Starting phenix.real_space_refine on Mon Aug 25 02:39:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c5r_16441/08_2025/8c5r_16441.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c5r_16441/08_2025/8c5r_16441.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c5r_16441/08_2025/8c5r_16441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c5r_16441/08_2025/8c5r_16441.map" model { file = "/net/cci-nas-00/data/ceres_data/8c5r_16441/08_2025/8c5r_16441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c5r_16441/08_2025/8c5r_16441.cif" } resolution = 3.7 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= -0.000 sd= 0.052 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 15984 2.51 5 N 4158 2.21 5 O 4713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24969 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8328 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 6 Chain: "B" Number of atoms: 8328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8328 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 53, 'TRANS': 1006} Chain breaks: 6 Chain: "C" Number of atoms: 8313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8313 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 53, 'TRANS': 1004} Chain breaks: 6 Time building chain proxies: 5.15, per 1000 atoms: 0.21 Number of scatterers: 24969 At special positions: 0 Unit cell: (144.768, 155.584, 193.024, 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 4713 8.00 N 4158 7.00 C 15984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 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=2.03 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=2.03 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 838.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5972 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 44 sheets defined 23.9% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.561A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.599A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.634A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.502A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 782 removed outlier: 4.498A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.540A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.043A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.663A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1031 removed outlier: 3.978A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 390 removed outlier: 3.552A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.698A pdb=" N SER B 443 " --> pdb=" O LYS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.605A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 4.163A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.534A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.667A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.250A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 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 966 removed outlier: 3.904A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.232A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.697A 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 365 through 370 removed outlier: 3.543A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.625A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.739A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.782A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.525A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.638A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.638A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 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 968 removed outlier: 4.028A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 968 " --> pdb=" O LYS C 964 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.663A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.848A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.066A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.894A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 263 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.655A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.517A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.333A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.397A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.380A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.652A 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) removed outlier: 4.789A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 326 through 327 removed outlier: 5.200A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.600A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.681A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.025A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR A 660 " --> pdb=" O SER A 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.025A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 3.503A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.246A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 removed outlier: 5.117A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.965A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.532A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.331A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 154 through 157 removed outlier: 6.482A pdb=" N ASP B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR B 259 " --> pdb=" O HIS B 245 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 314 removed outlier: 3.502A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.551A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.539A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.538A pdb=" N TYR B 453 " --> pdb=" O ARG B 493 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.945A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.415A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B1068 " --> pdb=" O THR B 719 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 789 removed outlier: 4.901A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.121A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA C 263 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ASN C 196 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LYS C 202 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.034A 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: 3.514A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.755A 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: 6.425A pdb=" N ASP C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 144 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.416A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.488A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.541A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.624A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.966A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.339A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.525A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.573A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 941 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.00 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8004 1.34 - 1.46: 6148 1.46 - 1.58: 11261 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 25557 Sorted by residual: bond pdb=" N PRO B 373 " pdb=" CD PRO B 373 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.69e+01 bond pdb=" N PRO C 213 " pdb=" CD PRO C 213 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N PRO A 213 " pdb=" CD PRO A 213 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" N PRO A 373 " pdb=" CD PRO A 373 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.53e+01 ... (remaining 25552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 34513 2.59 - 5.19: 226 5.19 - 7.78: 7 7.78 - 10.37: 4 10.37 - 12.96: 7 Bond angle restraints: 34757 Sorted by residual: angle pdb=" CA PRO A 213 " pdb=" N PRO A 213 " pdb=" CD PRO A 213 " ideal model delta sigma weight residual 112.00 99.04 12.96 1.40e+00 5.10e-01 8.57e+01 angle pdb=" CA PRO C 373 " pdb=" N PRO C 373 " pdb=" CD PRO C 373 " ideal model delta sigma weight residual 112.00 99.20 12.80 1.40e+00 5.10e-01 8.36e+01 angle pdb=" CA PRO C 213 " pdb=" N PRO C 213 " pdb=" CD PRO C 213 " ideal model delta sigma weight residual 112.00 99.22 12.78 1.40e+00 5.10e-01 8.33e+01 angle pdb=" CA PRO A 373 " pdb=" N PRO A 373 " pdb=" CD PRO A 373 " ideal model delta sigma weight residual 112.00 99.23 12.77 1.40e+00 5.10e-01 8.32e+01 angle pdb=" CA PRO B 213 " pdb=" N PRO B 213 " pdb=" CD PRO B 213 " ideal model delta sigma weight residual 112.00 99.26 12.74 1.40e+00 5.10e-01 8.29e+01 ... (remaining 34752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14856 17.99 - 35.99: 308 35.99 - 53.98: 62 53.98 - 71.98: 11 71.98 - 89.97: 10 Dihedral angle restraints: 15247 sinusoidal: 5974 harmonic: 9273 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 142.81 -49.81 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 142.72 -49.72 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CA ASN C 149 " pdb=" C ASN C 149 " pdb=" N LYS C 150 " pdb=" CA LYS C 150 " ideal model delta harmonic sigma weight residual -180.00 -158.81 -21.19 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 15244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2879 0.039 - 0.078: 671 0.078 - 0.118: 290 0.118 - 0.157: 80 0.157 - 0.196: 5 Chirality restraints: 3925 Sorted by residual: chirality pdb=" CA ILE A 211 " pdb=" N ILE A 211 " pdb=" C ILE A 211 " pdb=" CB ILE A 211 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.60e-01 chirality pdb=" CA ILE C 211 " pdb=" N ILE C 211 " pdb=" C ILE C 211 " pdb=" CB ILE C 211 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CA ILE C 714 " pdb=" N ILE C 714 " pdb=" C ILE C 714 " pdb=" CB ILE C 714 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 3922 not shown) Planarity restraints: 4495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " 0.055 5.00e-02 4.00e+02 7.65e-02 9.36e+00 pdb=" N PRO A 373 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 212 " -0.053 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO C 213 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 213 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 213 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 372 " -0.050 5.00e-02 4.00e+02 6.96e-02 7.74e+00 pdb=" N PRO C 373 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 373 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 373 " -0.037 5.00e-02 4.00e+02 ... (remaining 4492 not shown) Histogram of nonbonded interaction distances: 0.57 - 1.43: 29 1.43 - 2.30: 159 2.30 - 3.17: 21403 3.17 - 4.03: 64916 4.03 - 4.90: 120700 Warning: very small nonbonded interaction distances. Nonbonded interactions: 207207 Sorted by model distance: nonbonded pdb=" CG PHE B 643 " pdb=" CZ TYR B 655 " model vdw 0.567 3.480 nonbonded pdb=" CD2 PHE B 643 " pdb=" CE1 TYR B 655 " model vdw 0.618 3.640 nonbonded pdb=" CG PHE C 643 " pdb=" CZ TYR C 655 " model vdw 0.632 3.480 nonbonded pdb=" CB PHE C 643 " pdb=" CE2 TYR C 655 " model vdw 0.773 3.740 nonbonded pdb=" CE LYS C 439 " pdb=" CD GLN C 506 " model vdw 0.818 3.670 ... (remaining 207202 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147)) selection = (chain 'B' and (resid 14 through 676 or resid 690 through 827 or resid 855 throu \ gh 1147)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.540 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3687 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 : 0.006 0.624 25602 Z= 0.536 Angle : 0.586 12.964 34833 Z= 0.327 Chirality : 0.044 0.196 3925 Planarity : 0.003 0.076 4495 Dihedral : 8.088 89.972 9161 Min Nonbonded Distance : 0.567 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.09 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (0.12), residues: 3136 helix: -1.45 (0.15), residues: 666 sheet: -1.97 (0.17), residues: 694 loop : -2.52 (0.12), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.014 0.001 TYR C 873 PHE 0.014 0.001 PHE C 490 TRP 0.009 0.001 TRP A 152 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00304 (25557) covalent geometry : angle 0.58650 (34757) SS BOND : bond 0.00147 ( 38) SS BOND : angle 0.54263 ( 76) hydrogen bonds : bond 0.24352 ( 927) hydrogen bonds : angle 9.52211 ( 2607) Misc. bond : bond 0.30859 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 0.685 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 727 LEU cc_start: 0.7602 (mt) cc_final: 0.7362 (mt) REVERT: A 800 PHE cc_start: 0.6179 (m-80) cc_final: 0.4407 (m-80) REVERT: A 874 THR cc_start: 0.6447 (p) cc_final: 0.6121 (p) REVERT: A 904 TYR cc_start: 0.5590 (t80) cc_final: 0.4977 (t80) REVERT: A 1049 LEU cc_start: 0.7539 (mt) cc_final: 0.7285 (mt) REVERT: B 882 ILE cc_start: 0.7097 (mt) cc_final: 0.6849 (mt) REVERT: B 1009 THR cc_start: 0.7656 (m) cc_final: 0.7216 (m) REVERT: B 1039 ARG cc_start: 0.7977 (mtp180) cc_final: 0.6930 (mmm-85) REVERT: C 962 LEU cc_start: 0.5773 (tp) cc_final: 0.5429 (tt) REVERT: C 1110 TYR cc_start: 0.6515 (t80) cc_final: 0.6120 (t80) outliers start: 0 outliers final: 0 residues processed: 560 average time/residue: 0.1519 time to fit residues: 131.8237 Evaluate side-chains 274 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1071 GLN B 49 HIS B 99 ASN B 388 ASN B 613 GLN B 901 GLN B 955 ASN B 957 GLN B1125 ASN B1134 ASN B1135 ASN C 506 GLN C 762 GLN C 935 GLN C 954 HIS C1002 GLN C1005 GLN C1054 GLN C1106 GLN C1135 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.224258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.183019 restraints weight = 44726.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.177966 restraints weight = 63601.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.170497 restraints weight = 44115.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.170450 restraints weight = 51863.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.170584 restraints weight = 43171.498| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 25602 Z= 0.294 Angle : 0.809 12.060 34833 Z= 0.428 Chirality : 0.052 0.243 3925 Planarity : 0.006 0.074 4495 Dihedral : 4.907 29.435 3412 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.76 % Allowed : 6.24 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.33 (0.13), residues: 3136 helix: -0.45 (0.17), residues: 659 sheet: -1.45 (0.17), residues: 723 loop : -2.07 (0.13), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 273 TYR 0.027 0.003 TYR B 873 PHE 0.033 0.003 PHE A1121 TRP 0.020 0.003 TRP C 436 HIS 0.015 0.003 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00674 (25557) covalent geometry : angle 0.80848 (34757) SS BOND : bond 0.00413 ( 38) SS BOND : angle 1.12348 ( 76) hydrogen bonds : bond 0.05635 ( 927) hydrogen bonds : angle 6.83272 ( 2607) Misc. bond : bond 0.00535 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 317 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.4954 (t0) cc_final: 0.4669 (m-30) REVERT: A 598 ILE cc_start: 0.8687 (mt) cc_final: 0.8469 (mt) REVERT: A 740 MET cc_start: 0.7960 (mmm) cc_final: 0.7729 (tpt) REVERT: A 873 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.8390 (m-10) REVERT: B 646 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6459 (mmt90) REVERT: B 664 ILE cc_start: 0.8053 (mp) cc_final: 0.7813 (mp) REVERT: B 789 TYR cc_start: 0.8373 (m-80) cc_final: 0.8123 (m-80) REVERT: B 931 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7237 (tt) REVERT: B 933 LYS cc_start: 0.7588 (mttt) cc_final: 0.7226 (ttpt) REVERT: B 1003 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.8154 (t) REVERT: B 1094 VAL cc_start: 0.7643 (OUTLIER) cc_final: 0.6706 (t) REVERT: B 1097 SER cc_start: 0.8869 (t) cc_final: 0.8303 (p) REVERT: B 1102 TRP cc_start: 0.8743 (m100) cc_final: 0.7953 (m100) REVERT: C 52 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.7854 (tp-100) REVERT: C 91 TYR cc_start: 0.7287 (t80) cc_final: 0.7050 (t80) REVERT: C 458 LYS cc_start: 0.7285 (mttt) cc_final: 0.6645 (pttp) REVERT: C 729 VAL cc_start: 0.7551 (t) cc_final: 0.7073 (p) REVERT: C 887 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7741 (m) REVERT: C 1110 TYR cc_start: 0.8196 (t80) cc_final: 0.7820 (t80) outliers start: 77 outliers final: 40 residues processed: 383 average time/residue: 0.1409 time to fit residues: 85.1669 Evaluate side-chains 252 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 205 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 273 ARG Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 124 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 214 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 181 optimal weight: 0.4980 chunk 173 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 247 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1071 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B1005 GLN B1054 GLN C 437 ASN C 506 GLN C 935 GLN C 955 ASN C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.225673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.183122 restraints weight = 44693.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.176396 restraints weight = 60506.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.168261 restraints weight = 41452.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.169298 restraints weight = 41409.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.169570 restraints weight = 33654.608| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25602 Z= 0.140 Angle : 0.551 8.536 34833 Z= 0.289 Chirality : 0.045 0.228 3925 Planarity : 0.004 0.055 4495 Dihedral : 4.159 22.848 3412 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.04 % Allowed : 9.51 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.14), residues: 3136 helix: 0.53 (0.19), residues: 664 sheet: -1.02 (0.18), residues: 707 loop : -1.80 (0.13), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.018 0.001 TYR B 265 PHE 0.025 0.001 PHE C 43 TRP 0.021 0.002 TRP C 64 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00314 (25557) covalent geometry : angle 0.55063 (34757) SS BOND : bond 0.00262 ( 38) SS BOND : angle 0.79063 ( 76) hydrogen bonds : bond 0.04261 ( 927) hydrogen bonds : angle 5.97823 ( 2607) Misc. bond : bond 0.00414 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 259 time to evaluate : 0.561 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 224 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5688 (pt0) REVERT: A 306 PHE cc_start: 0.3985 (m-80) cc_final: 0.3778 (m-80) REVERT: A 644 GLN cc_start: 0.8596 (tp40) cc_final: 0.7822 (tt0) REVERT: B 1003 SER cc_start: 0.8552 (OUTLIER) cc_final: 0.8204 (t) REVERT: B 1102 TRP cc_start: 0.8650 (m100) cc_final: 0.8328 (m100) REVERT: B 1121 PHE cc_start: 0.6484 (OUTLIER) cc_final: 0.5402 (t80) REVERT: C 52 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8168 (tp-100) REVERT: C 458 LYS cc_start: 0.7166 (mttt) cc_final: 0.6555 (pttp) REVERT: C 756 TYR cc_start: 0.6110 (m-80) cc_final: 0.5790 (m-80) outliers start: 57 outliers final: 34 residues processed: 305 average time/residue: 0.1357 time to fit residues: 67.0308 Evaluate side-chains 241 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 203 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1013 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 224 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 262 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1071 GLN A1101 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN B1005 GLN B1113 GLN B1119 ASN C 474 GLN C 564 GLN C 965 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.218491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.176819 restraints weight = 43774.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 89)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.170118 restraints weight = 63368.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.162683 restraints weight = 56591.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.163915 restraints weight = 48207.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.164035 restraints weight = 38647.127| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25602 Z= 0.189 Angle : 0.604 9.626 34833 Z= 0.316 Chirality : 0.046 0.213 3925 Planarity : 0.005 0.081 4495 Dihedral : 4.427 24.671 3412 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.69 % Allowed : 10.33 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.14), residues: 3136 helix: 0.49 (0.19), residues: 657 sheet: -0.97 (0.18), residues: 680 loop : -1.73 (0.13), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 357 TYR 0.024 0.002 TYR C 38 PHE 0.028 0.002 PHE C 375 TRP 0.016 0.002 TRP C 64 HIS 0.009 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00443 (25557) covalent geometry : angle 0.60114 (34757) SS BOND : bond 0.00525 ( 38) SS BOND : angle 1.36731 ( 76) hydrogen bonds : bond 0.04298 ( 927) hydrogen bonds : angle 5.89426 ( 2607) Misc. bond : bond 0.00542 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 247 time to evaluate : 0.870 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 527 PRO cc_start: 0.4339 (Cg_endo) cc_final: 0.4104 (Cg_exo) REVERT: A 896 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8781 (mt) REVERT: A 1118 ASP cc_start: 0.6741 (t70) cc_final: 0.6450 (t0) REVERT: B 49 HIS cc_start: 0.5378 (t70) cc_final: 0.5085 (t-170) REVERT: B 969 LYS cc_start: 0.7147 (mttt) cc_final: 0.6788 (pttt) REVERT: B 996 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7683 (mm) REVERT: B 1002 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: B 1003 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8275 (t) REVERT: B 1121 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.5769 (t80) REVERT: C 28 TYR cc_start: 0.5906 (m-80) cc_final: 0.5370 (m-80) REVERT: C 52 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8099 (tp-100) REVERT: C 88 ASP cc_start: 0.5962 (p0) cc_final: 0.5458 (m-30) REVERT: C 204 TYR cc_start: 0.5379 (m-80) cc_final: 0.4614 (m-80) REVERT: C 458 LYS cc_start: 0.7199 (mttt) cc_final: 0.6615 (pttp) REVERT: C 756 TYR cc_start: 0.6655 (m-80) cc_final: 0.6303 (m-80) outliers start: 75 outliers final: 50 residues processed: 308 average time/residue: 0.1307 time to fit residues: 66.3051 Evaluate side-chains 257 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 14 optimal weight: 9.9990 chunk 315 optimal weight: 4.9990 chunk 269 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 156 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 243 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 872 GLN A1005 GLN A1054 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN B1119 ASN C 207 HIS C 282 ASN C 394 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1010 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.208207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.166033 restraints weight = 43406.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.162304 restraints weight = 57392.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.162873 restraints weight = 57030.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.162538 restraints weight = 42066.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.162506 restraints weight = 39756.490| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.8863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 25602 Z= 0.357 Angle : 0.818 13.121 34833 Z= 0.435 Chirality : 0.054 0.519 3925 Planarity : 0.006 0.078 4495 Dihedral : 5.648 43.163 3412 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.77 % Allowed : 11.08 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.09 (0.14), residues: 3136 helix: -0.40 (0.18), residues: 645 sheet: -0.89 (0.19), residues: 650 loop : -2.01 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 905 TYR 0.024 0.003 TYR C 38 PHE 0.032 0.003 PHE C 275 TRP 0.032 0.003 TRP C 436 HIS 0.014 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00847 (25557) covalent geometry : angle 0.81394 (34757) SS BOND : bond 0.00631 ( 38) SS BOND : angle 1.88998 ( 76) hydrogen bonds : bond 0.05251 ( 927) hydrogen bonds : angle 6.75215 ( 2607) Misc. bond : bond 0.00429 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 261 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7572 (ttmm) REVERT: A 919 ASN cc_start: 0.8358 (m-40) cc_final: 0.8090 (m110) REVERT: B 49 HIS cc_start: 0.5224 (t70) cc_final: 0.4865 (t-170) REVERT: B 281 GLU cc_start: 0.5207 (OUTLIER) cc_final: 0.4469 (pp20) REVERT: B 931 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8108 (tt) REVERT: B 962 LEU cc_start: 0.8913 (mt) cc_final: 0.8649 (mp) REVERT: B 1002 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7888 (tm-30) REVERT: C 88 ASP cc_start: 0.6524 (p0) cc_final: 0.5890 (m-30) REVERT: C 458 LYS cc_start: 0.7238 (mttt) cc_final: 0.6758 (pptt) REVERT: C 756 TYR cc_start: 0.7137 (m-80) cc_final: 0.6794 (m-80) outliers start: 105 outliers final: 72 residues processed: 343 average time/residue: 0.1262 time to fit residues: 71.1043 Evaluate side-chains 281 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 205 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 886 TRP Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1115 ILE Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1072 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 76 optimal weight: 1.9990 chunk 243 optimal weight: 0.5980 chunk 194 optimal weight: 0.0570 chunk 279 optimal weight: 6.9990 chunk 216 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 120 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1071 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN B1119 ASN C 52 GLN C 137 ASN C 239 GLN C 282 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.215494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.172743 restraints weight = 43677.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.167820 restraints weight = 66422.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.161108 restraints weight = 43619.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.160757 restraints weight = 50603.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.161683 restraints weight = 39219.102| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.8789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25602 Z= 0.118 Angle : 0.572 8.895 34833 Z= 0.296 Chirality : 0.045 0.272 3925 Planarity : 0.004 0.056 4495 Dihedral : 4.557 24.893 3412 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.87 % Allowed : 14.06 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.14), residues: 3136 helix: 0.55 (0.20), residues: 651 sheet: -0.80 (0.19), residues: 675 loop : -1.73 (0.13), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 357 TYR 0.037 0.001 TYR B1007 PHE 0.025 0.002 PHE A 43 TRP 0.030 0.002 TRP A 104 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00267 (25557) covalent geometry : angle 0.56822 (34757) SS BOND : bond 0.00289 ( 38) SS BOND : angle 1.54440 ( 76) hydrogen bonds : bond 0.03884 ( 927) hydrogen bonds : angle 5.78419 ( 2607) Misc. bond : bond 0.00352 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6003 (tt) cc_final: 0.5735 (mp) REVERT: A 765 ARG cc_start: 0.7503 (ttm-80) cc_final: 0.7302 (mtm110) REVERT: A 896 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8744 (mt) REVERT: B 49 HIS cc_start: 0.5152 (t70) cc_final: 0.4827 (t-170) REVERT: B 129 LYS cc_start: 0.5985 (mmtt) cc_final: 0.4774 (mtpt) REVERT: B 224 GLU cc_start: 0.6294 (mt-10) cc_final: 0.5559 (pp20) REVERT: B 644 GLN cc_start: 0.5678 (mm-40) cc_final: 0.5211 (pm20) REVERT: B 1017 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7067 (tm-30) REVERT: C 204 TYR cc_start: 0.5852 (m-80) cc_final: 0.5435 (m-80) REVERT: C 458 LYS cc_start: 0.7253 (mttt) cc_final: 0.6722 (pptt) REVERT: C 756 TYR cc_start: 0.7195 (m-80) cc_final: 0.6983 (m-80) outliers start: 52 outliers final: 32 residues processed: 296 average time/residue: 0.1339 time to fit residues: 64.8467 Evaluate side-chains 247 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 970 PHE Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 34 optimal weight: 7.9990 chunk 263 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 255 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 295 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN B 81 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS B 613 GLN B 644 GLN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 137 ASN C 282 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.205829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.162389 restraints weight = 43520.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.157691 restraints weight = 57019.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.158582 restraints weight = 51441.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.158556 restraints weight = 39411.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.158534 restraints weight = 34507.452| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.9786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.099 25602 Z= 0.376 Angle : 0.806 9.857 34833 Z= 0.429 Chirality : 0.052 0.224 3925 Planarity : 0.006 0.074 4495 Dihedral : 5.498 23.919 3412 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.48 % Allowed : 13.63 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.14), residues: 3136 helix: -0.21 (0.19), residues: 642 sheet: -0.91 (0.19), residues: 658 loop : -2.01 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 44 TYR 0.042 0.003 TYR A 904 PHE 0.036 0.003 PHE C 375 TRP 0.043 0.004 TRP A 886 HIS 0.015 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00887 (25557) covalent geometry : angle 0.80183 (34757) SS BOND : bond 0.00495 ( 38) SS BOND : angle 1.99720 ( 76) hydrogen bonds : bond 0.05236 ( 927) hydrogen bonds : angle 6.67873 ( 2607) Misc. bond : bond 0.00573 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 223 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 310 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7481 (pttt) REVERT: B 49 HIS cc_start: 0.5301 (t70) cc_final: 0.4917 (t-170) REVERT: B 224 GLU cc_start: 0.6578 (mt-10) cc_final: 0.5989 (pp20) REVERT: B 281 GLU cc_start: 0.5257 (OUTLIER) cc_final: 0.4738 (pp20) REVERT: B 355 ARG cc_start: 0.3719 (ptt90) cc_final: 0.3459 (ptt180) REVERT: B 509 ARG cc_start: 0.0716 (mtm180) cc_final: -0.0632 (mtp180) REVERT: B 995 ARG cc_start: 0.5947 (mpt180) cc_final: 0.5473 (mtt180) REVERT: B 1072 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: C 153 MET cc_start: 0.3766 (tpp) cc_final: 0.3503 (tpt) REVERT: C 458 LYS cc_start: 0.7366 (mttt) cc_final: 0.6817 (pptt) REVERT: C 756 TYR cc_start: 0.7536 (m-80) cc_final: 0.6926 (m-80) outliers start: 97 outliers final: 72 residues processed: 303 average time/residue: 0.1229 time to fit residues: 62.6847 Evaluate side-chains 284 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 209 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 696 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1006 THR Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1115 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 269 optimal weight: 0.8980 chunk 305 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 chunk 181 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 200 optimal weight: 0.5980 chunk 251 optimal weight: 10.0000 chunk 231 optimal weight: 0.8980 chunk 85 optimal weight: 0.2980 chunk 309 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 901 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 282 ASN C 564 GLN C 901 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.212329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.170570 restraints weight = 43129.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.165870 restraints weight = 66192.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.160456 restraints weight = 47945.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.161048 restraints weight = 39220.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.161033 restraints weight = 38575.854| |-----------------------------------------------------------------------------| r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.9707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25602 Z= 0.123 Angle : 0.581 7.849 34833 Z= 0.301 Chirality : 0.045 0.226 3925 Planarity : 0.004 0.055 4495 Dihedral : 4.598 23.534 3412 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.83 % Allowed : 15.82 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.14), residues: 3136 helix: 0.50 (0.20), residues: 654 sheet: -0.81 (0.20), residues: 653 loop : -1.71 (0.13), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 815 TYR 0.025 0.001 TYR A 904 PHE 0.036 0.002 PHE C 375 TRP 0.041 0.002 TRP A 104 HIS 0.005 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00281 (25557) covalent geometry : angle 0.57804 (34757) SS BOND : bond 0.00262 ( 38) SS BOND : angle 1.38053 ( 76) hydrogen bonds : bond 0.03854 ( 927) hydrogen bonds : angle 5.78747 ( 2607) Misc. bond : bond 0.00321 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 249 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.6063 (m-30) cc_final: 0.5843 (m-30) REVERT: A 203 ILE cc_start: 0.6345 (tp) cc_final: 0.6129 (pt) REVERT: A 752 LEU cc_start: 0.7428 (mt) cc_final: 0.6419 (tp) REVERT: A 765 ARG cc_start: 0.7676 (ttm-80) cc_final: 0.7427 (mtm110) REVERT: A 896 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8768 (mt) REVERT: A 1001 LEU cc_start: 0.8166 (mt) cc_final: 0.7161 (pp) REVERT: B 49 HIS cc_start: 0.5192 (t70) cc_final: 0.4884 (t-170) REVERT: B 129 LYS cc_start: 0.6109 (mmtt) cc_final: 0.4778 (mtpt) REVERT: B 303 LEU cc_start: 0.7855 (mm) cc_final: 0.7234 (pp) REVERT: B 872 GLN cc_start: 0.7900 (tt0) cc_final: 0.7694 (pt0) REVERT: B 995 ARG cc_start: 0.5742 (mpt180) cc_final: 0.5497 (mtt180) REVERT: B 1017 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7087 (tm-30) REVERT: C 153 MET cc_start: 0.3789 (tpp) cc_final: 0.3553 (tpt) REVERT: C 458 LYS cc_start: 0.7222 (mttt) cc_final: 0.6711 (pptt) outliers start: 51 outliers final: 38 residues processed: 291 average time/residue: 0.1177 time to fit residues: 56.2116 Evaluate side-chains 255 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 46 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 96 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 305 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 755 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.211582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.169264 restraints weight = 43172.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.168948 restraints weight = 63041.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.162239 restraints weight = 51353.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.156082 restraints weight = 44861.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.157539 restraints weight = 39517.568| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.9858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 25602 Z= 0.138 Angle : 0.590 9.050 34833 Z= 0.304 Chirality : 0.045 0.226 3925 Planarity : 0.004 0.053 4495 Dihedral : 4.484 22.660 3412 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.76 % Allowed : 16.18 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.14), residues: 3136 helix: 0.56 (0.20), residues: 660 sheet: -0.64 (0.20), residues: 656 loop : -1.66 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 577 TYR 0.025 0.001 TYR B 741 PHE 0.034 0.002 PHE C 375 TRP 0.043 0.002 TRP A 104 HIS 0.004 0.001 HIS C1101 Details of bonding type rmsd covalent geometry : bond 0.00323 (25557) covalent geometry : angle 0.58755 (34757) SS BOND : bond 0.00267 ( 38) SS BOND : angle 1.29662 ( 76) hydrogen bonds : bond 0.03873 ( 927) hydrogen bonds : angle 5.70756 ( 2607) Misc. bond : bond 0.00429 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 226 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6079 (mp) cc_final: 0.5839 (tt) REVERT: A 203 ILE cc_start: 0.6306 (tp) cc_final: 0.6088 (pt) REVERT: A 896 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8810 (mt) REVERT: A 1001 LEU cc_start: 0.8186 (mt) cc_final: 0.7308 (pp) REVERT: B 49 HIS cc_start: 0.5276 (t70) cc_final: 0.4904 (t-170) REVERT: B 129 LYS cc_start: 0.6209 (mmtt) cc_final: 0.4885 (mtpt) REVERT: B 281 GLU cc_start: 0.5307 (OUTLIER) cc_final: 0.4775 (pp20) REVERT: B 303 LEU cc_start: 0.7868 (mm) cc_final: 0.7238 (pp) REVERT: B 995 ARG cc_start: 0.5916 (mpt180) cc_final: 0.5613 (mtt180) REVERT: C 137 ASN cc_start: 0.7019 (m110) cc_final: 0.6509 (t0) REVERT: C 458 LYS cc_start: 0.7203 (mttt) cc_final: 0.6675 (pptt) outliers start: 49 outliers final: 43 residues processed: 264 average time/residue: 0.1349 time to fit residues: 59.0851 Evaluate side-chains 259 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 651 ILE Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1024 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 137 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 312 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 chunk 200 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 163 optimal weight: 0.0970 chunk 240 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN A 544 ASN A 804 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.212085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.170161 restraints weight = 43431.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.170025 restraints weight = 61107.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.164835 restraints weight = 53093.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.157078 restraints weight = 41451.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.157260 restraints weight = 40968.895| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 1.0012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25602 Z= 0.135 Angle : 0.591 11.469 34833 Z= 0.304 Chirality : 0.045 0.230 3925 Planarity : 0.004 0.053 4495 Dihedral : 4.406 22.134 3412 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.69 % Allowed : 16.61 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.14), residues: 3136 helix: 0.58 (0.20), residues: 669 sheet: -0.59 (0.20), residues: 653 loop : -1.59 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 577 TYR 0.022 0.001 TYR B1007 PHE 0.031 0.002 PHE C 375 TRP 0.058 0.002 TRP A 104 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00317 (25557) covalent geometry : angle 0.58858 (34757) SS BOND : bond 0.00258 ( 38) SS BOND : angle 1.22102 ( 76) hydrogen bonds : bond 0.03754 ( 927) hydrogen bonds : angle 5.59752 ( 2607) Misc. bond : bond 0.00344 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6272 Ramachandran restraints generated. 3136 Oldfield, 0 Emsley, 3136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6577 (mp) cc_final: 0.6340 (tt) REVERT: A 203 ILE cc_start: 0.6239 (tp) cc_final: 0.6027 (pt) REVERT: A 896 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8799 (mt) REVERT: A 1001 LEU cc_start: 0.8215 (mt) cc_final: 0.7233 (pp) REVERT: B 49 HIS cc_start: 0.5573 (t70) cc_final: 0.5220 (t-170) REVERT: B 129 LYS cc_start: 0.6173 (mmtt) cc_final: 0.4889 (mtpt) REVERT: B 303 LEU cc_start: 0.7753 (mm) cc_final: 0.7168 (pp) REVERT: B 1017 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7136 (tm-30) REVERT: C 137 ASN cc_start: 0.7075 (m110) cc_final: 0.6491 (t0) REVERT: C 458 LYS cc_start: 0.7210 (mttt) cc_final: 0.6669 (pptt) outliers start: 47 outliers final: 41 residues processed: 259 average time/residue: 0.1206 time to fit residues: 52.4084 Evaluate side-chains 248 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 881 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 85 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 258 optimal weight: 0.0980 chunk 221 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** 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 = 0.4571 r_free = 0.4571 target = 0.210163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.169003 restraints weight = 43238.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.163167 restraints weight = 65110.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.157924 restraints weight = 56081.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.158957 restraints weight = 51136.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.159505 restraints weight = 36370.879| |-----------------------------------------------------------------------------| r_work (final): 0.4000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 1.0200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 25602 Z= 0.173 Angle : 0.614 9.697 34833 Z= 0.318 Chirality : 0.046 0.230 3925 Planarity : 0.004 0.052 4495 Dihedral : 4.543 22.907 3412 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.01 % Allowed : 16.43 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.38 (0.14), residues: 3136 helix: 0.48 (0.20), residues: 668 sheet: -0.67 (0.20), residues: 676 loop : -1.61 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 765 TYR 0.034 0.001 TYR B1007 PHE 0.031 0.002 PHE C 375 TRP 0.072 0.002 TRP A 104 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00411 (25557) covalent geometry : angle 0.61085 (34757) SS BOND : bond 0.00275 ( 38) SS BOND : angle 1.46992 ( 76) hydrogen bonds : bond 0.03920 ( 927) hydrogen bonds : angle 5.71031 ( 2607) Misc. bond : bond 0.00303 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3899.17 seconds wall clock time: 68 minutes 10.01 seconds (4090.01 seconds total)