Starting phenix.real_space_refine on Fri Sep 19 13:30:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ljr_23400/09_2025/7ljr_23400.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ljr_23400/09_2025/7ljr_23400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ljr_23400/09_2025/7ljr_23400.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ljr_23400/09_2025/7ljr_23400.map" model { file = "/net/cci-nas-00/data/ceres_data/7ljr_23400/09_2025/7ljr_23400.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ljr_23400/09_2025/7ljr_23400.cif" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.046 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 112 5.16 5 C 16767 2.51 5 N 4376 2.21 5 O 5036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 148 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26291 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7597 Classifications: {'peptide': 972} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 7604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7604 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 11 Chain: "S" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1694 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 213} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "T" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1573 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 195} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 5.49, per 1000 atoms: 0.21 Number of scatterers: 26291 At special positions: 0 Unit cell: (133.308, 156.584, 221.122, 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 112 16.00 O 5036 8.00 N 4376 7.00 C 16767 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 954.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6330 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 50 sheets defined 24.8% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.675A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.856A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.467A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.067A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.635A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.118A 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 913 through 919 removed outlier: 3.689A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 941 through 944 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.703A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) 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: 3.759A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.118A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 4.209A pdb=" N LEU A1145 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 616 through 620 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 756 removed outlier: 4.446A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.600A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 4.452A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (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 907 removed outlier: 3.812A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 918 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 967 removed outlier: 3.554A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.339A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 342 removed outlier: 4.473A pdb=" N PHE C 342 " --> pdb=" O GLY C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.794A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 616 through 620 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.791A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.608A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.361A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.954A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.019A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) 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 967 removed outlier: 3.505A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.636A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.986A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1145 Processing helix chain 'S' and resid 44 through 50 removed outlier: 4.483A pdb=" N PHE S 48 " --> pdb=" O GLY S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 110 Processing helix chain 'S' and resid 120 through 124 removed outlier: 3.544A pdb=" N ASP S 123 " --> pdb=" O TYR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 158 No H-bonds generated for 'chain 'S' and resid 156 through 158' Processing helix chain 'S' and resid 185 through 187 No H-bonds generated for 'chain 'S' and resid 185 through 187' Processing helix chain 'S' and resid 216 through 218 No H-bonds generated for 'chain 'S' and resid 216 through 218' Processing helix chain 'S' and resid 230 through 233 Processing helix chain 'T' and resid 140 through 147 Processing helix chain 'T' and resid 202 through 208 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.983A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 44 removed outlier: 5.582A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.802A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.893A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.171A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.654A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.277A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.882A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 656 removed outlier: 5.913A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.850A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.850A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 5.539A pdb=" N VAL A1122 " --> pdb=" O PHE A1089 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A1089 " --> pdb=" O VAL A1122 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY A1124 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.476A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.069A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.983A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.299A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.212A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 334 through 335 removed outlier: 6.609A pdb=" N ASN B 334 " --> pdb=" O VAL B 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 377 through 379 removed outlier: 3.812A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 656 removed outlier: 4.305A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.858A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD1, first strand: chain 'B' and resid 1086 through 1090 removed outlier: 4.685A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.210A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.410A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 50 through 55 removed outlier: 7.169A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.221A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.262A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 357 through 358 Processing sheet with id=AD9, first strand: chain 'C' and resid 376 through 379 removed outlier: 3.891A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 656 removed outlier: 4.458A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.645A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.645A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.350A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 5.214A pdb=" N VAL C1122 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE C1089 " --> pdb=" O VAL C1122 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLY C1124 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 38 through 42 Processing sheet with id=AE7, first strand: chain 'S' and resid 77 through 79 removed outlier: 5.258A pdb=" N TRP S 66 " --> pdb=" O ARG S 57 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ARG S 57 " --> pdb=" O TRP S 66 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 149 through 153 removed outlier: 4.970A pdb=" N ALA S 166 " --> pdb=" O VAL S 213 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL S 213 " --> pdb=" O ALA S 166 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLY S 168 " --> pdb=" O VAL S 211 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL S 211 " --> pdb=" O GLY S 168 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEU S 170 " --> pdb=" O SER S 209 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER S 209 " --> pdb=" O LEU S 170 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LYS S 172 " --> pdb=" O LEU S 207 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU S 207 " --> pdb=" O LYS S 172 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 160 through 161 removed outlier: 3.511A pdb=" N THR S 164 " --> pdb=" O SER S 161 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ALA S 166 " --> pdb=" O VAL S 213 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL S 213 " --> pdb=" O ALA S 166 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLY S 168 " --> pdb=" O VAL S 211 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL S 211 " --> pdb=" O GLY S 168 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N LEU S 170 " --> pdb=" O SER S 209 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER S 209 " --> pdb=" O LEU S 170 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LYS S 172 " --> pdb=" O LEU S 207 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N LEU S 207 " --> pdb=" O LYS S 172 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'S' and resid 182 through 183 Processing sheet with id=AF2, first strand: chain 'T' and resid 29 through 32 Processing sheet with id=AF3, first strand: chain 'T' and resid 65 through 68 removed outlier: 6.589A pdb=" N TRP T 55 " --> pdb=" O LEU T 67 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLN T 109 " --> pdb=" O LEU T 53 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TRP T 55 " --> pdb=" O TYR T 107 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR T 107 " --> pdb=" O TRP T 55 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN T 57 " --> pdb=" O VAL T 105 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL T 105 " --> pdb=" O GLN T 57 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 133 through 137 removed outlier: 5.043A pdb=" N TYR T 192 " --> pdb=" O ASN T 157 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER T 181 " --> pdb=" O SER T 195 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 172 through 174 1056 hydrogen bonds defined for protein. 2829 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.32 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6970 1.33 - 1.46: 5231 1.46 - 1.58: 14538 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 26877 Sorted by residual: bond pdb=" CA PRO A 862 " pdb=" C PRO A 862 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.42e+01 bond pdb=" N VAL A 130 " pdb=" CA VAL A 130 " ideal model delta sigma weight residual 1.455 1.493 -0.037 1.04e-02 9.25e+03 1.29e+01 bond pdb=" CA ALA C 411 " pdb=" C ALA C 411 " ideal model delta sigma weight residual 1.519 1.557 -0.038 1.09e-02 8.42e+03 1.23e+01 bond pdb=" CA PRO B 862 " pdb=" C PRO B 862 " ideal model delta sigma weight residual 1.517 1.540 -0.023 6.70e-03 2.23e+04 1.14e+01 bond pdb=" CZ ARG B 454 " pdb=" NH2 ARG B 454 " ideal model delta sigma weight residual 1.330 1.288 0.042 1.30e-02 5.92e+03 1.06e+01 ... (remaining 26872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 29717 2.37 - 4.75: 6367 4.75 - 7.12: 439 7.12 - 9.50: 31 9.50 - 11.87: 3 Bond angle restraints: 36557 Sorted by residual: angle pdb=" CA PHE B 515 " pdb=" CB PHE B 515 " pdb=" CG PHE B 515 " ideal model delta sigma weight residual 113.80 124.63 -10.83 1.00e+00 1.00e+00 1.17e+02 angle pdb=" CA PHE S 129 " pdb=" CB PHE S 129 " pdb=" CG PHE S 129 " ideal model delta sigma weight residual 113.80 121.25 -7.45 1.00e+00 1.00e+00 5.55e+01 angle pdb=" CA PRO T 27 " pdb=" N PRO T 27 " pdb=" CD PRO T 27 " ideal model delta sigma weight residual 112.00 102.02 9.98 1.40e+00 5.10e-01 5.08e+01 angle pdb=" CA ASP C 737 " pdb=" CB ASP C 737 " pdb=" CG ASP C 737 " ideal model delta sigma weight residual 112.60 106.23 6.37 1.00e+00 1.00e+00 4.05e+01 angle pdb=" CA PHE B 392 " pdb=" CB PHE B 392 " pdb=" CG PHE B 392 " ideal model delta sigma weight residual 113.80 119.73 -5.93 1.00e+00 1.00e+00 3.52e+01 ... (remaining 36552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 14672 17.91 - 35.82: 1000 35.82 - 53.73: 164 53.73 - 71.64: 47 71.64 - 89.56: 38 Dihedral angle restraints: 15921 sinusoidal: 6099 harmonic: 9822 Sorted by residual: dihedral pdb=" CA LYS B 113 " pdb=" C LYS B 113 " pdb=" N THR B 114 " pdb=" CA THR B 114 " ideal model delta harmonic sigma weight residual 180.00 150.00 30.00 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ALA C 522 " pdb=" C ALA C 522 " pdb=" N THR C 523 " pdb=" CA THR C 523 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA LYS B 97 " pdb=" C LYS B 97 " pdb=" N SER B 98 " pdb=" CA SER B 98 " ideal model delta harmonic sigma weight residual 180.00 -150.04 -29.96 0 5.00e+00 4.00e-02 3.59e+01 ... (remaining 15918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2636 0.085 - 0.169: 1274 0.169 - 0.254: 215 0.254 - 0.339: 37 0.339 - 0.424: 12 Chirality restraints: 4174 Sorted by residual: chirality pdb=" CA ARG C 983 " pdb=" N ARG C 983 " pdb=" C ARG C 983 " pdb=" CB ARG C 983 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" CA ASP B 198 " pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CB ASP B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.30e+00 chirality pdb=" CA TYR S 120 " pdb=" N TYR S 120 " pdb=" C TYR S 120 " pdb=" CB TYR S 120 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 4171 not shown) Planarity restraints: 4724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 917 " 0.236 2.00e-02 2.50e+03 1.33e-01 3.56e+02 pdb=" CG TYR A 917 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 917 " -0.096 2.00e-02 2.50e+03 pdb=" CD2 TYR A 917 " -0.136 2.00e-02 2.50e+03 pdb=" CE1 TYR A 917 " -0.100 2.00e-02 2.50e+03 pdb=" CE2 TYR A 917 " -0.067 2.00e-02 2.50e+03 pdb=" CZ TYR A 917 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 917 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " 0.170 2.00e-02 2.50e+03 9.62e-02 2.31e+02 pdb=" CG TRP A 886 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " -0.108 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " -0.070 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " -0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " -0.141 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.093 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " 0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 707 " 0.200 2.00e-02 2.50e+03 1.07e-01 2.29e+02 pdb=" CG TYR B 707 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR B 707 " -0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR B 707 " -0.097 2.00e-02 2.50e+03 pdb=" CE1 TYR B 707 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TYR B 707 " -0.053 2.00e-02 2.50e+03 pdb=" CZ TYR B 707 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 707 " 0.154 2.00e-02 2.50e+03 ... (remaining 4721 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 13393 2.99 - 3.47: 27658 3.47 - 3.94: 45086 3.94 - 4.42: 50828 4.42 - 4.90: 84002 Nonbonded interactions: 220967 Sorted by model distance: nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.509 3.040 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.517 3.040 nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.520 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OE1 GLU C 918 " model vdw 2.521 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.525 3.040 ... (remaining 220962 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 27 through 444 or resid 447 through 452 or (resid 453 and \ (name N or name CA or name C or name O or name CB )) or resid 454 or resid 462 t \ hrough 468 or resid 489 through 501 or resid 503 through 1147)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 452 or (resid 453 and (name N or name CA or nam \ e C or name O or name CB )) or resid 454 through 1147)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.550 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 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 : 0.013 0.046 26877 Z= 0.750 Angle : 1.827 11.874 36557 Z= 1.215 Chirality : 0.095 0.424 4174 Planarity : 0.015 0.133 4724 Dihedral : 13.960 89.556 9591 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.82 % Allowed : 9.15 % Favored : 90.03 % Rotamer: Outliers : 1.12 % Allowed : 4.69 % Favored : 94.19 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.13), residues: 3310 helix: -0.87 (0.17), residues: 660 sheet: -0.28 (0.23), residues: 469 loop : -1.70 (0.12), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG A 102 TYR 0.236 0.025 TYR A 917 PHE 0.092 0.014 PHE A 927 TRP 0.172 0.033 TRP S 66 HIS 0.016 0.003 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01275 (26877) covalent geometry : angle 1.82658 (36557) hydrogen bonds : bond 0.14308 ( 1035) hydrogen bonds : angle 8.74513 ( 2829) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 0.917 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 317 ASN cc_start: 0.7645 (m-40) cc_final: 0.7435 (m-40) REVERT: C 902 MET cc_start: 0.8831 (mmm) cc_final: 0.8579 (mmm) outliers start: 33 outliers final: 10 residues processed: 265 average time/residue: 0.2136 time to fit residues: 86.0126 Evaluate side-chains 105 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 122 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 66 HIS A 655 HIS A 901 GLN B 134 GLN B 343 ASN B 360 ASN B 450 ASN B 675 GLN B 762 GLN C 66 HIS C1101 HIS C1119 ASN S 54 ASN S 58 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.105511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.082324 restraints weight = 108929.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.079935 restraints weight = 78295.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.080664 restraints weight = 70128.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.081164 restraints weight = 49526.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.081290 restraints weight = 46212.836| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26877 Z= 0.150 Angle : 0.680 13.148 36557 Z= 0.368 Chirality : 0.046 0.171 4174 Planarity : 0.005 0.081 4724 Dihedral : 7.176 51.806 3617 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.68 % Favored : 95.17 % Rotamer: Outliers : 1.63 % Allowed : 8.12 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.14), residues: 3310 helix: 0.68 (0.20), residues: 664 sheet: -0.44 (0.19), residues: 678 loop : -1.36 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG T 161 TYR 0.027 0.002 TYR C 423 PHE 0.043 0.002 PHE B 135 TRP 0.018 0.003 TRP A 64 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00313 (26877) covalent geometry : angle 0.68033 (36557) hydrogen bonds : bond 0.04835 ( 1035) hydrogen bonds : angle 6.67369 ( 2829) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.6925 (t80) cc_final: 0.6584 (t80) REVERT: A 429 PHE cc_start: 0.8083 (t80) cc_final: 0.7818 (t80) REVERT: B 135 PHE cc_start: 0.5887 (m-80) cc_final: 0.5556 (m-80) REVERT: B 819 GLU cc_start: 0.7304 (mt-10) cc_final: 0.6941 (mt-10) REVERT: B 1019 ARG cc_start: 0.8211 (ttp-110) cc_final: 0.7847 (ttp80) REVERT: C 518 LEU cc_start: 0.5063 (OUTLIER) cc_final: 0.4797 (pt) REVERT: C 553 THR cc_start: 0.8438 (OUTLIER) cc_final: 0.7903 (p) REVERT: T 78 ILE cc_start: 0.1409 (mp) cc_final: 0.0958 (tp) outliers start: 48 outliers final: 28 residues processed: 191 average time/residue: 0.1820 time to fit residues: 55.9222 Evaluate side-chains 134 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain T residue 33 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 267 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 156 optimal weight: 0.7980 chunk 212 optimal weight: 9.9990 chunk 309 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 299 optimal weight: 0.9980 chunk 216 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 901 GLN C 675 GLN ** S 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.102829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.079561 restraints weight = 108881.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.077051 restraints weight = 76617.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.077956 restraints weight = 82342.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.077678 restraints weight = 59672.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.077800 restraints weight = 51108.050| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 26877 Z= 0.249 Angle : 0.694 13.548 36557 Z= 0.369 Chirality : 0.046 0.176 4174 Planarity : 0.005 0.050 4724 Dihedral : 6.544 50.258 3612 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.01 % Favored : 93.87 % Rotamer: Outliers : 1.94 % Allowed : 9.99 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.14), residues: 3310 helix: 0.52 (0.20), residues: 654 sheet: -0.75 (0.18), residues: 743 loop : -1.34 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 995 TYR 0.020 0.002 TYR A 695 PHE 0.038 0.002 PHE B 429 TRP 0.015 0.002 TRP S 66 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00547 (26877) covalent geometry : angle 0.69414 (36557) hydrogen bonds : bond 0.04806 ( 1035) hydrogen bonds : angle 6.51563 ( 2829) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 111 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7127 (t80) cc_final: 0.6766 (t80) REVERT: A 878 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8303 (mp) REVERT: A 1130 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7887 (tp) REVERT: B 135 PHE cc_start: 0.6494 (m-80) cc_final: 0.6039 (m-80) REVERT: B 351 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6723 (p90) REVERT: B 380 TYR cc_start: 0.8126 (m-80) cc_final: 0.7864 (m-10) REVERT: B 396 TYR cc_start: 0.6402 (OUTLIER) cc_final: 0.6188 (m-80) REVERT: B 406 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: B 819 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7413 (mt-10) REVERT: C 266 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: C 493 GLN cc_start: 0.2713 (OUTLIER) cc_final: 0.1639 (tp40) REVERT: C 553 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8235 (p) REVERT: C 1051 SER cc_start: 0.8193 (m) cc_final: 0.7768 (p) REVERT: T 78 ILE cc_start: 0.1748 (mp) cc_final: 0.1337 (tp) outliers start: 57 outliers final: 36 residues processed: 163 average time/residue: 0.1716 time to fit residues: 45.1416 Evaluate side-chains 136 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 92 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 136 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 328 optimal weight: 8.9990 chunk 326 optimal weight: 8.9990 chunk 227 optimal weight: 20.0000 chunk 62 optimal weight: 0.0570 chunk 259 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 305 optimal weight: 20.0000 chunk 262 optimal weight: 0.6980 chunk 142 optimal weight: 8.9990 chunk 267 optimal weight: 0.9990 chunk 332 optimal weight: 10.0000 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN B 343 ASN C 61 ASN ** S 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.104340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.081066 restraints weight = 108616.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.078606 restraints weight = 80057.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.079387 restraints weight = 73683.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.079692 restraints weight = 50829.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.079876 restraints weight = 47668.469| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26877 Z= 0.134 Angle : 0.593 13.814 36557 Z= 0.313 Chirality : 0.044 0.178 4174 Planarity : 0.004 0.055 4724 Dihedral : 5.937 42.527 3610 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.02 % Favored : 94.86 % Rotamer: Outliers : 2.21 % Allowed : 10.53 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.14), residues: 3310 helix: 0.90 (0.20), residues: 652 sheet: -0.77 (0.18), residues: 753 loop : -1.18 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 237 TYR 0.021 0.001 TYR S 122 PHE 0.023 0.001 PHE B 515 TRP 0.011 0.001 TRP S 66 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00286 (26877) covalent geometry : angle 0.59326 (36557) hydrogen bonds : bond 0.04102 ( 1035) hydrogen bonds : angle 6.10157 ( 2829) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 112 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7218 (t80) cc_final: 0.6850 (t80) REVERT: A 619 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7132 (mp0) REVERT: A 786 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.8048 (pmtt) REVERT: A 878 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8253 (mp) REVERT: B 135 PHE cc_start: 0.6290 (m-80) cc_final: 0.5929 (m-80) REVERT: B 231 ILE cc_start: 0.8545 (mp) cc_final: 0.8296 (pt) REVERT: B 380 TYR cc_start: 0.7949 (m-80) cc_final: 0.7694 (m-10) REVERT: C 231 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7309 (mm) REVERT: C 266 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7739 (m-80) REVERT: C 518 LEU cc_start: 0.5745 (OUTLIER) cc_final: 0.5037 (pt) REVERT: C 856 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8122 (t0) REVERT: C 1051 SER cc_start: 0.8210 (m) cc_final: 0.7555 (p) REVERT: S 228 ASN cc_start: 0.7135 (t0) cc_final: 0.6930 (t0) REVERT: T 124 GLU cc_start: 0.5023 (mp0) cc_final: 0.4740 (mp0) outliers start: 65 outliers final: 30 residues processed: 171 average time/residue: 0.1718 time to fit residues: 47.8181 Evaluate side-chains 133 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 97 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 396 TYR Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain T residue 33 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 101 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 312 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 148 optimal weight: 0.0010 chunk 231 optimal weight: 6.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 448 ASN B 498 GLN ** S 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.103706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.080044 restraints weight = 108326.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.077633 restraints weight = 70125.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.078246 restraints weight = 69989.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.078610 restraints weight = 49057.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.078796 restraints weight = 44213.163| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26877 Z= 0.161 Angle : 0.591 13.131 36557 Z= 0.310 Chirality : 0.044 0.165 4174 Planarity : 0.004 0.048 4724 Dihedral : 5.737 42.967 3609 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.68 % Favored : 94.20 % Rotamer: Outliers : 1.90 % Allowed : 11.18 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.14), residues: 3310 helix: 1.00 (0.20), residues: 656 sheet: -0.62 (0.19), residues: 718 loop : -1.18 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.021 0.002 TYR S 122 PHE 0.033 0.002 PHE B 429 TRP 0.011 0.001 TRP B 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00354 (26877) covalent geometry : angle 0.59093 (36557) hydrogen bonds : bond 0.04088 ( 1035) hydrogen bonds : angle 6.02746 ( 2829) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 102 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7278 (t80) cc_final: 0.6875 (t80) REVERT: A 511 VAL cc_start: 0.8995 (t) cc_final: 0.8698 (m) REVERT: A 533 LEU cc_start: 0.8223 (tt) cc_final: 0.7462 (mp) REVERT: A 878 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8213 (mp) REVERT: A 1130 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8033 (tp) REVERT: B 135 PHE cc_start: 0.6474 (m-80) cc_final: 0.6042 (m-80) REVERT: B 231 ILE cc_start: 0.8654 (mp) cc_final: 0.8413 (pt) REVERT: B 242 LEU cc_start: 0.8272 (mp) cc_final: 0.7772 (tp) REVERT: B 532 ASN cc_start: 0.8974 (t0) cc_final: 0.8749 (t0) REVERT: B 819 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7190 (mt-10) REVERT: C 231 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7435 (mm) REVERT: C 266 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: C 294 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7447 (p0) REVERT: C 518 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5219 (pt) REVERT: C 856 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.8101 (t0) REVERT: C 1051 SER cc_start: 0.8105 (m) cc_final: 0.7699 (p) REVERT: S 67 MET cc_start: 0.5679 (mtm) cc_final: 0.5259 (mtm) outliers start: 56 outliers final: 33 residues processed: 152 average time/residue: 0.1793 time to fit residues: 44.4018 Evaluate side-chains 133 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 93 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 225 CYS Chi-restraints excluded: chain T residue 136 ILE Chi-restraints excluded: chain T residue 214 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 191 optimal weight: 0.2980 chunk 145 optimal weight: 0.0980 chunk 310 optimal weight: 50.0000 chunk 82 optimal weight: 0.7980 chunk 166 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 235 optimal weight: 0.0070 chunk 91 optimal weight: 0.8980 chunk 295 optimal weight: 30.0000 chunk 234 optimal weight: 9.9990 chunk 37 optimal weight: 0.0770 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 969 ASN C 955 ASN C1135 ASN ** T 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.105723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.082328 restraints weight = 109339.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.079662 restraints weight = 71441.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.080311 restraints weight = 70107.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.080710 restraints weight = 48986.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.080953 restraints weight = 44918.401| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 26877 Z= 0.102 Angle : 0.556 12.671 36557 Z= 0.290 Chirality : 0.043 0.166 4174 Planarity : 0.004 0.058 4724 Dihedral : 5.234 33.638 3607 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.77 % Favored : 95.14 % Rotamer: Outliers : 1.66 % Allowed : 11.65 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.15), residues: 3310 helix: 1.32 (0.20), residues: 652 sheet: -0.61 (0.19), residues: 742 loop : -0.98 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 50 TYR 0.019 0.001 TYR C 423 PHE 0.022 0.001 PHE A 374 TRP 0.033 0.001 TRP A 436 HIS 0.005 0.000 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00210 (26877) covalent geometry : angle 0.55619 (36557) hydrogen bonds : bond 0.03613 ( 1035) hydrogen bonds : angle 5.67208 ( 2829) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 128 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.6807 (t80) cc_final: 0.6533 (t80) REVERT: A 387 LEU cc_start: 0.8857 (mt) cc_final: 0.8644 (mt) REVERT: A 533 LEU cc_start: 0.8094 (tt) cc_final: 0.7602 (mp) REVERT: A 878 LEU cc_start: 0.8327 (tp) cc_final: 0.8021 (mp) REVERT: B 135 PHE cc_start: 0.6457 (m-80) cc_final: 0.6183 (m-80) REVERT: B 242 LEU cc_start: 0.8337 (mp) cc_final: 0.7934 (tp) REVERT: C 231 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7409 (mm) REVERT: C 518 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5290 (pt) REVERT: C 1051 SER cc_start: 0.8030 (m) cc_final: 0.7751 (p) outliers start: 49 outliers final: 27 residues processed: 169 average time/residue: 0.1677 time to fit residues: 46.5933 Evaluate side-chains 124 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 225 CYS Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 136 ILE Chi-restraints excluded: chain T residue 214 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 285 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 263 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 335 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 121 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 ASN B 343 ASN B 762 GLN B1088 HIS C1106 GLN ** S 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 228 ASN ** T 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.104535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.081748 restraints weight = 108526.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.079470 restraints weight = 63008.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.080340 restraints weight = 65285.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.080309 restraints weight = 47664.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.081188 restraints weight = 41925.398| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26877 Z= 0.225 Angle : 0.617 12.706 36557 Z= 0.323 Chirality : 0.045 0.224 4174 Planarity : 0.005 0.056 4724 Dihedral : 5.372 34.267 3605 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.68 % Favored : 94.23 % Rotamer: Outliers : 1.94 % Allowed : 12.33 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.14), residues: 3310 helix: 1.02 (0.20), residues: 658 sheet: -0.67 (0.19), residues: 759 loop : -1.07 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 50 TYR 0.030 0.002 TYR B 380 PHE 0.032 0.002 PHE B 515 TRP 0.016 0.001 TRP A 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00503 (26877) covalent geometry : angle 0.61749 (36557) hydrogen bonds : bond 0.04199 ( 1035) hydrogen bonds : angle 5.91989 ( 2829) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 87 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.7128 (t80) cc_final: 0.6718 (t80) REVERT: A 1130 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8120 (tp) REVERT: B 135 PHE cc_start: 0.6493 (m-80) cc_final: 0.6248 (m-80) REVERT: B 242 LEU cc_start: 0.8329 (mp) cc_final: 0.7775 (tp) REVERT: B 406 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6424 (pm20) REVERT: C 266 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7663 (m-80) REVERT: C 518 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5303 (pt) REVERT: S 67 MET cc_start: 0.5968 (mtm) cc_final: 0.5395 (mtm) outliers start: 57 outliers final: 42 residues processed: 138 average time/residue: 0.1461 time to fit residues: 34.6995 Evaluate side-chains 126 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 80 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 225 CYS Chi-restraints excluded: chain T residue 33 SER Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 136 ILE Chi-restraints excluded: chain T residue 214 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 333 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 299 optimal weight: 20.0000 chunk 259 optimal weight: 0.9980 chunk 193 optimal weight: 0.0980 chunk 314 optimal weight: 30.0000 chunk 276 optimal weight: 4.9990 chunk 228 optimal weight: 30.0000 chunk 101 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 302 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN B 613 GLN B 762 GLN ** T 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.106374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.083610 restraints weight = 109084.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.081890 restraints weight = 62883.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.082512 restraints weight = 56024.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.083030 restraints weight = 41366.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.083025 restraints weight = 37621.077| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26877 Z= 0.111 Angle : 0.557 12.586 36557 Z= 0.288 Chirality : 0.044 0.225 4174 Planarity : 0.004 0.052 4724 Dihedral : 5.110 33.642 3605 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.14 % Rotamer: Outliers : 1.80 % Allowed : 12.43 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.15), residues: 3310 helix: 1.25 (0.20), residues: 655 sheet: -0.60 (0.18), residues: 777 loop : -0.97 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 995 TYR 0.019 0.001 TYR B 380 PHE 0.024 0.001 PHE A 429 TRP 0.011 0.001 TRP B 436 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00238 (26877) covalent geometry : angle 0.55692 (36557) hydrogen bonds : bond 0.03680 ( 1035) hydrogen bonds : angle 5.64674 ( 2829) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 86 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 LEU cc_start: 0.8877 (mt) cc_final: 0.8673 (mt) REVERT: A 1130 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8121 (tp) REVERT: B 242 LEU cc_start: 0.8358 (mp) cc_final: 0.7864 (tp) REVERT: B 368 LEU cc_start: 0.8498 (mt) cc_final: 0.8242 (mp) REVERT: B 900 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6970 (ptm) REVERT: C 118 LEU cc_start: 0.8880 (tt) cc_final: 0.8186 (mm) REVERT: C 518 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5131 (pt) REVERT: S 67 MET cc_start: 0.5951 (mtm) cc_final: 0.5433 (mtm) outliers start: 53 outliers final: 40 residues processed: 132 average time/residue: 0.1655 time to fit residues: 36.9873 Evaluate side-chains 123 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 80 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 343 ASN Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 225 CYS Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 136 ILE Chi-restraints excluded: chain T residue 214 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 323 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 249 optimal weight: 0.5980 chunk 333 optimal weight: 50.0000 chunk 181 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 180 optimal weight: 2.9990 chunk 217 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 GLN B 762 GLN C 913 GLN S 228 ASN ** T 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.104153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.080856 restraints weight = 108941.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.078807 restraints weight = 68357.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.079742 restraints weight = 69825.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.079699 restraints weight = 49640.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.080848 restraints weight = 44277.364| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26877 Z= 0.150 Angle : 0.568 12.556 36557 Z= 0.295 Chirality : 0.044 0.216 4174 Planarity : 0.004 0.053 4724 Dihedral : 5.087 33.851 3605 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.29 % Favored : 94.65 % Rotamer: Outliers : 1.60 % Allowed : 12.74 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.15), residues: 3310 helix: 1.20 (0.20), residues: 660 sheet: -0.60 (0.18), residues: 778 loop : -0.95 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 995 TYR 0.019 0.001 TYR C 266 PHE 0.022 0.001 PHE A 429 TRP 0.046 0.002 TRP A 436 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00332 (26877) covalent geometry : angle 0.56769 (36557) hydrogen bonds : bond 0.03815 ( 1035) hydrogen bonds : angle 5.67715 ( 2829) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 80 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1130 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8269 (tp) REVERT: B 229 LEU cc_start: 0.8648 (pt) cc_final: 0.8409 (pt) REVERT: B 242 LEU cc_start: 0.8361 (mp) cc_final: 0.7845 (tp) REVERT: B 368 LEU cc_start: 0.8500 (mt) cc_final: 0.8257 (mt) REVERT: B 900 MET cc_start: 0.6979 (OUTLIER) cc_final: 0.6706 (ptm) REVERT: C 518 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5079 (pt) REVERT: S 67 MET cc_start: 0.5883 (mtm) cc_final: 0.5372 (mtm) outliers start: 47 outliers final: 38 residues processed: 121 average time/residue: 0.1551 time to fit residues: 33.0784 Evaluate side-chains 118 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 122 TYR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 225 CYS Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 136 ILE Chi-restraints excluded: chain T residue 214 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 68 optimal weight: 0.0970 chunk 329 optimal weight: 40.0000 chunk 159 optimal weight: 3.9990 chunk 286 optimal weight: 0.6980 chunk 120 optimal weight: 4.9990 chunk 271 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 264 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 220 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.104243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.081088 restraints weight = 108306.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.078836 restraints weight = 73226.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.079625 restraints weight = 67647.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.079975 restraints weight = 48038.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.080206 restraints weight = 45637.508| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26877 Z= 0.142 Angle : 0.560 12.200 36557 Z= 0.291 Chirality : 0.043 0.175 4174 Planarity : 0.004 0.053 4724 Dihedral : 5.025 33.837 3605 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.14 % Favored : 94.77 % Rotamer: Outliers : 1.60 % Allowed : 12.60 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.15), residues: 3310 helix: 1.21 (0.20), residues: 661 sheet: -0.66 (0.18), residues: 787 loop : -0.91 (0.15), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 995 TYR 0.019 0.001 TYR A 369 PHE 0.034 0.001 PHE A 220 TRP 0.032 0.001 TRP A 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00313 (26877) covalent geometry : angle 0.56036 (36557) hydrogen bonds : bond 0.03753 ( 1035) hydrogen bonds : angle 5.65188 ( 2829) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6620 Ramachandran restraints generated. 3310 Oldfield, 0 Emsley, 3310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 84 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1130 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8246 (tp) REVERT: B 229 LEU cc_start: 0.8695 (pt) cc_final: 0.8453 (pt) REVERT: B 242 LEU cc_start: 0.8400 (mp) cc_final: 0.7892 (tp) REVERT: B 368 LEU cc_start: 0.8519 (mt) cc_final: 0.8259 (mp) REVERT: B 900 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6757 (ptm) REVERT: C 518 LEU cc_start: 0.5948 (OUTLIER) cc_final: 0.5145 (pt) REVERT: S 67 MET cc_start: 0.5920 (mtm) cc_final: 0.5231 (mtp) outliers start: 47 outliers final: 38 residues processed: 126 average time/residue: 0.1578 time to fit residues: 34.4494 Evaluate side-chains 117 residues out of total 2947 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 76 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 983 ARG Chi-restraints excluded: chain C residue 1123 SER Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 225 CYS Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 136 ILE Chi-restraints excluded: chain T residue 214 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 292 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 251 optimal weight: 0.5980 chunk 129 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.106211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.083584 restraints weight = 108426.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.081701 restraints weight = 64940.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.082162 restraints weight = 63156.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.082600 restraints weight = 45391.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.082797 restraints weight = 40654.620| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26877 Z= 0.119 Angle : 0.544 12.075 36557 Z= 0.282 Chirality : 0.043 0.169 4174 Planarity : 0.004 0.052 4724 Dihedral : 4.891 33.708 3605 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 1.43 % Allowed : 12.81 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 3310 helix: 1.34 (0.20), residues: 662 sheet: -0.64 (0.18), residues: 791 loop : -0.83 (0.15), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 995 TYR 0.019 0.001 TYR A 369 PHE 0.033 0.001 PHE A 220 TRP 0.026 0.001 TRP A 436 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00260 (26877) covalent geometry : angle 0.54419 (36557) hydrogen bonds : bond 0.03622 ( 1035) hydrogen bonds : angle 5.55230 ( 2829) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4054.74 seconds wall clock time: 71 minutes 47.66 seconds (4307.66 seconds total)