13), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 237 TYR 0.024 0.002 TYR C 707 PHE 0.033 0.002 PHE C 92 TRP 0.020 0.002 TRP A 886 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00440 (25384) covalent geometry : angle 0.62017 (34515) SS BOND : bond 0.00405 ( 39) SS BOND : angle 1.65609 ( 78) hydrogen bonds : bond 0.05161 ( 924) hydrogen bonds : angle 5.72562 ( 2616) *********************** 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 613 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 531 time to evaluate : 0.668 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 190 ARG cc_start: 0.7939 (ttm110) cc_final: 0.7531 (ttm110) REVERT: A 207 HIS cc_start: 0.7230 (m170) cc_final: 0.6865 (m170) REVERT: A 239 GLN cc_start: 0.7891 (tt0) cc_final: 0.7581 (tp40) REVERT: A 267 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8488 (t) REVERT: A 304 LYS cc_start: 0.8977 (mttt) cc_final: 0.8769 (mmtp) REVERT: A 307 THR cc_start: 0.8738 (m) cc_final: 0.8371 (p) REVERT: A 557 LYS cc_start: 0.5543 (pptt) cc_final: 0.5249 (mttt) REVERT: A 580 GLN cc_start: 0.6936 (mt0) cc_final: 0.6647 (tm-30) REVERT: A 585 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7084 (pp) REVERT: A 591 SER cc_start: 0.9158 (t) cc_final: 0.8841 (p) REVERT: A 780 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8099 (mt-10) REVERT: A 884 SER cc_start: 0.9082 (m) cc_final: 0.8698 (t) REVERT: A 933 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8354 (mttp) REVERT: A 945 LEU cc_start: 0.7770 (mm) cc_final: 0.7494 (mm) REVERT: A 1002 GLN cc_start: 0.8393 (tp40) cc_final: 0.7786 (tp40) REVERT: A 1038 LYS cc_start: 0.9103 (mttt) cc_final: 0.8822 (mtpp) REVERT: B 45 SER cc_start: 0.8791 (p) cc_final: 0.8533 (t) REVERT: B 190 ARG cc_start: 0.7851 (mtm180) cc_final: 0.7503 (mtt90) REVERT: B 191 GLU cc_start: 0.7800 (pt0) cc_final: 0.7450 (mt-10) REVERT: B 195 LYS cc_start: 0.7867 (tptt) cc_final: 0.7505 (ptmt) REVERT: B 237 ARG cc_start: 0.8553 (mtm-85) cc_final: 0.7468 (ptt90) REVERT: B 278 LYS cc_start: 0.8896 (tttt) cc_final: 0.8483 (ttpt) REVERT: B 528 LYS cc_start: 0.7159 (ttpt) cc_final: 0.5245 (mmtp) REVERT: B 583 GLU cc_start: 0.7532 (pm20) cc_final: 0.7316 (pm20) REVERT: B 643 PHE cc_start: 0.8320 (t80) cc_final: 0.8088 (t80) REVERT: B 790 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8509 (mtpp) REVERT: B 882 ILE cc_start: 0.8879 (mt) cc_final: 0.8672 (mt) REVERT: C 202 LYS cc_start: 0.7722 (mttt) cc_final: 0.7334 (mtpp) REVERT: C 319 ARG cc_start: 0.7879 (mmm160) cc_final: 0.7565 (mpt180) REVERT: C 607 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8270 (mm-40) REVERT: C 643 PHE cc_start: 0.8206 (t80) cc_final: 0.7997 (t80) REVERT: C 710 ASN cc_start: 0.8667 (p0) cc_final: 0.8386 (p0) REVERT: C 725 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7413 (mt-10) REVERT: C 739 THR cc_start: 0.8262 (m) cc_final: 0.7990 (p) REVERT: C 776 LYS cc_start: 0.8626 (mmmm) cc_final: 0.8361 (tppp) REVERT: C 947 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7675 (mttm) REVERT: C 965 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8450 (mm-40) REVERT: C 985 ASP cc_start: 0.7254 (m-30) cc_final: 0.6578 (m-30) REVERT: C 988 GLU cc_start: 0.7846 (pm20) cc_final: 0.7404 (pm20) REVERT: C 1002 GLN cc_start: 0.8513 (tp40) cc_final: 0.8169 (tp40) REVERT: C 1081 ILE cc_start: 0.8446 (pt) cc_final: 0.8188 (pt) outliers start: 82 outliers final: 53 residues processed: 569 average time/residue: 0.1641 time to fit residues: 144.0999 Evaluate side-chains 533 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 477 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 200 TYR Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 267 VAL 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 585 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 615 VAL 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 1030 SER Chi-restraints excluded: chain A residue 1045 LYS 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 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 532 ASN 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 973 ILE 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 189 LEU 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 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 1040 VAL Chi-restraints excluded: chain C residue 1125 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 174 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 213 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 258 optimal weight: 0.8980 chunk 278 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 212 optimal weight: 0.6980 chunk 264 optimal weight: 0.0060 chunk 108 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 690 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN B 207 HIS 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.161873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.126242 restraints weight = 48195.414| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.10 r_work: 0.3498 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25423 Z= 0.171 Angle : 0.599 8.607 34593 Z= 0.313 Chirality : 0.045 0.253 3904 Planarity : 0.004 0.075 4462 Dihedral : 4.428 20.965 3391 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.10 % Allowed : 12.60 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3114 helix: 1.24 (0.21), residues: 655 sheet: 0.29 (0.19), residues: 654 loop : -0.88 (0.13), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 346 TYR 0.025 0.002 TYR C 707 PHE 0.035 0.002 PHE B 342 TRP 0.017 0.002 TRP C 64 HIS 0.006 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00386 (25384) covalent geometry : angle 0.59501 (34515) SS BOND : bond 0.00704 ( 39) SS BOND : angle 1.51258 ( 78) hydrogen bonds : bond 0.04674 ( 924) hydrogen bonds : angle 5.42669 ( 2616) *********************** 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 576 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 490 time to evaluate : 0.663 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 190 ARG cc_start: 0.7972 (ttm110) cc_final: 0.7670 (ttm110) REVERT: A 207 HIS cc_start: 0.7152 (m170) cc_final: 0.6697 (m-70) REVERT: A 239 GLN cc_start: 0.8221 (tt0) cc_final: 0.7740 (tp40) REVERT: A 307 THR cc_start: 0.8787 (m) cc_final: 0.8404 (p) REVERT: A 581 THR cc_start: 0.7646 (p) cc_final: 0.6620 (p) REVERT: A 588 THR cc_start: 0.8331 (m) cc_final: 0.7801 (p) REVERT: A 591 SER cc_start: 0.9206 (t) cc_final: 0.8704 (p) REVERT: A 748 GLU cc_start: 0.8269 (mp0) cc_final: 0.8036 (mp0) REVERT: A 869 MET cc_start: 0.8636 (mtp) cc_final: 0.8417 (mtp) REVERT: A 902 MET cc_start: 0.8389 (mmm) cc_final: 0.8166 (mmp) REVERT: A 933 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8405 (mttp) REVERT: A 1002 GLN cc_start: 0.8306 (tp40) cc_final: 0.7847 (tp40) REVERT: A 1030 SER cc_start: 0.8986 (OUTLIER) cc_final: 0.8565 (t) REVERT: A 1038 LYS cc_start: 0.9178 (mttt) cc_final: 0.8890 (mtpp) REVERT: B 100 ILE cc_start: 0.8709 (mm) cc_final: 0.8417 (mm) REVERT: B 104 TRP cc_start: 0.8841 (m-90) cc_final: 0.8379 (m-90) REVERT: B 160 TYR cc_start: 0.7498 (p90) cc_final: 0.7295 (p90) REVERT: B 191 GLU cc_start: 0.7802 (pt0) cc_final: 0.7432 (mt-10) REVERT: B 195 LYS cc_start: 0.7974 (tptt) cc_final: 0.7570 (ptmt) REVERT: B 237 ARG cc_start: 0.8546 (mtm-85) cc_final: 0.8156 (mtm110) REVERT: B 278 LYS cc_start: 0.8832 (tttt) cc_final: 0.8418 (ttmm) REVERT: B 286 THR cc_start: 0.8383 (OUTLIER) cc_final: 0.8155 (p) REVERT: B 304 LYS cc_start: 0.8871 (mmmm) cc_final: 0.8530 (ttmm) REVERT: B 329 PHE cc_start: 0.6699 (t80) cc_final: 0.6470 (t80) REVERT: B 335 LEU cc_start: 0.9130 (tp) cc_final: 0.8906 (mm) REVERT: B 386 LYS cc_start: 0.8345 (mmmt) cc_final: 0.7841 (mptt) REVERT: B 528 LYS cc_start: 0.7095 (ttpt) cc_final: 0.5257 (mttm) REVERT: B 537 LYS cc_start: 0.8533 (tttt) cc_final: 0.8298 (tttm) REVERT: B 737 ASP cc_start: 0.7870 (t0) cc_final: 0.7602 (t0) REVERT: B 790 LYS cc_start: 0.8779 (mtmt) cc_final: 0.8546 (mtpp) REVERT: B 882 ILE cc_start: 0.8898 (mt) cc_final: 0.8694 (mt) REVERT: B 888 PHE cc_start: 0.8716 (p90) cc_final: 0.8325 (p90) REVERT: B 896 ILE cc_start: 0.8512 (tp) cc_final: 0.8310 (tt) REVERT: B 935 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8288 (tm-30) REVERT: B 936 ASP cc_start: 0.8252 (m-30) cc_final: 0.7966 (m-30) REVERT: B 1002 GLN cc_start: 0.8248 (tp40) cc_final: 0.7577 (tp40) REVERT: B 1038 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8627 (mmtp) REVERT: C 195 LYS cc_start: 0.8304 (pttt) cc_final: 0.8052 (pttt) REVERT: C 196 ASN cc_start: 0.7159 (m-40) cc_final: 0.6929 (m-40) REVERT: C 197 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7911 (pt) REVERT: C 202 LYS cc_start: 0.7904 (mttt) cc_final: 0.7616 (mttp) REVERT: C 238 PHE cc_start: 0.7370 (p90) cc_final: 0.7152 (p90) REVERT: C 281 GLU cc_start: 0.6843 (pm20) cc_final: 0.6582 (pp20) REVERT: C 298 GLU cc_start: 0.8571 (tp30) cc_final: 0.8186 (tp30) REVERT: C 304 LYS cc_start: 0.8800 (mmmm) cc_final: 0.8544 (mmmm) REVERT: C 577 ARG cc_start: 0.7031 (mtp85) cc_final: 0.6598 (mtp85) REVERT: C 710 ASN cc_start: 0.8782 (p0) cc_final: 0.8506 (p0) REVERT: C 725 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7434 (mt-10) REVERT: C 739 THR cc_start: 0.8500 (m) cc_final: 0.8138 (p) REVERT: C 745 ASP cc_start: 0.6605 (m-30) cc_final: 0.6289 (p0) REVERT: C 776 LYS cc_start: 0.8606 (mmmm) cc_final: 0.8330 (tppp) REVERT: C 822 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8436 (mm) REVERT: C 936 ASP cc_start: 0.8101 (t70) cc_final: 0.7889 (m-30) REVERT: C 947 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7654 (mttm) REVERT: C 955 ASN cc_start: 0.8400 (t0) cc_final: 0.8141 (t0) REVERT: C 965 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8502 (mm-40) REVERT: C 1002 GLN cc_start: 0.8503 (tp40) cc_final: 0.7793 (tp40) REVERT: C 1081 ILE cc_start: 0.8537 (pt) cc_final: 0.8315 (mm) REVERT: C 1097 SER cc_start: 0.8822 (t) cc_final: 0.8484 (p) outliers start: 86 outliers final: 50 residues processed: 530 average time/residue: 0.1646 time to fit residues: 133.9503 Evaluate side-chains 512 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 456 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 555 SER Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET 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 286 THR Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 538 CYS 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 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 973 ILE 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 142 ASP Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 197 ILE 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 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 752 LEU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 790 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 979 ASP Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 62 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 196 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 262 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 GLN A 955 ASN B1074 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN 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 = 0.159599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124008 restraints weight = 47847.160| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.08 r_work: 0.3467 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25423 Z= 0.169 Angle : 0.590 8.673 34593 Z= 0.308 Chirality : 0.044 0.251 3904 Planarity : 0.004 0.042 4462 Dihedral : 4.429 23.537 3391 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.14 % Allowed : 12.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3114 helix: 1.35 (0.21), residues: 653 sheet: 0.39 (0.19), residues: 664 loop : -0.86 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 346 TYR 0.024 0.001 TYR C 707 PHE 0.045 0.002 PHE B 342 TRP 0.020 0.001 TRP C 64 HIS 0.005 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00390 (25384) covalent geometry : angle 0.58635 (34515) SS BOND : bond 0.00376 ( 39) SS BOND : angle 1.53376 ( 78) hydrogen bonds : bond 0.04646 ( 924) hydrogen bonds : angle 5.26401 ( 2616) *********************** 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 581 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 494 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8021 (ttm110) cc_final: 0.7599 (ttm110) REVERT: A 192 PHE cc_start: 0.8711 (m-80) cc_final: 0.8107 (m-10) REVERT: A 207 HIS cc_start: 0.7119 (m170) cc_final: 0.6815 (m-70) REVERT: A 307 THR cc_start: 0.8797 (m) cc_final: 0.8434 (p) REVERT: A 588 THR cc_start: 0.8304 (m) cc_final: 0.7807 (p) REVERT: A 902 MET cc_start: 0.8392 (mmm) cc_final: 0.8078 (mmt) REVERT: A 933 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8415 (mttp) REVERT: A 953 ASN cc_start: 0.8363 (m-40) cc_final: 0.8157 (m-40) REVERT: A 1002 GLN cc_start: 0.8287 (tp40) cc_final: 0.7842 (tp40) REVERT: A 1030 SER cc_start: 0.8993 (m) cc_final: 0.8618 (t) REVERT: A 1038 LYS cc_start: 0.9235 (mttt) cc_final: 0.8905 (mmmm) REVERT: B 81 ASN cc_start: 0.9009 (t0) cc_final: 0.8427 (t0) REVERT: B 160 TYR cc_start: 0.7383 (p90) cc_final: 0.7176 (p90) REVERT: B 191 GLU cc_start: 0.7863 (pt0) cc_final: 0.7544 (mt-10) REVERT: B 195 LYS cc_start: 0.8032 (tptt) cc_final: 0.7661 (ptpt) REVERT: B 237 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.8145 (mtp180) REVERT: B 239 GLN cc_start: 0.7642 (mt0) cc_final: 0.7138 (mt0) REVERT: B 278 LYS cc_start: 0.8800 (tttt) cc_final: 0.8465 (ttmm) REVERT: B 286 THR cc_start: 0.8366 (OUTLIER) cc_final: 0.8163 (p) REVERT: B 335 LEU cc_start: 0.9146 (tp) cc_final: 0.8910 (mm) REVERT: B 354 ASN cc_start: 0.7836 (t0) cc_final: 0.7630 (t0) REVERT: B 356 LYS cc_start: 0.8288 (tppt) cc_final: 0.8073 (tptm) REVERT: B 386 LYS cc_start: 0.8387 (mmmt) cc_final: 0.7981 (mttt) REVERT: B 387 LEU cc_start: 0.8592 (mt) cc_final: 0.8347 (mt) REVERT: B 400 PHE cc_start: 0.6608 (p90) cc_final: 0.6353 (p90) REVERT: B 425 LEU cc_start: 0.7956 (mt) cc_final: 0.7748 (mm) REVERT: B 528 LYS cc_start: 0.7106 (ttpt) cc_final: 0.5301 (mttm) REVERT: B 537 LYS cc_start: 0.8461 (tttt) cc_final: 0.8241 (tttp) REVERT: B 547 LYS cc_start: 0.8319 (mttt) cc_final: 0.7995 (mttm) REVERT: B 657 ASN cc_start: 0.8300 (p0) cc_final: 0.8017 (m-40) REVERT: B 737 ASP cc_start: 0.7922 (t0) cc_final: 0.7510 (t0) REVERT: B 748 GLU cc_start: 0.7408 (pt0) cc_final: 0.6609 (pt0) REVERT: B 882 ILE cc_start: 0.8890 (mt) cc_final: 0.8687 (mt) REVERT: B 935 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8297 (tm-30) REVERT: B 936 ASP cc_start: 0.8251 (m-30) cc_final: 0.8022 (m-30) REVERT: B 964 LYS cc_start: 0.8857 (tppp) cc_final: 0.8509 (tppp) REVERT: B 1002 GLN cc_start: 0.8284 (tp40) cc_final: 0.7581 (tp40) REVERT: B 1092 GLU cc_start: 0.7971 (tp30) cc_final: 0.7768 (tp30) REVERT: B 1123 SER cc_start: 0.8795 (t) cc_final: 0.8358 (m) REVERT: C 195 LYS cc_start: 0.8257 (pttt) cc_final: 0.8044 (pttt) REVERT: C 197 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.8024 (pt) REVERT: C 202 LYS cc_start: 0.8068 (mttt) cc_final: 0.7738 (mttp) REVERT: C 281 GLU cc_start: 0.6796 (pm20) cc_final: 0.6572 (pp20) REVERT: C 298 GLU cc_start: 0.8618 (tp30) cc_final: 0.8222 (tp30) REVERT: C 304 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8521 (mmmm) REVERT: C 577 ARG cc_start: 0.7087 (mtp85) cc_final: 0.6533 (mtp85) REVERT: C 710 ASN cc_start: 0.8859 (p0) cc_final: 0.8525 (p0) REVERT: C 739 THR cc_start: 0.8536 (m) cc_final: 0.8252 (p) REVERT: C 745 ASP cc_start: 0.6600 (m-30) cc_final: 0.6312 (p0) REVERT: C 776 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8307 (tppp) REVERT: C 884 SER cc_start: 0.8961 (t) cc_final: 0.8634 (p) REVERT: C 902 MET cc_start: 0.8216 (mmt) cc_final: 0.7686 (mmt) REVERT: C 965 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8489 (mm-40) REVERT: C 1002 GLN cc_start: 0.8513 (tp40) cc_final: 0.7959 (tp40) REVERT: C 1081 ILE cc_start: 0.8520 (pt) cc_final: 0.8271 (pt) outliers start: 87 outliers final: 62 residues processed: 544 average time/residue: 0.1690 time to fit residues: 141.4023 Evaluate side-chains 523 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 458 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 240 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 820 ASP Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 933 LYS 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 1132 ILE Chi-restraints excluded: chain B residue 30 ASN 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 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 538 CYS 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 641 ASN 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 973 ILE Chi-restraints excluded: chain B residue 1117 THR 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 157 PHE Chi-restraints excluded: chain C residue 197 ILE 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 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 697 MET Chi-restraints excluded: chain C residue 705 VAL 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 764 LYS Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 859 THR 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 1104 VAL Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 9 optimal weight: 3.9990 chunk 266 optimal weight: 0.8980 chunk 311 optimal weight: 0.3980 chunk 224 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 179 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 675 GLN A 901 GLN A 913 GLN A 955 ASN B 506 GLN B1074 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.159797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124103 restraints weight = 47986.077| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 3.10 r_work: 0.3468 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.6396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25423 Z= 0.137 Angle : 0.573 9.500 34593 Z= 0.298 Chirality : 0.044 0.206 3904 Planarity : 0.004 0.042 4462 Dihedral : 4.340 22.804 3391 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.07 % Allowed : 13.97 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3114 helix: 1.40 (0.21), residues: 667 sheet: 0.43 (0.19), residues: 645 loop : -0.82 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 346 TYR 0.021 0.001 TYR A 265 PHE 0.047 0.002 PHE B 342 TRP 0.021 0.001 TRP C 64 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00313 (25384) covalent geometry : angle 0.57048 (34515) SS BOND : bond 0.00338 ( 39) SS BOND : angle 1.31325 ( 78) hydrogen bonds : bond 0.04349 ( 924) hydrogen bonds : angle 5.12502 ( 2616) *********************** 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 555 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 470 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8016 (ttm110) cc_final: 0.7570 (ttm110) REVERT: A 202 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8671 (mttp) REVERT: A 207 HIS cc_start: 0.7059 (m170) cc_final: 0.6793 (m170) REVERT: A 239 GLN cc_start: 0.8163 (tt0) cc_final: 0.7611 (tp40) REVERT: A 307 THR cc_start: 0.8801 (m) cc_final: 0.8446 (p) REVERT: A 329 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.7193 (m-10) REVERT: A 588 THR cc_start: 0.8267 (m) cc_final: 0.7788 (p) REVERT: A 933 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8381 (mttp) REVERT: A 953 ASN cc_start: 0.8357 (m-40) cc_final: 0.8133 (m-40) REVERT: A 1002 GLN cc_start: 0.8203 (tp40) cc_final: 0.7820 (tp40) REVERT: A 1017 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7487 (tp30) REVERT: A 1030 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8637 (t) REVERT: A 1038 LYS cc_start: 0.9233 (mttt) cc_final: 0.8903 (mmmm) REVERT: B 81 ASN cc_start: 0.8931 (t0) cc_final: 0.8571 (t0) REVERT: B 191 GLU cc_start: 0.7910 (pt0) cc_final: 0.7598 (mt-10) REVERT: B 195 LYS cc_start: 0.8115 (tptt) cc_final: 0.7760 (ptmt) REVERT: B 278 LYS cc_start: 0.8805 (tttt) cc_final: 0.8402 (ttpt) REVERT: B 335 LEU cc_start: 0.9122 (tp) cc_final: 0.8886 (mm) REVERT: B 356 LYS cc_start: 0.8301 (tppt) cc_final: 0.8086 (tptm) REVERT: B 386 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8083 (mttt) REVERT: B 387 LEU cc_start: 0.8634 (mt) cc_final: 0.8364 (mt) REVERT: B 400 PHE cc_start: 0.6657 (p90) cc_final: 0.6352 (p90) REVERT: B 425 LEU cc_start: 0.7985 (mt) cc_final: 0.7766 (mm) REVERT: B 528 LYS cc_start: 0.7151 (ttpt) cc_final: 0.5213 (mmmm) REVERT: B 537 LYS cc_start: 0.8536 (tttt) cc_final: 0.8297 (tttp) REVERT: B 547 LYS cc_start: 0.8367 (mttt) cc_final: 0.8027 (mttm) REVERT: B 551 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8352 (m) REVERT: B 571 ASP cc_start: 0.8054 (m-30) cc_final: 0.7848 (t70) REVERT: B 583 GLU cc_start: 0.7583 (pm20) cc_final: 0.7048 (pm20) REVERT: B 737 ASP cc_start: 0.7825 (t0) cc_final: 0.7407 (t70) REVERT: B 748 GLU cc_start: 0.7007 (pt0) cc_final: 0.6497 (pt0) REVERT: B 765 ARG cc_start: 0.7918 (tmm-80) cc_final: 0.6944 (ttm-80) REVERT: B 790 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8504 (mtpp) REVERT: B 935 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8291 (tm-30) REVERT: B 936 ASP cc_start: 0.8279 (m-30) cc_final: 0.8007 (m-30) REVERT: B 964 LYS cc_start: 0.8835 (tppp) cc_final: 0.8620 (ttmm) REVERT: B 981 PHE cc_start: 0.7250 (t80) cc_final: 0.7002 (t80) REVERT: B 985 ASP cc_start: 0.7976 (p0) cc_final: 0.7776 (p0) REVERT: B 1002 GLN cc_start: 0.8186 (tp40) cc_final: 0.7586 (tp40) REVERT: B 1005 GLN cc_start: 0.8523 (tp40) cc_final: 0.8311 (tp40) REVERT: B 1092 GLU cc_start: 0.7916 (tp30) cc_final: 0.7675 (tp30) REVERT: B 1123 SER cc_start: 0.8710 (t) cc_final: 0.8259 (m) REVERT: C 202 LYS cc_start: 0.8088 (mttt) cc_final: 0.7789 (mttp) REVERT: C 237 ARG cc_start: 0.7364 (mmm-85) cc_final: 0.7150 (mmm-85) REVERT: C 298 GLU cc_start: 0.8636 (tp30) cc_final: 0.8231 (tp30) REVERT: C 304 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8428 (mmmm) REVERT: C 577 ARG cc_start: 0.6954 (mtp85) cc_final: 0.6609 (mtp85) REVERT: C 578 ASP cc_start: 0.7431 (t0) cc_final: 0.7210 (t70) REVERT: C 710 ASN cc_start: 0.8874 (p0) cc_final: 0.8522 (p0) REVERT: C 725 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7540 (mt-10) REVERT: C 739 THR cc_start: 0.8641 (m) cc_final: 0.8388 (p) REVERT: C 745 ASP cc_start: 0.6589 (m-30) cc_final: 0.6332 (p0) REVERT: C 776 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8271 (tppp) REVERT: C 790 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7952 (ptpp) REVERT: C 884 SER cc_start: 0.8879 (t) cc_final: 0.8633 (p) REVERT: C 947 LYS cc_start: 0.7911 (mmmm) cc_final: 0.7574 (mttm) REVERT: C 957 GLN cc_start: 0.8392 (tt0) cc_final: 0.7892 (tt0) REVERT: C 965 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8469 (mm-40) REVERT: C 1002 GLN cc_start: 0.8484 (tp40) cc_final: 0.7826 (tp40) REVERT: C 1081 ILE cc_start: 0.8558 (pt) cc_final: 0.8342 (mm) outliers start: 85 outliers final: 65 residues processed: 518 average time/residue: 0.1726 time to fit residues: 135.9295 Evaluate side-chains 525 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 453 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 329 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 576 VAL 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 933 LYS Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 227 VAL 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 286 THR Chi-restraints excluded: chain B residue 306 PHE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 538 CYS Chi-restraints excluded: chain B residue 551 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 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 973 ILE 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 157 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 289 VAL 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 697 MET Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 764 LYS Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 183 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 114 optimal weight: 6.9990 chunk 182 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 955 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN B 544 ASN C 196 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 913 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.157027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121653 restraints weight = 47772.335| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.06 r_work: 0.3427 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 25423 Z= 0.201 Angle : 0.630 11.199 34593 Z= 0.329 Chirality : 0.045 0.189 3904 Planarity : 0.004 0.042 4462 Dihedral : 4.524 24.360 3391 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.18 % Allowed : 14.48 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.14), residues: 3114 helix: 1.23 (0.21), residues: 677 sheet: 0.29 (0.19), residues: 668 loop : -0.86 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C1019 TYR 0.023 0.002 TYR A 265 PHE 0.047 0.002 PHE B 342 TRP 0.022 0.002 TRP C 64 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00470 (25384) covalent geometry : angle 0.62322 (34515) SS BOND : bond 0.00374 ( 39) SS BOND : angle 2.08029 ( 78) hydrogen bonds : bond 0.04829 ( 924) hydrogen bonds : angle 5.17286 ( 2616) *********************** 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 566 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 478 time to evaluate : 0.818 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 190 ARG cc_start: 0.7993 (ttm110) cc_final: 0.7657 (ttm110) REVERT: A 197 ILE cc_start: 0.7760 (mt) cc_final: 0.7509 (mt) REVERT: A 202 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8568 (mttp) REVERT: A 307 THR cc_start: 0.8885 (m) cc_final: 0.8515 (p) REVERT: A 329 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: A 902 MET cc_start: 0.8440 (mmm) cc_final: 0.8125 (tpp) REVERT: A 969 LYS cc_start: 0.9129 (mtmm) cc_final: 0.8893 (mtmm) REVERT: A 1002 GLN cc_start: 0.8312 (tp40) cc_final: 0.8067 (tp40) REVERT: A 1017 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7630 (mm-30) REVERT: A 1030 SER cc_start: 0.8970 (m) cc_final: 0.8653 (t) REVERT: A 1038 LYS cc_start: 0.9246 (mttt) cc_final: 0.8929 (mmmm) REVERT: B 191 GLU cc_start: 0.7945 (pt0) cc_final: 0.7619 (mt-10) REVERT: B 195 LYS cc_start: 0.8210 (tptt) cc_final: 0.7878 (ptmt) REVERT: B 237 ARG cc_start: 0.8568 (mtm-85) cc_final: 0.8349 (mtp180) REVERT: B 278 LYS cc_start: 0.8774 (tttt) cc_final: 0.8398 (ttpt) REVERT: B 335 LEU cc_start: 0.9205 (tp) cc_final: 0.8980 (mm) REVERT: B 386 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8271 (mttt) REVERT: B 387 LEU cc_start: 0.8748 (mt) cc_final: 0.8450 (mt) REVERT: B 400 PHE cc_start: 0.6703 (p90) cc_final: 0.6331 (p90) REVERT: B 537 LYS cc_start: 0.8506 (tttt) cc_final: 0.8243 (tttp) REVERT: B 547 LYS cc_start: 0.8493 (mttt) cc_final: 0.8137 (mttm) REVERT: B 551 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8375 (m) REVERT: B 558 LYS cc_start: 0.8661 (mptt) cc_final: 0.8461 (mttt) REVERT: B 571 ASP cc_start: 0.8069 (m-30) cc_final: 0.7811 (t70) REVERT: B 737 ASP cc_start: 0.7925 (t0) cc_final: 0.7588 (t70) REVERT: B 765 ARG cc_start: 0.7949 (tmm-80) cc_final: 0.6943 (ttm-80) REVERT: B 935 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8312 (tm-30) REVERT: B 936 ASP cc_start: 0.8275 (m-30) cc_final: 0.7943 (m-30) REVERT: B 964 LYS cc_start: 0.8839 (tppp) cc_final: 0.8621 (ttmm) REVERT: B 1002 GLN cc_start: 0.8327 (tp40) cc_final: 0.7672 (tp40) REVERT: B 1111 GLU cc_start: 0.8452 (tp30) cc_final: 0.8238 (tt0) REVERT: B 1123 SER cc_start: 0.8773 (t) cc_final: 0.8269 (m) REVERT: C 48 LEU cc_start: 0.9069 (mm) cc_final: 0.8865 (mp) REVERT: C 202 LYS cc_start: 0.8168 (mttt) cc_final: 0.7811 (mttp) REVERT: C 298 GLU cc_start: 0.8667 (tp30) cc_final: 0.8283 (tp30) REVERT: C 304 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8538 (mmmm) REVERT: C 558 LYS cc_start: 0.8414 (mttt) cc_final: 0.8175 (tttm) REVERT: C 577 ARG cc_start: 0.6811 (mtp85) cc_final: 0.6495 (mtp85) REVERT: C 578 ASP cc_start: 0.7806 (t0) cc_final: 0.7586 (t70) REVERT: C 710 ASN cc_start: 0.8964 (p0) cc_final: 0.8640 (p0) REVERT: C 725 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7499 (mt-10) REVERT: C 739 THR cc_start: 0.8709 (m) cc_final: 0.8477 (p) REVERT: C 745 ASP cc_start: 0.6782 (m-30) cc_final: 0.6435 (p0) REVERT: C 776 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8296 (tppp) REVERT: C 825 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8217 (mtpp) REVERT: C 955 ASN cc_start: 0.8337 (t0) cc_final: 0.7982 (t0) REVERT: C 957 GLN cc_start: 0.8409 (tt0) cc_final: 0.7886 (tt0) REVERT: C 965 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8457 (mm-40) REVERT: C 1002 GLN cc_start: 0.8558 (tp40) cc_final: 0.7919 (tp40) REVERT: C 1081 ILE cc_start: 0.8535 (pt) cc_final: 0.8309 (pt) outliers start: 88 outliers final: 68 residues processed: 523 average time/residue: 0.1696 time to fit residues: 135.4575 Evaluate side-chains 532 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 459 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 128 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 329 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 576 VAL 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 30 ASN Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 227 VAL 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 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 544 ASN Chi-restraints excluded: chain B residue 551 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 753 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 973 ILE 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 157 PHE Chi-restraints excluded: chain C residue 240 THR 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 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 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 776 LYS Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 115 optimal weight: 4.9990 chunk 181 optimal weight: 0.0020 chunk 288 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.157551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122286 restraints weight = 47755.631| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 3.06 r_work: 0.3437 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.6895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 25423 Z= 0.150 Angle : 0.605 10.003 34593 Z= 0.316 Chirality : 0.044 0.180 3904 Planarity : 0.004 0.042 4462 Dihedral : 4.454 22.777 3391 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.82 % Allowed : 15.13 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3114 helix: 1.34 (0.21), residues: 683 sheet: 0.35 (0.19), residues: 657 loop : -0.86 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.019 0.001 TYR A 265 PHE 0.052 0.002 PHE B 342 TRP 0.019 0.001 TRP C 64 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00347 (25384) covalent geometry : angle 0.59976 (34515) SS BOND : bond 0.00446 ( 39) SS BOND : angle 1.84404 ( 78) hydrogen bonds : bond 0.04441 ( 924) hydrogen bonds : angle 5.09822 ( 2616) *********************** 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 543 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 465 time to evaluate : 0.857 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: A 190 ARG cc_start: 0.8022 (ttm110) cc_final: 0.7682 (ttm110) REVERT: A 239 GLN cc_start: 0.8192 (tt0) cc_final: 0.7602 (tp-100) REVERT: A 307 THR cc_start: 0.8889 (m) cc_final: 0.8520 (p) REVERT: A 329 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.7342 (m-10) REVERT: A 902 MET cc_start: 0.8411 (mmm) cc_final: 0.8126 (tpp) REVERT: A 933 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8371 (mttp) REVERT: A 969 LYS cc_start: 0.9136 (mtmm) cc_final: 0.8897 (mtmm) REVERT: A 990 GLU cc_start: 0.7356 (tm-30) cc_final: 0.7118 (tm-30) REVERT: A 1002 GLN cc_start: 0.8220 (tp40) cc_final: 0.7913 (tp40) REVERT: A 1030 SER cc_start: 0.8968 (m) cc_final: 0.8668 (t) REVERT: A 1038 LYS cc_start: 0.9236 (mttt) cc_final: 0.8918 (mmmm) REVERT: B 41 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7049 (mmmm) REVERT: B 191 GLU cc_start: 0.7915 (pt0) cc_final: 0.7696 (mt-10) REVERT: B 195 LYS cc_start: 0.8196 (tptt) cc_final: 0.7890 (ptmt) REVERT: B 237 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.8349 (mtp180) REVERT: B 278 LYS cc_start: 0.8842 (tttt) cc_final: 0.8463 (ttpt) REVERT: B 335 LEU cc_start: 0.9128 (tp) cc_final: 0.8898 (mm) REVERT: B 386 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8237 (mttt) REVERT: B 387 LEU cc_start: 0.8779 (mt) cc_final: 0.8478 (mt) REVERT: B 400 PHE cc_start: 0.6755 (p90) cc_final: 0.6311 (p90) REVERT: B 537 LYS cc_start: 0.8504 (tttt) cc_final: 0.8294 (tttp) REVERT: B 547 LYS cc_start: 0.8517 (mttt) cc_final: 0.8141 (mttm) REVERT: B 551 VAL cc_start: 0.8797 (OUTLIER) cc_final: 0.8312 (m) REVERT: B 571 ASP cc_start: 0.8017 (m-30) cc_final: 0.7767 (t70) REVERT: B 737 ASP cc_start: 0.7849 (t0) cc_final: 0.7513 (t70) REVERT: B 765 ARG cc_start: 0.7919 (tmm-80) cc_final: 0.6893 (ttm-80) REVERT: B 935 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8308 (tm-30) REVERT: B 936 ASP cc_start: 0.8296 (m-30) cc_final: 0.7970 (m-30) REVERT: B 964 LYS cc_start: 0.8835 (tppp) cc_final: 0.8613 (ttmm) REVERT: B 995 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.8006 (ttm-80) REVERT: B 1002 GLN cc_start: 0.8241 (tp40) cc_final: 0.7572 (tp40) REVERT: B 1038 LYS cc_start: 0.9007 (mmmm) cc_final: 0.8760 (mmtp) REVERT: B 1111 GLU cc_start: 0.8505 (tp30) cc_final: 0.8284 (tt0) REVERT: B 1123 SER cc_start: 0.8690 (t) cc_final: 0.8151 (m) REVERT: C 202 LYS cc_start: 0.8159 (mttt) cc_final: 0.7875 (mptt) REVERT: C 298 GLU cc_start: 0.8630 (tp30) cc_final: 0.8246 (tp30) REVERT: C 304 LYS cc_start: 0.8756 (mmmm) cc_final: 0.8400 (mmmm) REVERT: C 558 LYS cc_start: 0.8404 (mttt) cc_final: 0.8174 (tttp) REVERT: C 577 ARG cc_start: 0.6871 (mtp85) cc_final: 0.6536 (mtp85) REVERT: C 710 ASN cc_start: 0.8935 (p0) cc_final: 0.8594 (p0) REVERT: C 725 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7495 (mt-10) REVERT: C 739 THR cc_start: 0.8694 (m) cc_final: 0.8478 (p) REVERT: C 745 ASP cc_start: 0.6740 (m-30) cc_final: 0.6478 (p0) REVERT: C 773 GLU cc_start: 0.8338 (tp30) cc_final: 0.8135 (tt0) REVERT: C 776 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8261 (tppp) REVERT: C 780 GLU cc_start: 0.8200 (tp30) cc_final: 0.7994 (tp30) REVERT: C 825 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8290 (mtpp) REVERT: C 955 ASN cc_start: 0.8314 (t0) cc_final: 0.7959 (t0) REVERT: C 957 GLN cc_start: 0.8394 (tt0) cc_final: 0.7852 (tt0) REVERT: C 965 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8450 (mm-40) REVERT: C 1002 GLN cc_start: 0.8456 (tp40) cc_final: 0.7841 (tp40) REVERT: C 1019 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7158 (ttp80) REVERT: C 1081 ILE cc_start: 0.8571 (pt) cc_final: 0.8340 (pt) outliers start: 78 outliers final: 65 residues processed: 506 average time/residue: 0.1712 time to fit residues: 131.8429 Evaluate side-chains 525 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 456 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 128 ILE Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 329 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 576 VAL 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 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 30 ASN Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 227 VAL 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 551 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 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 973 ILE 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 157 PHE 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 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 697 MET 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 790 LYS Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 268 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 288 optimal weight: 0.0570 chunk 81 optimal weight: 1.9990 chunk 181 optimal weight: 0.4980 chunk 290 optimal weight: 0.9980 chunk 95 optimal weight: 0.0980 chunk 65 optimal weight: 0.6980 chunk 73 optimal weight: 0.0980 chunk 137 optimal weight: 0.9980 overall best weight: 0.2898 ------------------------------------------------------------------------------- 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 A 955 ASN B 657 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 = 0.4130 r_free = 0.4130 target = 0.159024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123599 restraints weight = 47792.732| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 3.08 r_work: 0.3469 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 25423 Z= 0.118 Angle : 0.587 10.031 34593 Z= 0.306 Chirality : 0.044 0.179 3904 Planarity : 0.004 0.046 4462 Dihedral : 4.304 23.665 3391 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.20 % Allowed : 16.32 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.15), residues: 3114 helix: 1.50 (0.21), residues: 683 sheet: 0.33 (0.19), residues: 677 loop : -0.77 (0.14), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1019 TYR 0.018 0.001 TYR A 265 PHE 0.061 0.002 PHE B 342 TRP 0.020 0.001 TRP C 64 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00272 (25384) covalent geometry : angle 0.58344 (34515) SS BOND : bond 0.00323 ( 39) SS BOND : angle 1.48757 ( 78) hydrogen bonds : bond 0.04003 ( 924) hydrogen bonds : angle 4.97335 ( 2616) *********************** 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 535 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 474 time to evaluate : 0.880 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 190 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7718 (ttm110) REVERT: A 197 ILE cc_start: 0.7895 (mt) cc_final: 0.7646 (mp) REVERT: A 202 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8661 (mttp) REVERT: A 239 GLN cc_start: 0.8159 (tt0) cc_final: 0.7773 (tp40) REVERT: A 240 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7648 (t) REVERT: A 307 THR cc_start: 0.8874 (m) cc_final: 0.8508 (p) REVERT: A 329 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7313 (m-10) REVERT: A 588 THR cc_start: 0.8385 (m) cc_final: 0.7978 (p) REVERT: A 763 LEU cc_start: 0.8231 (mt) cc_final: 0.7826 (mp) REVERT: A 933 LYS cc_start: 0.8624 (ttmm) cc_final: 0.8419 (mttp) REVERT: A 969 LYS cc_start: 0.9129 (mtmm) cc_final: 0.8862 (mtmm) REVERT: A 1002 GLN cc_start: 0.8148 (tp40) cc_final: 0.7689 (tp40) REVERT: A 1030 SER cc_start: 0.8978 (m) cc_final: 0.8680 (t) REVERT: A 1038 LYS cc_start: 0.9228 (mttt) cc_final: 0.8922 (mmmm) REVERT: B 195 LYS cc_start: 0.8081 (tptt) cc_final: 0.7804 (ptmt) REVERT: B 237 ARG cc_start: 0.8529 (mtm-85) cc_final: 0.8319 (mtp180) REVERT: B 240 THR cc_start: 0.6480 (OUTLIER) cc_final: 0.6210 (t) REVERT: B 278 LYS cc_start: 0.8866 (tttt) cc_final: 0.8486 (ttpt) REVERT: B 335 LEU cc_start: 0.8980 (tp) cc_final: 0.8711 (mm) REVERT: B 386 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8163 (mttt) REVERT: B 387 LEU cc_start: 0.8770 (mt) cc_final: 0.8455 (mt) REVERT: B 400 PHE cc_start: 0.6567 (p90) cc_final: 0.6144 (p90) REVERT: B 454 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.6902 (mtm-85) REVERT: B 547 LYS cc_start: 0.8462 (mttt) cc_final: 0.8155 (mttm) REVERT: B 551 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8314 (m) REVERT: B 571 ASP cc_start: 0.7965 (m-30) cc_final: 0.7743 (t70) REVERT: B 737 ASP cc_start: 0.7739 (t0) cc_final: 0.7375 (t70) REVERT: B 765 ARG cc_start: 0.7835 (tmm-80) cc_final: 0.6789 (ttm-80) REVERT: B 935 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 936 ASP cc_start: 0.8251 (m-30) cc_final: 0.7936 (m-30) REVERT: B 964 LYS cc_start: 0.8830 (tppp) cc_final: 0.8575 (ttmm) REVERT: B 984 LEU cc_start: 0.8480 (mm) cc_final: 0.8218 (mp) REVERT: B 995 ARG cc_start: 0.8106 (ttm-80) cc_final: 0.7893 (ttm-80) REVERT: B 1002 GLN cc_start: 0.8100 (tp40) cc_final: 0.7462 (tp40) REVERT: B 1019 ARG cc_start: 0.8218 (tpp-160) cc_final: 0.7813 (tpm170) REVERT: B 1038 LYS cc_start: 0.9013 (mmmm) cc_final: 0.8773 (mmtp) REVERT: B 1111 GLU cc_start: 0.8468 (tp30) cc_final: 0.8249 (tt0) REVERT: B 1123 SER cc_start: 0.8553 (t) cc_final: 0.7944 (m) REVERT: C 197 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.8036 (pt) REVERT: C 202 LYS cc_start: 0.8110 (mttt) cc_final: 0.7825 (mptt) REVERT: C 237 ARG cc_start: 0.7360 (mmm-85) cc_final: 0.7145 (mmm-85) REVERT: C 280 ASN cc_start: 0.8169 (p0) cc_final: 0.7962 (p0) REVERT: C 298 GLU cc_start: 0.8615 (tp30) cc_final: 0.8236 (tp30) REVERT: C 304 LYS cc_start: 0.8754 (mmmm) cc_final: 0.8385 (mmmm) REVERT: C 558 LYS cc_start: 0.8367 (mttt) cc_final: 0.8105 (tttp) REVERT: C 577 ARG cc_start: 0.6811 (mtp85) cc_final: 0.6446 (mtp85) REVERT: C 710 ASN cc_start: 0.8905 (p0) cc_final: 0.8548 (p0) REVERT: C 725 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7462 (mt-10) REVERT: C 739 THR cc_start: 0.8620 (m) cc_final: 0.8404 (p) REVERT: C 825 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8291 (mtpp) REVERT: C 955 ASN cc_start: 0.8295 (t0) cc_final: 0.7934 (t0) REVERT: C 957 GLN cc_start: 0.8413 (tt0) cc_final: 0.7858 (tt0) REVERT: C 1002 GLN cc_start: 0.8368 (tp40) cc_final: 0.7794 (tp40) REVERT: C 1081 ILE cc_start: 0.8559 (pt) cc_final: 0.8329 (pt) REVERT: C 1123 SER cc_start: 0.8992 (t) cc_final: 0.8655 (m) outliers start: 61 outliers final: 47 residues processed: 506 average time/residue: 0.1708 time to fit residues: 131.5213 Evaluate side-chains 508 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 454 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 202 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 365 TYR Chi-restraints excluded: chain A residue 576 VAL 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 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 30 ASN 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 306 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 556 ASN 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 973 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 197 ILE 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 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 790 LYS Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP 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 85 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 255 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 263 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 0.0470 chunk 194 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- 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** A1119 ASN B 544 ASN B 657 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.157062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121674 restraints weight = 48033.386| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.06 r_work: 0.3440 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.7157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 25423 Z= 0.156 Angle : 0.615 10.319 34593 Z= 0.321 Chirality : 0.044 0.202 3904 Planarity : 0.004 0.059 4462 Dihedral : 4.412 24.160 3391 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.09 % Allowed : 17.00 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3114 helix: 1.43 (0.21), residues: 685 sheet: 0.42 (0.19), residues: 674 loop : -0.82 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 355 TYR 0.024 0.001 TYR C 707 PHE 0.059 0.002 PHE B 342 TRP 0.019 0.001 TRP B 353 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00365 (25384) covalent geometry : angle 0.61052 (34515) SS BOND : bond 0.00382 ( 39) SS BOND : angle 1.69235 ( 78) hydrogen bonds : bond 0.04342 ( 924) hydrogen bonds : angle 5.02860 ( 2616) ********************** 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 524 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 466 time to evaluate : 0.900 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 190 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7750 (ttm110) REVERT: A 239 GLN cc_start: 0.8234 (tt0) cc_final: 0.7957 (tt0) REVERT: A 240 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7630 (t) REVERT: A 307 THR cc_start: 0.8862 (m) cc_final: 0.8415 (p) REVERT: A 588 THR cc_start: 0.8414 (m) cc_final: 0.7977 (p) REVERT: A 933 LYS cc_start: 0.8655 (ttmm) cc_final: 0.8398 (mttp) REVERT: A 1002 GLN cc_start: 0.8223 (tp40) cc_final: 0.7794 (tp40) REVERT: A 1017 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7393 (mm-30) REVERT: A 1030 SER cc_start: 0.8974 (m) cc_final: 0.8682 (t) REVERT: A 1038 LYS cc_start: 0.9229 (mttt) cc_final: 0.8923 (mmmm) REVERT: B 41 LYS cc_start: 0.7756 (mmmt) cc_final: 0.7490 (mmmt) REVERT: B 195 LYS cc_start: 0.8169 (tptt) cc_final: 0.7890 (ptmt) REVERT: B 278 LYS cc_start: 0.8853 (tttt) cc_final: 0.8486 (ttpt) REVERT: B 335 LEU cc_start: 0.9097 (tp) cc_final: 0.8813 (mm) REVERT: B 386 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8312 (mttt) REVERT: B 387 LEU cc_start: 0.8880 (mt) cc_final: 0.8580 (mt) REVERT: B 400 PHE cc_start: 0.6521 (p90) cc_final: 0.6080 (p90) REVERT: B 454 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7216 (mtm-85) REVERT: B 547 LYS cc_start: 0.8519 (mttt) cc_final: 0.8205 (mttm) REVERT: B 551 VAL cc_start: 0.8826 (OUTLIER) cc_final: 0.8344 (m) REVERT: B 558 LYS cc_start: 0.8760 (mttt) cc_final: 0.8374 (mttt) REVERT: B 737 ASP cc_start: 0.7870 (t0) cc_final: 0.7485 (t70) REVERT: B 765 ARG cc_start: 0.7912 (tmm-80) cc_final: 0.6851 (ttm-80) REVERT: B 935 GLN cc_start: 0.8632 (tm-30) cc_final: 0.8261 (tm-30) REVERT: B 936 ASP cc_start: 0.8261 (m-30) cc_final: 0.7922 (m-30) REVERT: B 964 LYS cc_start: 0.8866 (tppp) cc_final: 0.8632 (ttmm) REVERT: B 984 LEU cc_start: 0.8444 (mm) cc_final: 0.8239 (mp) REVERT: B 995 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7998 (ttm-80) REVERT: B 1002 GLN cc_start: 0.8272 (tp40) cc_final: 0.7724 (tp40) REVERT: B 1019 ARG cc_start: 0.8245 (tpp-160) cc_final: 0.7888 (tpm170) REVERT: B 1038 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8772 (mmtp) REVERT: B 1111 GLU cc_start: 0.8498 (tp30) cc_final: 0.8285 (tt0) REVERT: C 197 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7946 (pt) REVERT: C 200 TYR cc_start: 0.6572 (m-80) cc_final: 0.6059 (m-80) REVERT: C 202 LYS cc_start: 0.8127 (mttt) cc_final: 0.7831 (mptt) REVERT: C 298 GLU cc_start: 0.8608 (tp30) cc_final: 0.8235 (tp30) REVERT: C 355 ARG cc_start: 0.7077 (ptt-90) cc_final: 0.6877 (ptt-90) REVERT: C 558 LYS cc_start: 0.8503 (mttt) cc_final: 0.8156 (tttp) REVERT: C 725 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7480 (mt-10) REVERT: C 780 GLU cc_start: 0.8302 (tp30) cc_final: 0.8075 (tp30) REVERT: C 825 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8331 (mtpp) REVERT: C 955 ASN cc_start: 0.8355 (t0) cc_final: 0.7982 (t0) REVERT: C 957 GLN cc_start: 0.8422 (tt0) cc_final: 0.7859 (tt0) REVERT: C 965 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8521 (tp40) REVERT: C 1002 GLN cc_start: 0.8420 (tp40) cc_final: 0.7858 (tp40) REVERT: C 1081 ILE cc_start: 0.8556 (pt) cc_final: 0.8337 (pt) REVERT: C 1123 SER cc_start: 0.8957 (t) cc_final: 0.8627 (m) outliers start: 58 outliers final: 49 residues processed: 497 average time/residue: 0.1711 time to fit residues: 129.5792 Evaluate side-chains 502 residues out of total 2770 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 448 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 202 LYS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 240 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 576 VAL 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 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 266 TYR Chi-restraints excluded: chain B residue 277 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 551 VAL Chi-restraints excluded: chain B residue 556 ASN 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 973 ILE Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 197 ILE 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 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 790 LYS Chi-restraints excluded: chain C residue 825 LYS Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1136 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 314 random chunks: chunk 63 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 313 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 1 optimal weight: 0.0270 chunk 32 optimal weight: 1.9990 overall best weight: 0.7840 ------------------------------------------------------------------------------- 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 B 657 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.157156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.121680 restraints weight = 47957.953| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.07 r_work: 0.3435 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.7177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.212 25423 Z= 0.210 Angle : 0.803 59.145 34593 Z= 0.437 Chirality : 0.046 0.817 3904 Planarity : 0.004 0.066 4462 Dihedral : 4.415 24.131 3391 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.17 % Allowed : 17.11 % Favored : 80.72 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.15), residues: 3114 helix: 1.42 (0.21), residues: 685 sheet: 0.39 (0.19), residues: 676 loop : -0.83 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 237 TYR 0.022 0.001 TYR C 707 PHE 0.056 0.002 PHE B 342 TRP 0.017 0.001 TRP B 353 HIS 0.010 0.001 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00473 (25384) covalent geometry : angle 0.77327 (34515) SS BOND : bond 0.01632 ( 39) SS BOND : angle 4.62041 ( 78) hydrogen bonds : bond 0.04353 ( 924) hydrogen bonds : angle 5.03124 ( 2616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6135.42 seconds wall clock time: 105 minutes 38.65 seconds (6338.65 seconds total)