Starting phenix.real_space_refine on Sat Jun 21 10:00:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c5r_16441/06_2025/8c5r_16441.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c5r_16441/06_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_16441/06_2025/8c5r_16441.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c5r_16441/06_2025/8c5r_16441.map" model { file = "/net/cci-nas-00/data/ceres_data/8c5r_16441/06_2025/8c5r_16441.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c5r_16441/06_2025/8c5r_16441.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 15.56, per 1000 atoms: 0.62 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: 6.14 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 3.68 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: 11.12 Time building geometry restraints manager: 7.25 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: 0.010 Normalize map: mean=0, sd=1: 7.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.180 Set scattering table: 0.210 Process input model: 58.890 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.050 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.009 0.001 TRP A 152 HIS 0.004 0.001 HIS A1048 PHE 0.014 0.001 PHE C 490 TYR 0.014 0.001 TYR C 873 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.24352 ( 927) hydrogen bonds : angle 9.52211 ( 2607) SS BOND : bond 0.00147 ( 38) SS BOND : angle 0.54263 ( 76) covalent geometry : bond 0.00304 (25557) covalent geometry : angle 0.58650 (34757) 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 : 3.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 LEU cc_start: 0.7602 (mt) cc_final: 0.7355 (mt) REVERT: A 800 PHE cc_start: 0.6179 (m-80) cc_final: 0.4410 (m-80) REVERT: A 874 THR cc_start: 0.6447 (p) cc_final: 0.6116 (p) REVERT: A 904 TYR cc_start: 0.5590 (t80) cc_final: 0.4982 (t80) REVERT: A 1049 LEU cc_start: 0.7539 (mt) cc_final: 0.7280 (mt) REVERT: B 882 ILE cc_start: 0.7097 (mt) cc_final: 0.6848 (mt) REVERT: B 1009 THR cc_start: 0.7656 (m) cc_final: 0.7219 (m) REVERT: B 1039 ARG cc_start: 0.7977 (mtp180) cc_final: 0.6931 (mmm-85) REVERT: C 962 LEU cc_start: 0.5773 (tp) cc_final: 0.5431 (tt) REVERT: C 1110 TYR cc_start: 0.6515 (t80) cc_final: 0.6121 (t80) outliers start: 0 outliers final: 0 residues processed: 560 average time/residue: 0.3999 time to fit residues: 347.1413 Evaluate side-chains 273 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 248 optimal weight: 20.0000 chunk 96 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 184 optimal weight: 3.9990 chunk 287 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** A 774 GLN A1011 GLN A1071 GLN B 49 HIS B 99 ASN B 388 ASN B 901 GLN B 955 ASN B 957 GLN B1125 ASN B1134 ASN C 506 GLN C 762 GLN C 784 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 = 0.4751 r_free = 0.4751 target = 0.228940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.193469 restraints weight = 44668.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.195701 restraints weight = 86715.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.197024 restraints weight = 54861.847| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 25602 Z= 0.242 Angle : 0.733 10.684 34833 Z= 0.387 Chirality : 0.050 0.210 3925 Planarity : 0.005 0.069 4495 Dihedral : 4.545 28.554 3412 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.47 % Allowed : 5.99 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.13), residues: 3136 helix: -0.15 (0.18), residues: 660 sheet: -1.36 (0.18), residues: 706 loop : -1.98 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 436 HIS 0.012 0.002 HIS A 66 PHE 0.029 0.003 PHE A1121 TYR 0.034 0.002 TYR B 655 ARG 0.020 0.001 ARG A 498 Details of bonding type rmsd hydrogen bonds : bond 0.05084 ( 927) hydrogen bonds : angle 6.57151 ( 2607) SS BOND : bond 0.00383 ( 38) SS BOND : angle 1.05828 ( 76) covalent geometry : bond 0.00540 (25557) covalent geometry : angle 0.73185 (34757) Misc. bond : bond 0.00480 ( 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 381 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 312 time to evaluate : 3.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 644 GLN cc_start: 0.8200 (tp40) cc_final: 0.7817 (tt0) REVERT: A 873 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.7294 (m-10) REVERT: B 664 ILE cc_start: 0.7853 (mp) cc_final: 0.7542 (mp) REVERT: B 1102 TRP cc_start: 0.8521 (m100) cc_final: 0.8241 (m-10) REVERT: C 458 LYS cc_start: 0.6756 (mttt) cc_final: 0.6463 (pttp) REVERT: C 697 MET cc_start: 0.7356 (tmm) cc_final: 0.6909 (ttt) outliers start: 69 outliers final: 39 residues processed: 369 average time/residue: 0.3671 time to fit residues: 216.9678 Evaluate side-chains 254 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 214 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR 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 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU 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 1034 LEU Chi-restraints excluded: chain A residue 1097 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 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 791 THR 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 273 ARG Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1012 LEU 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 95 optimal weight: 0.2980 chunk 22 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 224 optimal weight: 20.0000 chunk 173 optimal weight: 0.8980 chunk 152 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 872 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN A1101 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 901 GLN B1048 HIS B1113 GLN B1119 ASN C 207 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 955 ASN C 965 GLN C1002 GLN C1054 GLN C1088 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.213448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.170306 restraints weight = 43909.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.167208 restraints weight = 64446.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.166680 restraints weight = 61014.711| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.7901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.125 25602 Z= 0.363 Angle : 0.858 9.379 34833 Z= 0.456 Chirality : 0.055 0.304 3925 Planarity : 0.006 0.072 4495 Dihedral : 5.655 27.053 3412 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.91 % Allowed : 8.97 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.13), residues: 3136 helix: -0.29 (0.18), residues: 657 sheet: -1.22 (0.18), residues: 709 loop : -2.10 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 886 HIS 0.013 0.002 HIS C1064 PHE 0.031 0.003 PHE B1042 TYR 0.028 0.003 TYR B 789 ARG 0.008 0.001 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.05979 ( 927) hydrogen bonds : angle 6.96281 ( 2607) SS BOND : bond 0.00908 ( 38) SS BOND : angle 1.45495 ( 76) covalent geometry : bond 0.00849 (25557) covalent geometry : angle 0.85586 (34757) Misc. bond : bond 0.00571 ( 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 402 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 293 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 LYS cc_start: 0.5507 (tttt) cc_final: 0.5287 (pttp) REVERT: A 873 TYR cc_start: 0.8940 (OUTLIER) cc_final: 0.8659 (m-10) REVERT: A 905 ARG cc_start: 0.7822 (mtt90) cc_final: 0.6860 (mtt-85) REVERT: A 943 SER cc_start: 0.8214 (OUTLIER) cc_final: 0.7869 (t) REVERT: A 1130 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8479 (mt) REVERT: B 49 HIS cc_start: 0.5249 (t70) cc_final: 0.4862 (t-170) REVERT: B 224 GLU cc_start: 0.6092 (mt-10) cc_final: 0.5820 (pp20) REVERT: B 646 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.5438 (mmt90) REVERT: B 695 TYR cc_start: 0.8010 (p90) cc_final: 0.7619 (p90) REVERT: B 804 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7635 (mp10) REVERT: B 995 ARG cc_start: 0.5974 (mmt90) cc_final: 0.5707 (tpp80) REVERT: B 1002 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: B 1003 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8455 (t) REVERT: B 1017 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7511 (tm-30) REVERT: C 28 TYR cc_start: 0.5634 (m-80) cc_final: 0.5151 (m-80) REVERT: C 88 ASP cc_start: 0.6331 (p0) cc_final: 0.5694 (m-30) REVERT: C 596 SER cc_start: 0.8786 (m) cc_final: 0.8451 (t) REVERT: C 964 LYS cc_start: 0.7887 (mttm) cc_final: 0.7501 (mmmt) REVERT: C 997 ILE cc_start: 0.7510 (mt) cc_final: 0.7273 (mm) outliers start: 109 outliers final: 61 residues processed: 378 average time/residue: 0.3426 time to fit residues: 208.3262 Evaluate side-chains 273 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 206 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 693 ILE 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 761 THR 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 886 TRP Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 943 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 1030 SER Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU 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 760 CYS Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1002 GLN 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 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 1117 THR Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR 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 289 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 796 TYR Chi-restraints excluded: chain C residue 811 LYS 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 1134 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 9 optimal weight: 8.9990 chunk 221 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 308 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 290 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 251 optimal weight: 7.9990 chunk 167 optimal weight: 0.5980 chunk 48 optimal weight: 8.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 872 GLN A 965 GLN A1071 GLN B 81 ASN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 360 ASN B 755 GLN B 895 GLN B1005 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 506 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.215812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.169907 restraints weight = 43995.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.167962 restraints weight = 49026.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.159991 restraints weight = 32024.356| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.8133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25602 Z= 0.161 Angle : 0.594 8.417 34833 Z= 0.311 Chirality : 0.046 0.235 3925 Planarity : 0.004 0.059 4495 Dihedral : 4.746 24.029 3412 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.69 % Allowed : 11.76 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.14), residues: 3136 helix: 0.36 (0.19), residues: 652 sheet: -1.09 (0.18), residues: 709 loop : -1.79 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 64 HIS 0.006 0.001 HIS C 519 PHE 0.023 0.002 PHE A 168 TYR 0.021 0.001 TYR B1007 ARG 0.010 0.000 ARG B 357 Details of bonding type rmsd hydrogen bonds : bond 0.04211 ( 927) hydrogen bonds : angle 6.13385 ( 2607) SS BOND : bond 0.00352 ( 38) SS BOND : angle 1.66330 ( 76) covalent geometry : bond 0.00380 (25557) covalent geometry : angle 0.58914 (34757) Misc. bond : bond 0.00369 ( 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 333 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 258 time to evaluate : 3.815 Fit side-chains revert: symmetry clash REVERT: A 201 PHE cc_start: 0.5634 (t80) cc_final: 0.5315 (t80) REVERT: A 873 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8653 (m-10) REVERT: A 896 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8678 (mt) REVERT: A 905 ARG cc_start: 0.7811 (mtt90) cc_final: 0.6823 (mtt-85) REVERT: B 224 GLU cc_start: 0.6202 (mt-10) cc_final: 0.5505 (pp20) REVERT: B 281 GLU cc_start: 0.4809 (OUTLIER) cc_final: 0.4028 (pp20) REVERT: B 664 ILE cc_start: 0.8144 (mp) cc_final: 0.7943 (mt) REVERT: B 1017 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7304 (tm-30) REVERT: B 1119 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8453 (t0) REVERT: B 1121 PHE cc_start: 0.7065 (OUTLIER) cc_final: 0.5950 (t80) REVERT: C 28 TYR cc_start: 0.5680 (m-80) cc_final: 0.5234 (m-80) REVERT: C 88 ASP cc_start: 0.5968 (p0) cc_final: 0.5490 (m-30) REVERT: C 170 TYR cc_start: 0.4518 (t80) cc_final: 0.4260 (t80) REVERT: C 458 LYS cc_start: 0.7256 (mttt) cc_final: 0.6769 (pptt) REVERT: C 740 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.7352 (tmm) REVERT: C 887 THR cc_start: 0.8003 (OUTLIER) cc_final: 0.7676 (m) outliers start: 75 outliers final: 44 residues processed: 320 average time/residue: 0.5056 time to fit residues: 269.3306 Evaluate side-chains 259 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 3.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 658 ASN 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 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 866 THR Chi-restraints excluded: chain A residue 873 TYR 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 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 281 GLU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 383 SER 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 859 THR Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1074 ASN 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 1119 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 748 GLU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 62 optimal weight: 0.7980 chunk 287 optimal weight: 4.9990 chunk 249 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 chunk 273 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 276 optimal weight: 0.4980 chunk 121 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 255 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 360 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.217211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.173051 restraints weight = 44075.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.170307 restraints weight = 55328.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.171557 restraints weight = 46898.909| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.8414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25602 Z= 0.146 Angle : 0.562 8.172 34833 Z= 0.292 Chirality : 0.045 0.246 3925 Planarity : 0.004 0.058 4495 Dihedral : 4.448 20.978 3412 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.62 % Allowed : 12.70 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3136 helix: 0.58 (0.19), residues: 657 sheet: -0.91 (0.19), residues: 696 loop : -1.67 (0.14), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 104 HIS 0.005 0.001 HIS A 66 PHE 0.021 0.002 PHE B 823 TYR 0.018 0.001 TYR C 91 ARG 0.005 0.000 ARG B 646 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 927) hydrogen bonds : angle 5.89551 ( 2607) SS BOND : bond 0.00287 ( 38) SS BOND : angle 1.39523 ( 76) covalent geometry : bond 0.00344 (25557) covalent geometry : angle 0.55840 (34757) Misc. bond : bond 0.00279 ( 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 318 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 245 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.4122 (m-10) cc_final: 0.3876 (m-80) REVERT: A 765 ARG cc_start: 0.7696 (ttm-80) cc_final: 0.7307 (mtm110) REVERT: A 873 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.8678 (m-10) REVERT: A 896 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8649 (mt) REVERT: B 64 TRP cc_start: 0.5171 (t60) cc_final: 0.4939 (t60) REVERT: B 129 LYS cc_start: 0.5808 (mmtt) cc_final: 0.4627 (mtpt) REVERT: B 177 MET cc_start: 0.1307 (tpt) cc_final: 0.1050 (tpt) REVERT: B 224 GLU cc_start: 0.6177 (mt-10) cc_final: 0.5717 (pp20) REVERT: B 281 GLU cc_start: 0.4931 (OUTLIER) cc_final: 0.4336 (pp20) REVERT: B 664 ILE cc_start: 0.8252 (mp) cc_final: 0.8040 (mt) REVERT: B 765 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7818 (ptp90) REVERT: B 962 LEU cc_start: 0.8857 (mm) cc_final: 0.8645 (mm) REVERT: B 1017 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7237 (tm-30) REVERT: B 1121 PHE cc_start: 0.7105 (OUTLIER) cc_final: 0.5947 (t80) REVERT: C 28 TYR cc_start: 0.5443 (m-80) cc_final: 0.4978 (m-80) REVERT: C 170 TYR cc_start: 0.4174 (t80) cc_final: 0.3945 (t80) REVERT: C 458 LYS cc_start: 0.7127 (mttt) cc_final: 0.6703 (pptt) outliers start: 73 outliers final: 51 residues processed: 302 average time/residue: 0.3322 time to fit residues: 164.2884 Evaluate side-chains 271 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 215 time to evaluate : 2.493 ------------------------------------------------------------------------------- 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 588 THR Chi-restraints excluded: chain A residue 655 TYR 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 734 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 784 GLN 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 896 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 937 SER 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 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 68 ILE Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 281 GLU 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 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 765 ARG Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1068 VAL 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 68 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 219 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 270 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 259 optimal weight: 0.0570 chunk 182 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 360 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN B1119 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** C 901 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 = 0.4624 r_free = 0.4624 target = 0.215430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.173413 restraints weight = 43515.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.164475 restraints weight = 59996.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.157859 restraints weight = 46322.586| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.8628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25602 Z= 0.128 Angle : 0.544 9.464 34833 Z= 0.281 Chirality : 0.044 0.179 3925 Planarity : 0.004 0.060 4495 Dihedral : 4.284 20.249 3412 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.69 % Allowed : 13.13 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.14), residues: 3136 helix: 0.74 (0.20), residues: 657 sheet: -0.80 (0.19), residues: 691 loop : -1.59 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 886 HIS 0.004 0.001 HIS C1064 PHE 0.020 0.001 PHE A 497 TYR 0.017 0.001 TYR B 265 ARG 0.004 0.000 ARG B 577 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 927) hydrogen bonds : angle 5.65497 ( 2607) SS BOND : bond 0.00296 ( 38) SS BOND : angle 1.24177 ( 76) covalent geometry : bond 0.00301 (25557) covalent geometry : angle 0.54180 (34757) Misc. bond : bond 0.00284 ( 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 316 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 241 time to evaluate : 2.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 TYR cc_start: 0.4981 (m-10) cc_final: 0.4536 (m-80) REVERT: A 765 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.7323 (mtm110) REVERT: A 768 THR cc_start: 0.8567 (p) cc_final: 0.8357 (t) REVERT: A 873 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8628 (m-10) REVERT: A 896 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8647 (mt) REVERT: B 64 TRP cc_start: 0.5591 (t60) cc_final: 0.5319 (t60) REVERT: B 129 LYS cc_start: 0.5868 (mmtt) cc_final: 0.4768 (mtpt) REVERT: B 224 GLU cc_start: 0.6238 (mt-10) cc_final: 0.5436 (pp20) REVERT: B 281 GLU cc_start: 0.5151 (OUTLIER) cc_final: 0.4349 (pp20) REVERT: B 1017 GLU cc_start: 0.7572 (tm-30) cc_final: 0.7290 (tm-30) REVERT: B 1119 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8436 (t0) REVERT: C 28 TYR cc_start: 0.5874 (m-80) cc_final: 0.5393 (m-80) REVERT: C 170 TYR cc_start: 0.4724 (t80) cc_final: 0.4519 (t80) REVERT: C 458 LYS cc_start: 0.7208 (mttt) cc_final: 0.6688 (pptt) REVERT: C 957 GLN cc_start: 0.7556 (tm-30) cc_final: 0.7246 (tm-30) REVERT: C 1072 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6402 (mp0) outliers start: 75 outliers final: 56 residues processed: 302 average time/residue: 0.3294 time to fit residues: 165.7660 Evaluate side-chains 286 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 225 time to evaluate : 2.575 ------------------------------------------------------------------------------- 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 568 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 696 THR 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 784 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 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 896 ILE Chi-restraints excluded: chain A residue 934 ILE 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 1030 SER 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 68 ILE Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 281 GLU 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 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 816 SER Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 796 TYR 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 1032 CYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 189 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 54 optimal weight: 20.0000 chunk 287 optimal weight: 5.9990 chunk 125 optimal weight: 0.8980 chunk 20 optimal weight: 20.0000 chunk 265 optimal weight: 9.9990 chunk 126 optimal weight: 0.3980 chunk 214 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1071 GLN B 49 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 317 ASN B 360 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1119 ASN C 239 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.212203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.168263 restraints weight = 43493.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.165437 restraints weight = 54528.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.166361 restraints weight = 49378.379| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.9080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 25602 Z= 0.185 Angle : 0.599 9.265 34833 Z= 0.310 Chirality : 0.046 0.174 3925 Planarity : 0.004 0.067 4495 Dihedral : 4.486 20.224 3412 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.94 % Allowed : 13.52 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 3136 helix: 0.47 (0.19), residues: 663 sheet: -0.71 (0.19), residues: 694 loop : -1.67 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 104 HIS 0.008 0.001 HIS C1064 PHE 0.047 0.002 PHE C 981 TYR 0.034 0.001 TYR B1007 ARG 0.010 0.001 ARG B1091 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 927) hydrogen bonds : angle 5.83377 ( 2607) SS BOND : bond 0.00277 ( 38) SS BOND : angle 1.27791 ( 76) covalent geometry : bond 0.00442 (25557) covalent geometry : angle 0.59692 (34757) Misc. bond : bond 0.00237 ( 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 321 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 239 time to evaluate : 5.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6950 (p0) REVERT: A 765 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7348 (mtm110) REVERT: A 873 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.8777 (m-10) REVERT: A 881 THR cc_start: 0.8430 (m) cc_final: 0.7391 (p) REVERT: A 896 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8792 (mt) REVERT: B 129 LYS cc_start: 0.5928 (mmtt) cc_final: 0.4905 (mtpt) REVERT: B 224 GLU cc_start: 0.6320 (mt-10) cc_final: 0.5755 (pp20) REVERT: B 281 GLU cc_start: 0.5111 (OUTLIER) cc_final: 0.4517 (pp20) REVERT: B 606 ASN cc_start: 0.6982 (t0) cc_final: 0.6736 (p0) REVERT: B 1017 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7235 (tm-30) REVERT: C 28 TYR cc_start: 0.5568 (m-80) cc_final: 0.5102 (m-80) REVERT: C 153 MET cc_start: 0.3743 (tpp) cc_final: 0.3434 (tpt) REVERT: C 170 TYR cc_start: 0.4283 (t80) cc_final: 0.4014 (t80) REVERT: C 458 LYS cc_start: 0.7181 (mttt) cc_final: 0.6707 (pptt) REVERT: C 664 ILE cc_start: 0.8547 (mt) cc_final: 0.8339 (mt) REVERT: C 740 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6973 (tmm) REVERT: C 957 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7333 (tm-30) outliers start: 82 outliers final: 62 residues processed: 302 average time/residue: 0.4571 time to fit residues: 230.0973 Evaluate side-chains 282 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 215 time to evaluate : 3.388 ------------------------------------------------------------------------------- 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 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 655 TYR Chi-restraints excluded: chain A residue 663 ASP 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 760 CYS Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 794 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 896 ILE Chi-restraints excluded: chain A residue 934 ILE 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 1030 SER 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 68 ILE Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 281 GLU 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 734 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1084 ASP Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1120 THR 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 68 ILE Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 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 967 SER Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 49 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 260 optimal weight: 20.0000 chunk 271 optimal weight: 4.9990 chunk 297 optimal weight: 5.9990 chunk 279 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 223 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1011 GLN A1071 GLN A1088 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1011 GLN C 52 GLN C 99 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 HIS ** 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 = 0.4535 r_free = 0.4535 target = 0.206820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.167180 restraints weight = 43323.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.164522 restraints weight = 72003.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.160369 restraints weight = 52759.079| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 1.0049 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= 0.301 Angle : 0.726 9.383 34833 Z= 0.383 Chirality : 0.050 0.282 3925 Planarity : 0.005 0.090 4495 Dihedral : 5.291 23.472 3412 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 3.37 % Allowed : 13.70 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.14), residues: 3136 helix: -0.02 (0.19), residues: 650 sheet: -0.81 (0.19), residues: 682 loop : -1.89 (0.13), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP A 104 HIS 0.011 0.002 HIS C1064 PHE 0.064 0.002 PHE C 981 TYR 0.036 0.002 TYR B1007 ARG 0.014 0.001 ARG B 466 Details of bonding type rmsd hydrogen bonds : bond 0.04725 ( 927) hydrogen bonds : angle 6.40929 ( 2607) SS BOND : bond 0.00933 ( 38) SS BOND : angle 1.81329 ( 76) covalent geometry : bond 0.00711 (25557) covalent geometry : angle 0.72203 (34757) Misc. bond : bond 0.00469 ( 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 329 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 235 time to evaluate : 2.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 881 THR cc_start: 0.8540 (m) cc_final: 0.7515 (p) REVERT: A 896 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8831 (mt) REVERT: B 129 LYS cc_start: 0.5959 (mmtt) cc_final: 0.4760 (mtpt) REVERT: B 224 GLU cc_start: 0.6712 (mt-10) cc_final: 0.5936 (pp20) REVERT: B 281 GLU cc_start: 0.5363 (OUTLIER) cc_final: 0.4823 (pp20) REVERT: B 577 ARG cc_start: 0.3425 (mmt90) cc_final: 0.2779 (ptm160) REVERT: B 695 TYR cc_start: 0.8064 (p90) cc_final: 0.7399 (p90) REVERT: C 137 ASN cc_start: 0.6850 (m110) cc_final: 0.6581 (t0) REVERT: C 170 TYR cc_start: 0.4201 (t80) cc_final: 0.3918 (t80) REVERT: C 228 ASP cc_start: 0.5789 (t0) cc_final: 0.5328 (m-30) REVERT: C 458 LYS cc_start: 0.7354 (mttt) cc_final: 0.6820 (pptt) REVERT: C 740 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7156 (tmm) REVERT: C 957 GLN cc_start: 0.7941 (tm-30) cc_final: 0.7615 (tm-30) outliers start: 94 outliers final: 75 residues processed: 314 average time/residue: 0.4787 time to fit residues: 255.9702 Evaluate side-chains 282 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 204 time to evaluate : 4.232 ------------------------------------------------------------------------------- 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 312 ILE 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 599 THR Chi-restraints excluded: chain A residue 663 ASP 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 732 THR 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 784 GLN Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 934 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 1005 GLN Chi-restraints excluded: chain A residue 1030 SER 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 68 ILE Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 281 GLU 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 608 VAL Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1084 ASP 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 1120 THR 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 68 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 796 TYR 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 967 SER Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1067 TYR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 295 optimal weight: 0.9980 chunk 288 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 308 optimal weight: 0.7980 chunk 307 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 302 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A 992 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 282 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS C 564 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.211503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.168003 restraints weight = 44184.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.164809 restraints weight = 54995.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.166214 restraints weight = 49703.702| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 1.0041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25602 Z= 0.132 Angle : 0.580 9.544 34833 Z= 0.301 Chirality : 0.045 0.219 3925 Planarity : 0.004 0.063 4495 Dihedral : 4.655 19.769 3412 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.40 % Allowed : 14.81 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3136 helix: 0.40 (0.19), residues: 664 sheet: -0.65 (0.20), residues: 660 loop : -1.70 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.003 TRP A 104 HIS 0.005 0.001 HIS A1088 PHE 0.053 0.002 PHE C 981 TYR 0.036 0.001 TYR A 904 ARG 0.007 0.000 ARG C 815 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 927) hydrogen bonds : angle 5.80129 ( 2607) SS BOND : bond 0.00270 ( 38) SS BOND : angle 1.39521 ( 76) covalent geometry : bond 0.00306 (25557) covalent geometry : angle 0.57722 (34757) Misc. bond : bond 0.00298 ( 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 304 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 237 time to evaluate : 5.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.5949 (mp) cc_final: 0.5674 (tt) REVERT: A 765 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7417 (mtm110) REVERT: A 886 TRP cc_start: 0.7343 (p90) cc_final: 0.7018 (p90) REVERT: A 896 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8744 (mt) REVERT: B 129 LYS cc_start: 0.6124 (mmtt) cc_final: 0.4965 (mtpt) REVERT: B 224 GLU cc_start: 0.6460 (mt-10) cc_final: 0.5672 (pp20) REVERT: B 281 GLU cc_start: 0.5291 (OUTLIER) cc_final: 0.4854 (pp20) REVERT: B 303 LEU cc_start: 0.7767 (mm) cc_final: 0.7286 (pp) REVERT: B 577 ARG cc_start: 0.3109 (mmt90) cc_final: 0.2631 (ptm160) REVERT: B 1017 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7234 (tm-30) REVERT: C 137 ASN cc_start: 0.6713 (m110) cc_final: 0.6448 (t0) REVERT: C 170 TYR cc_start: 0.4389 (t80) cc_final: 0.4129 (t80) REVERT: C 228 ASP cc_start: 0.5451 (t0) cc_final: 0.5131 (m-30) REVERT: C 458 LYS cc_start: 0.7179 (mttt) cc_final: 0.6678 (pptt) REVERT: C 740 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6947 (tmm) REVERT: C 957 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7593 (tm-30) REVERT: C 970 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.7072 (t80) REVERT: C 1072 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6319 (mp0) outliers start: 67 outliers final: 50 residues processed: 289 average time/residue: 0.5118 time to fit residues: 249.9421 Evaluate side-chains 261 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 2.848 ------------------------------------------------------------------------------- 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 588 THR Chi-restraints excluded: chain A residue 599 THR 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 760 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 784 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 934 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1030 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 68 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1068 VAL 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 68 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR 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 970 PHE Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 280 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 202 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 154 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 125 optimal weight: 0.0770 chunk 271 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.211300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.171656 restraints weight = 43856.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 86)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.165481 restraints weight = 70454.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.158974 restraints weight = 54452.968| |-----------------------------------------------------------------------------| r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 1.0077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 1.157 25602 Z= 0.392 Angle : 0.829 67.878 34833 Z= 0.415 Chirality : 0.049 1.010 3925 Planarity : 0.005 0.124 4495 Dihedral : 4.628 20.059 3412 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.44 % Rotamer: Outliers : 1.97 % Allowed : 15.93 % Favored : 82.10 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3136 helix: 0.43 (0.19), residues: 664 sheet: -0.63 (0.20), residues: 660 loop : -1.69 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP A 104 HIS 0.008 0.001 HIS C 519 PHE 0.050 0.002 PHE C 981 TYR 0.036 0.002 TYR B 741 ARG 0.010 0.000 ARG C 567 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 927) hydrogen bonds : angle 5.80110 ( 2607) SS BOND : bond 0.00267 ( 38) SS BOND : angle 1.35018 ( 76) covalent geometry : bond 0.00985 (25557) covalent geometry : angle 0.82785 (34757) Misc. bond : bond 0.06867 ( 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 260 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 205 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.6287 (mp) cc_final: 0.5952 (tt) REVERT: A 765 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7404 (mtm110) REVERT: A 886 TRP cc_start: 0.7615 (p90) cc_final: 0.7290 (p90) REVERT: A 896 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8644 (mt) REVERT: B 129 LYS cc_start: 0.6217 (mmtt) cc_final: 0.4977 (mtpt) REVERT: B 281 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.4825 (pp20) REVERT: B 303 LEU cc_start: 0.7827 (mm) cc_final: 0.7292 (pp) REVERT: B 577 ARG cc_start: 0.3547 (mmt90) cc_final: 0.2999 (ptm160) REVERT: B 1017 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7211 (tm-30) REVERT: C 137 ASN cc_start: 0.6949 (m110) cc_final: 0.6497 (t0) REVERT: C 170 TYR cc_start: 0.4705 (t80) cc_final: 0.4449 (t80) REVERT: C 228 ASP cc_start: 0.5649 (t0) cc_final: 0.5283 (m-30) REVERT: C 458 LYS cc_start: 0.7220 (mttt) cc_final: 0.6673 (pptt) REVERT: C 740 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.6992 (tmm) REVERT: C 957 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7578 (tm-30) REVERT: C 1072 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6249 (mp0) outliers start: 55 outliers final: 51 residues processed: 247 average time/residue: 0.3520 time to fit residues: 145.3452 Evaluate side-chains 258 residues out of total 2788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 203 time to evaluate : 2.460 ------------------------------------------------------------------------------- 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 285 ILE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 784 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 934 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1030 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 68 ILE Chi-restraints excluded: chain B residue 281 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 962 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1068 VAL 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 68 ILE Chi-restraints excluded: chain C residue 108 THR 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 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR 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 1032 CYS Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1134 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 292 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 chunk 315 optimal weight: 0.9990 chunk 316 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 chunk 291 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 106 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.211376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.167757 restraints weight = 43784.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.164803 restraints weight = 51089.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.165187 restraints weight = 48161.661| |-----------------------------------------------------------------------------| r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 1.0080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 1.750 25602 Z= 0.534 Angle : 0.914 68.692 34833 Z= 0.461 Chirality : 0.051 1.354 3925 Planarity : 0.004 0.063 4495 Dihedral : 4.624 25.371 3412 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.08 % Allowed : 15.75 % Favored : 82.17 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3136 helix: 0.43 (0.19), residues: 664 sheet: -0.63 (0.20), residues: 660 loop : -1.69 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP A 104 HIS 0.005 0.001 HIS C 519 PHE 0.047 0.002 PHE C 981 TYR 0.031 0.001 TYR B 741 ARG 0.008 0.000 ARG C 567 Details of bonding type rmsd hydrogen bonds : bond 0.03813 ( 927) hydrogen bonds : angle 5.80323 ( 2607) SS BOND : bond 0.00258 ( 38) SS BOND : angle 1.34624 ( 76) covalent geometry : bond 0.01286 (25557) covalent geometry : angle 0.91306 (34757) Misc. bond : bond 0.09164 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9360.02 seconds wall clock time: 169 minutes 20.97 seconds (10160.97 seconds total)