Starting phenix.real_space_refine on Thu Jul 31 07:03:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7niw_12367/07_2025/7niw_12367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7niw_12367/07_2025/7niw_12367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7niw_12367/07_2025/7niw_12367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7niw_12367/07_2025/7niw_12367.map" model { file = "/net/cci-nas-00/data/ceres_data/7niw_12367/07_2025/7niw_12367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7niw_12367/07_2025/7niw_12367.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 41 5.16 5 C 8055 2.51 5 N 2067 2.21 5 O 2311 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12477 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 8831 Classifications: {'peptide': 1140} Link IDs: {'PTRANS': 29, 'TRANS': 1110} Chain breaks: 2 Chain: "B" Number of atoms: 1616 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 211, 1610 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Conformer: "B" Number of residues, atoms: 211, 1607 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 200} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1631 Chain: "C" Number of atoms: 1757 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 234, 1757 Classifications: {'peptide': 234} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 222} Chain: "A" Number of atoms: 273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 273 Unusual residues: {'CLR': 6, 'DLP': 1, 'X2N': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 10.36, per 1000 atoms: 0.83 Number of scatterers: 12477 At special positions: 0 Unit cell: (120.12, 127.38, 128.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 41 16.00 P 1 15.00 F 2 9.00 O 2311 8.00 N 2067 7.00 C 8055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.02 Simple disulfide: pdb=" SG CYS C 160 " - pdb=" SG CYS C 216 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 2.0 seconds 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2922 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 22 sheets defined 49.7% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 50 through 69 removed outlier: 4.008A pdb=" N LYS A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 92 removed outlier: 4.251A pdb=" N LEU A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N MET A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 159 removed outlier: 3.787A pdb=" N GLU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG A 159 " --> pdb=" O HIS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 168 removed outlier: 3.640A pdb=" N ASN A 168 " --> pdb=" O TRP A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 190 removed outlier: 4.059A pdb=" N ASN A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 213 Processing helix chain 'A' and resid 213 through 252 removed outlier: 3.575A pdb=" N THR A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.548A pdb=" N GLU A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.531A pdb=" N VAL A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 325 removed outlier: 4.277A pdb=" N HIS A 282 " --> pdb=" O ARG A 278 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU A 288 " --> pdb=" O GLU A 284 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS A 292 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 349 removed outlier: 3.898A pdb=" N VAL A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 372 removed outlier: 3.502A pdb=" N ASP A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE A 357 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 485 through 495 removed outlier: 3.617A pdb=" N ASN A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 509 Processing helix chain 'A' and resid 535 through 548 removed outlier: 4.032A pdb=" N GLN A 539 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 577 removed outlier: 3.528A pdb=" N GLU A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 619 removed outlier: 3.739A pdb=" N LYS A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 629 removed outlier: 3.867A pdb=" N ASN A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 703 Processing helix chain 'A' and resid 707 through 723 Processing helix chain 'A' and resid 724 through 739 removed outlier: 3.813A pdb=" N PHE A 739 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 796 removed outlier: 3.901A pdb=" N GLN A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 766 " --> pdb=" O GLY A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 3.699A pdb=" N ASP A 805 " --> pdb=" O TRP A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 853 removed outlier: 3.867A pdb=" N ALA A 821 " --> pdb=" O LEU A 817 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA A 822 " --> pdb=" O ALA A 818 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY A 826 " --> pdb=" O ALA A 822 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ARG A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU A 832 " --> pdb=" O THR A 828 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 846 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 862 removed outlier: 3.787A pdb=" N LEU A 859 " --> pdb=" O GLN A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 902 removed outlier: 3.960A pdb=" N ILE A 867 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N GLY A 871 " --> pdb=" O ILE A 867 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE A 872 " --> pdb=" O ALA A 868 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA A 899 " --> pdb=" O ILE A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 909 Processing helix chain 'A' and resid 911 through 966 removed outlier: 3.686A pdb=" N PHE A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 917 " --> pdb=" O ARG A 913 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS A 922 " --> pdb=" O MET A 918 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY A 925 " --> pdb=" O GLU A 921 " (cutoff:3.500A) Proline residue: A 926 - end of helix removed outlier: 4.181A pdb=" N HIS A 935 " --> pdb=" O VAL A 931 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR A 940 " --> pdb=" O ILE A 936 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 948 " --> pdb=" O SER A 944 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR A 949 " --> pdb=" O GLN A 945 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE A 950 " --> pdb=" O ALA A 946 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 951 " --> pdb=" O PHE A 947 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR A 952 " --> pdb=" O MET A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 992 removed outlier: 3.593A pdb=" N GLY A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1000 Processing helix chain 'A' and resid 1002 through 1013 removed outlier: 3.808A pdb=" N LEU A1010 " --> pdb=" O HIS A1006 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A1012 " --> pdb=" O PHE A1008 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A1013 " --> pdb=" O MET A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1084 removed outlier: 3.930A pdb=" N LEU A1082 " --> pdb=" O VAL A1078 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU A1083 " --> pdb=" O VAL A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1103 No H-bonds generated for 'chain 'A' and resid 1101 through 1103' Processing helix chain 'A' and resid 1104 through 1109 Processing helix chain 'A' and resid 1126 through 1131 Processing helix chain 'A' and resid 1132 through 1134 No H-bonds generated for 'chain 'A' and resid 1132 through 1134' Processing helix chain 'A' and resid 1140 through 1151 Processing helix chain 'A' and resid 1153 through 1158 removed outlier: 3.551A pdb=" N ILE A1157 " --> pdb=" O ILE A1153 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A1158 " --> pdb=" O HIS A1154 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1153 through 1158' Processing helix chain 'A' and resid 1179 through 1191 removed outlier: 3.628A pdb=" N ALA A1184 " --> pdb=" O LYS A1180 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A1185 " --> pdb=" O GLN A1181 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A1190 " --> pdb=" O ALA A1186 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ARG A1191 " --> pdb=" O ARG A1187 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1222 removed outlier: 4.662A pdb=" N GLU A1215 " --> pdb=" O LYS A1211 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A1216 " --> pdb=" O VAL A1212 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A1220 " --> pdb=" O ALA A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1237 Processing helix chain 'B' and resid 122 through 127 removed outlier: 4.361A pdb=" N LYS B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 35 removed outlier: 3.616A pdb=" N SER C 34 " --> pdb=" O ASN C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 221 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 395 through 397 Processing sheet with id=AA2, first strand: chain 'A' and resid 425 through 427 removed outlier: 6.379A pdb=" N ALA A 426 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N PHE A 603 " --> pdb=" O ALA A 426 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 610 " --> pdb=" O GLY A 602 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 472 through 475 removed outlier: 6.446A pdb=" N LEU A 554 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE A 587 " --> pdb=" O LEU A 554 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 556 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1052 through 1053 removed outlier: 3.555A pdb=" N LEU A1057 " --> pdb=" O PHE A1036 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1052 through 1053 removed outlier: 5.659A pdb=" N GLU A1038 " --> pdb=" O THR A1092 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N THR A1092 " --> pdb=" O GLU A1038 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1113 through 1114 removed outlier: 7.283A pdb=" N GLY A1113 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU A1196 " --> pdb=" O ILE A1227 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A1067 " --> pdb=" O VAL A1228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1094 through 1095 Processing sheet with id=AA8, first strand: chain 'A' and resid 1124 through 1125 removed outlier: 3.961A pdb=" N CYS A1124 " --> pdb=" O VAL A1168 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1168 " --> pdb=" O CYS A1124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 6 through 7 Processing sheet with id=AB1, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AB2, first strand: chain 'B' and resid 63 through 66 Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 93 Processing sheet with id=AB4, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.598A pdb=" N SER B 115 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASN B 138 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 176 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.598A pdb=" N SER B 115 " --> pdb=" O ASN B 138 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ASN B 138 " --> pdb=" O LEU B 176 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 176 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 146 through 151 Processing sheet with id=AB7, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AB8, first strand: chain 'C' and resid 60 through 61 removed outlier: 3.912A pdb=" N TYR C 122 " --> pdb=" O ARG C 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AC1, first strand: chain 'C' and resid 96 through 97 removed outlier: 4.120A pdb=" N THR C 127 " --> pdb=" O TYR C 97 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.557A pdb=" N LEU C 161 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 201 " --> pdb=" O HIS C 184 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.557A pdb=" N LEU C 161 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 171 through 174 removed outlier: 3.561A pdb=" N CYS C 216 " --> pdb=" O LYS C 229 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS C 229 " --> pdb=" O CYS C 216 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1806 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: 4.82 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2020 1.31 - 1.44: 3442 1.44 - 1.57: 7203 1.57 - 1.70: 19 1.70 - 1.83: 64 Bond restraints: 12748 Sorted by residual: bond pdb=" CA LEU A1197 " pdb=" CB LEU A1197 " ideal model delta sigma weight residual 1.524 1.435 0.089 1.62e-02 3.81e+03 3.01e+01 bond pdb=" C31 DLP A1308 " pdb=" O2 DLP A1308 " ideal model delta sigma weight residual 1.331 1.438 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C11 DLP A1308 " pdb=" O3 DLP A1308 " ideal model delta sigma weight residual 1.327 1.420 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CBL X2N A1306 " pdb=" NBT X2N A1306 " ideal model delta sigma weight residual 1.406 1.331 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" CB GLN A 837 " pdb=" CG GLN A 837 " ideal model delta sigma weight residual 1.520 1.414 0.106 3.00e-02 1.11e+03 1.25e+01 ... (remaining 12743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 16124 2.35 - 4.70: 966 4.70 - 7.05: 157 7.05 - 9.40: 40 9.40 - 11.75: 8 Bond angle restraints: 17295 Sorted by residual: angle pdb=" N THR B 207 " pdb=" CA THR B 207 " pdb=" C THR B 207 " ideal model delta sigma weight residual 107.23 118.04 -10.81 1.67e+00 3.59e-01 4.19e+01 angle pdb=" N LEU A1089 " pdb=" CA LEU A1089 " pdb=" C LEU A1089 " ideal model delta sigma weight residual 111.36 106.02 5.34 1.09e+00 8.42e-01 2.40e+01 angle pdb=" CA TYR A 312 " pdb=" CB TYR A 312 " pdb=" CG TYR A 312 " ideal model delta sigma weight residual 113.90 122.61 -8.71 1.80e+00 3.09e-01 2.34e+01 angle pdb=" N PHE A 947 " pdb=" CA PHE A 947 " pdb=" C PHE A 947 " ideal model delta sigma weight residual 113.19 118.86 -5.67 1.19e+00 7.06e-01 2.27e+01 angle pdb=" N LEU B 136 " pdb=" CA LEU B 136 " pdb=" C LEU B 136 " ideal model delta sigma weight residual 109.79 116.91 -7.12 1.56e+00 4.11e-01 2.08e+01 ... (remaining 17290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.83: 7324 25.83 - 51.65: 504 51.65 - 77.48: 47 77.48 - 103.31: 14 103.31 - 129.14: 2 Dihedral angle restraints: 7891 sinusoidal: 3326 harmonic: 4565 Sorted by residual: dihedral pdb=" CA ASN A 91 " pdb=" C ASN A 91 " pdb=" N PHE A 92 " pdb=" CA PHE A 92 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA GLN A 911 " pdb=" C GLN A 911 " pdb=" N GLU A 912 " pdb=" CA GLU A 912 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA VAL A 869 " pdb=" C VAL A 869 " pdb=" N SER A 870 " pdb=" CA SER A 870 " ideal model delta harmonic sigma weight residual 180.00 154.04 25.96 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 7888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1565 0.081 - 0.161: 353 0.161 - 0.242: 40 0.242 - 0.322: 10 0.322 - 0.403: 6 Chirality restraints: 1974 Sorted by residual: chirality pdb=" C17 CLR A1304 " pdb=" C13 CLR A1304 " pdb=" C16 CLR A1304 " pdb=" C20 CLR A1304 " both_signs ideal model delta sigma weight residual False 2.55 2.96 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C17 CLR A1307 " pdb=" C13 CLR A1307 " pdb=" C16 CLR A1307 " pdb=" C20 CLR A1307 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C17 CLR A1305 " pdb=" C13 CLR A1305 " pdb=" C16 CLR A1305 " pdb=" C20 CLR A1305 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.39 2.00e-01 2.50e+01 3.84e+00 ... (remaining 1971 not shown) Planarity restraints: 2157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1132 " -0.025 2.00e-02 2.50e+03 1.88e-02 7.04e+00 pdb=" CG TYR A1132 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A1132 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A1132 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A1132 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A1132 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A1132 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1132 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 792 " -0.030 2.00e-02 2.50e+03 1.94e-02 6.62e+00 pdb=" CG PHE A 792 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE A 792 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 792 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 792 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 792 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 792 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 99 " 0.024 2.00e-02 2.50e+03 1.81e-02 5.72e+00 pdb=" CG PHE B 99 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 99 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 99 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 99 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 99 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 99 " 0.009 2.00e-02 2.50e+03 ... (remaining 2154 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 379 2.64 - 3.21: 12895 3.21 - 3.77: 18794 3.77 - 4.34: 25209 4.34 - 4.90: 40597 Nonbonded interactions: 97874 Sorted by model distance: nonbonded pdb=" O ASN A 332 " pdb=" ND2 ASN A 332 " model vdw 2.078 3.120 nonbonded pdb=" OG SER A 476 " pdb=" OE1 GLN A 477 " model vdw 2.090 3.040 nonbonded pdb=" O SER A 69 " pdb=" OG SER A 69 " model vdw 2.110 3.040 nonbonded pdb=" N GLN A 272 " pdb=" OE1 GLN A 272 " model vdw 2.180 3.120 nonbonded pdb=" O SER B 31 " pdb=" OG SER B 31 " model vdw 2.189 3.040 ... (remaining 97869 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.30 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: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.780 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.015 0.117 12752 Z= 0.675 Angle : 1.289 11.748 17303 Z= 0.686 Chirality : 0.070 0.403 1974 Planarity : 0.006 0.053 2157 Dihedral : 17.102 129.137 4957 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 27.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 15.49 % Favored : 84.32 % Rotamer: Outliers : 2.44 % Allowed : 13.98 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.15), residues: 1577 helix: -3.16 (0.13), residues: 712 sheet: -3.13 (0.28), residues: 227 loop : -3.81 (0.18), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP A 802 HIS 0.017 0.002 HIS A 67 PHE 0.040 0.004 PHE B 99 TYR 0.044 0.003 TYR A1132 ARG 0.012 0.001 ARG A1221 Details of bonding type rmsd hydrogen bonds : bond 0.19862 ( 625) hydrogen bonds : angle 8.41184 ( 1806) SS BOND : bond 0.00515 ( 4) SS BOND : angle 1.51536 ( 8) covalent geometry : bond 0.01519 (12748) covalent geometry : angle 1.28887 (17295) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 151 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7637 (tm-30) REVERT: A 190 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8204 (t0) REVERT: A 383 ARG cc_start: 0.7644 (mtp180) cc_final: 0.6440 (ttp80) REVERT: A 553 ILE cc_start: 0.8832 (mp) cc_final: 0.8605 (mp) REVERT: A 875 MET cc_start: 0.3854 (mmm) cc_final: 0.3647 (tmm) REVERT: A 884 ARG cc_start: 0.5732 (tpp-160) cc_final: 0.5350 (mtt180) REVERT: A 947 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8587 (t80) REVERT: B 139 ASN cc_start: 0.6873 (m-40) cc_final: 0.5915 (p0) REVERT: C 196 TYR cc_start: 0.7303 (m-80) cc_final: 0.6850 (m-80) REVERT: C 230 LYS cc_start: 0.7344 (ttpp) cc_final: 0.7136 (tttp) outliers start: 32 outliers final: 20 residues processed: 188 average time/residue: 0.2478 time to fit residues: 67.3868 Evaluate side-chains 131 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 132 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 7.9990 chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 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 282 HIS A 298 ASN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 416 ASN A 752 ASN A 823 GLN A 837 GLN ** A 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 HIS A1104 ASN A1129 ASN A1214 GLN B 39 GLN C 42 GLN C 191 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.168825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129837 restraints weight = 27220.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.128363 restraints weight = 27334.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.130959 restraints weight = 21678.188| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12752 Z= 0.169 Angle : 0.713 8.736 17303 Z= 0.371 Chirality : 0.044 0.210 1974 Planarity : 0.004 0.039 2157 Dihedral : 11.024 130.456 2223 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.13 % Allowed : 17.72 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.18), residues: 1577 helix: -1.06 (0.17), residues: 745 sheet: -2.68 (0.28), residues: 254 loop : -3.27 (0.21), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.004 0.001 HIS A1154 PHE 0.033 0.002 PHE A 728 TYR 0.026 0.002 TYR A 249 ARG 0.008 0.001 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.06854 ( 625) hydrogen bonds : angle 5.65327 ( 1806) SS BOND : bond 0.00146 ( 4) SS BOND : angle 1.16234 ( 8) covalent geometry : bond 0.00349 (12748) covalent geometry : angle 0.71228 (17295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 1.238 Fit side-chains REVERT: A 119 TYR cc_start: 0.7730 (m-80) cc_final: 0.7435 (m-80) REVERT: A 218 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8429 (mm) REVERT: A 383 ARG cc_start: 0.7610 (mtp180) cc_final: 0.6495 (ttp-170) REVERT: A 537 GLN cc_start: 0.5699 (mt0) cc_final: 0.5303 (mt0) REVERT: A 553 ILE cc_start: 0.8829 (mp) cc_final: 0.8581 (mp) REVERT: A 875 MET cc_start: 0.3945 (mmm) cc_final: 0.3646 (tmm) REVERT: A 884 ARG cc_start: 0.5547 (tpp-160) cc_final: 0.5203 (mtm180) REVERT: A 947 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8746 (t80) REVERT: B 139 ASN cc_start: 0.6592 (m-40) cc_final: 0.6037 (p0) REVERT: C 196 TYR cc_start: 0.7061 (m-80) cc_final: 0.6438 (m-80) outliers start: 41 outliers final: 23 residues processed: 180 average time/residue: 0.2252 time to fit residues: 60.5511 Evaluate side-chains 142 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 171 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 112 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN ** A 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.165826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.121641 restraints weight = 34665.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.120359 restraints weight = 24923.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.122608 restraints weight = 15879.103| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3588 r_free = 0.3588 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12752 Z= 0.214 Angle : 0.694 8.940 17303 Z= 0.362 Chirality : 0.044 0.226 1974 Planarity : 0.004 0.037 2157 Dihedral : 10.504 133.403 2205 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 4.28 % Allowed : 20.09 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.19), residues: 1577 helix: -0.45 (0.18), residues: 746 sheet: -2.40 (0.29), residues: 250 loop : -3.09 (0.21), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 802 HIS 0.005 0.001 HIS A 67 PHE 0.022 0.002 PHE B 99 TYR 0.026 0.002 TYR A 919 ARG 0.006 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.06990 ( 625) hydrogen bonds : angle 5.43756 ( 1806) SS BOND : bond 0.00163 ( 4) SS BOND : angle 1.03113 ( 8) covalent geometry : bond 0.00486 (12748) covalent geometry : angle 0.69390 (17295) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 125 time to evaluate : 1.307 Fit side-chains REVERT: A 383 ARG cc_start: 0.7637 (mtp180) cc_final: 0.6531 (ttp-170) REVERT: A 553 ILE cc_start: 0.8730 (mp) cc_final: 0.8498 (mp) REVERT: A 556 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6520 (mt) REVERT: A 753 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8579 (tt) REVERT: A 884 ARG cc_start: 0.5559 (tpp-160) cc_final: 0.5166 (mtm180) REVERT: A 947 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8802 (t80) REVERT: A 1112 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8491 (mt) REVERT: A 1129 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8506 (t0) REVERT: B 139 ASN cc_start: 0.6668 (m-40) cc_final: 0.5994 (p0) REVERT: C 196 TYR cc_start: 0.7014 (m-80) cc_final: 0.6575 (m-80) outliers start: 56 outliers final: 40 residues processed: 173 average time/residue: 0.2063 time to fit residues: 55.0168 Evaluate side-chains 160 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 753 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1129 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1207 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 111 optimal weight: 4.9990 chunk 86 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: A 349 GLN A 464 ASN ** A 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.171063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.129525 restraints weight = 39948.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.127296 restraints weight = 24554.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.129865 restraints weight = 20206.763| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12752 Z= 0.137 Angle : 0.603 7.824 17303 Z= 0.314 Chirality : 0.041 0.185 1974 Planarity : 0.004 0.039 2157 Dihedral : 9.818 132.852 2202 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.43 % Allowed : 21.08 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.20), residues: 1577 helix: 0.26 (0.19), residues: 742 sheet: -2.08 (0.29), residues: 246 loop : -2.74 (0.22), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.016 0.001 HIS A 614 PHE 0.018 0.001 PHE A1036 TYR 0.018 0.001 TYR A 952 ARG 0.007 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.05994 ( 625) hydrogen bonds : angle 4.96742 ( 1806) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.60782 ( 8) covalent geometry : bond 0.00292 (12748) covalent geometry : angle 0.60297 (17295) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 135 time to evaluate : 1.286 Fit side-chains REVERT: A 119 TYR cc_start: 0.7603 (m-80) cc_final: 0.7385 (m-80) REVERT: A 147 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7476 (ttp-170) REVERT: A 383 ARG cc_start: 0.7606 (mtp180) cc_final: 0.6414 (ttp80) REVERT: A 444 ARG cc_start: 0.7747 (ttt180) cc_final: 0.6872 (ttt180) REVERT: A 537 GLN cc_start: 0.5598 (mt0) cc_final: 0.5101 (mp10) REVERT: A 553 ILE cc_start: 0.8678 (mp) cc_final: 0.8440 (mp) REVERT: A 556 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6524 (mt) REVERT: A 884 ARG cc_start: 0.5527 (tpp-160) cc_final: 0.5140 (mtm180) REVERT: A 947 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8779 (t80) REVERT: A 948 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7696 (tmm) REVERT: A 1036 PHE cc_start: 0.7761 (m-80) cc_final: 0.7415 (m-80) REVERT: B 50 TYR cc_start: 0.8434 (p90) cc_final: 0.8214 (p90) REVERT: B 139 ASN cc_start: 0.6605 (m-40) cc_final: 0.6016 (p0) REVERT: B 210 PHE cc_start: 0.5324 (p90) cc_final: 0.5065 (p90) REVERT: C 196 TYR cc_start: 0.6935 (m-80) cc_final: 0.6709 (m-80) outliers start: 58 outliers final: 36 residues processed: 185 average time/residue: 0.2120 time to fit residues: 59.4386 Evaluate side-chains 159 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1021 SER Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 155 optimal weight: 30.0000 chunk 146 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 69 optimal weight: 0.0270 chunk 99 optimal weight: 0.9990 chunk 32 optimal weight: 0.0030 chunk 58 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 119 optimal weight: 0.2980 chunk 74 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.3048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 929 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.175375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.138016 restraints weight = 33518.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.139879 restraints weight = 39159.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.143213 restraints weight = 18388.189| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 12752 Z= 0.117 Angle : 0.559 6.887 17303 Z= 0.290 Chirality : 0.040 0.144 1974 Planarity : 0.003 0.041 2157 Dihedral : 9.231 135.170 2201 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.90 % Allowed : 22.54 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.21), residues: 1577 helix: 0.76 (0.19), residues: 736 sheet: -1.65 (0.30), residues: 248 loop : -2.48 (0.23), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 614 PHE 0.015 0.001 PHE A 337 TYR 0.017 0.001 TYR A 467 ARG 0.005 0.000 ARG A 144 Details of bonding type rmsd hydrogen bonds : bond 0.05323 ( 625) hydrogen bonds : angle 4.59517 ( 1806) SS BOND : bond 0.00160 ( 4) SS BOND : angle 0.45852 ( 8) covalent geometry : bond 0.00233 (12748) covalent geometry : angle 0.55895 (17295) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: A 154 PHE cc_start: 0.7642 (t80) cc_final: 0.7270 (t80) REVERT: A 383 ARG cc_start: 0.7482 (mtp180) cc_final: 0.6443 (ttp80) REVERT: A 444 ARG cc_start: 0.7669 (ttt180) cc_final: 0.6845 (ttt180) REVERT: A 537 GLN cc_start: 0.5745 (mt0) cc_final: 0.5337 (mt0) REVERT: A 553 ILE cc_start: 0.8759 (mp) cc_final: 0.8521 (mp) REVERT: A 556 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6403 (mt) REVERT: A 884 ARG cc_start: 0.5323 (tpp-160) cc_final: 0.5029 (mtm180) REVERT: A 894 LYS cc_start: 0.7413 (mttm) cc_final: 0.7071 (mttm) REVERT: A 914 LYS cc_start: 0.7920 (pttt) cc_final: 0.7679 (tptt) REVERT: A 947 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8830 (t80) REVERT: A 948 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7590 (tmm) REVERT: A 1036 PHE cc_start: 0.7607 (m-80) cc_final: 0.7084 (m-80) REVERT: B 50 TYR cc_start: 0.8380 (p90) cc_final: 0.8162 (p90) REVERT: B 139 ASN cc_start: 0.6451 (m-40) cc_final: 0.5980 (p0) REVERT: B 210 PHE cc_start: 0.5241 (p90) cc_final: 0.4982 (p90) REVERT: C 196 TYR cc_start: 0.7028 (m-80) cc_final: 0.6720 (m-10) outliers start: 51 outliers final: 31 residues processed: 195 average time/residue: 0.2395 time to fit residues: 69.0591 Evaluate side-chains 166 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 90 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 133 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN C 191 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.168813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.125152 restraints weight = 35835.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.123186 restraints weight = 23707.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125459 restraints weight = 16984.208| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3615 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3615 r_free = 0.3615 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3615 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12752 Z= 0.220 Angle : 0.665 9.775 17303 Z= 0.345 Chirality : 0.044 0.192 1974 Planarity : 0.004 0.041 2157 Dihedral : 9.553 138.850 2195 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 5.42 % Allowed : 22.23 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.20), residues: 1577 helix: 0.44 (0.18), residues: 746 sheet: -1.79 (0.30), residues: 247 loop : -2.39 (0.23), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 112 HIS 0.006 0.001 HIS A 67 PHE 0.029 0.002 PHE A 769 TYR 0.030 0.002 TYR C 53 ARG 0.006 0.001 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.06453 ( 625) hydrogen bonds : angle 4.88438 ( 1806) SS BOND : bond 0.00265 ( 4) SS BOND : angle 1.53108 ( 8) covalent geometry : bond 0.00505 (12748) covalent geometry : angle 0.66417 (17295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 133 time to evaluate : 1.413 Fit side-chains REVERT: A 154 PHE cc_start: 0.7852 (t80) cc_final: 0.7460 (t80) REVERT: A 312 TYR cc_start: 0.7906 (OUTLIER) cc_final: 0.7430 (t80) REVERT: A 383 ARG cc_start: 0.7559 (mtp180) cc_final: 0.6327 (ttp80) REVERT: A 444 ARG cc_start: 0.7741 (ttt180) cc_final: 0.6832 (ttt180) REVERT: A 537 GLN cc_start: 0.5720 (mt0) cc_final: 0.5319 (mt0) REVERT: A 553 ILE cc_start: 0.8666 (mp) cc_final: 0.8450 (mp) REVERT: A 556 LEU cc_start: 0.6888 (OUTLIER) cc_final: 0.6503 (mt) REVERT: A 884 ARG cc_start: 0.5273 (tpp-160) cc_final: 0.4990 (mtm180) REVERT: A 886 LYS cc_start: 0.7266 (mtmm) cc_final: 0.6761 (tptt) REVERT: A 914 LYS cc_start: 0.8069 (pttt) cc_final: 0.7721 (tptt) REVERT: A 947 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8790 (t80) REVERT: A 1112 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8489 (mt) REVERT: B 139 ASN cc_start: 0.6580 (m-40) cc_final: 0.5977 (p0) REVERT: B 210 PHE cc_start: 0.5330 (p90) cc_final: 0.5110 (p90) REVERT: C 196 TYR cc_start: 0.7113 (m-80) cc_final: 0.6866 (m-80) outliers start: 70 outliers final: 51 residues processed: 190 average time/residue: 0.2072 time to fit residues: 59.8838 Evaluate side-chains 180 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 125 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 930 SER Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 60 optimal weight: 0.9990 chunk 57 optimal weight: 30.0000 chunk 105 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 157 optimal weight: 0.0000 chunk 83 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.173170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128481 restraints weight = 35186.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.128272 restraints weight = 22295.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.129367 restraints weight = 16350.666| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3676 r_free = 0.3676 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12752 Z= 0.124 Angle : 0.590 12.004 17303 Z= 0.301 Chirality : 0.040 0.205 1974 Planarity : 0.003 0.042 2157 Dihedral : 9.135 137.317 2195 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.13 % Allowed : 23.68 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.21), residues: 1577 helix: 0.83 (0.19), residues: 737 sheet: -1.57 (0.31), residues: 242 loop : -2.29 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS C 38 PHE 0.024 0.001 PHE A 770 TYR 0.017 0.001 TYR A 467 ARG 0.007 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.05579 ( 625) hydrogen bonds : angle 4.63011 ( 1806) SS BOND : bond 0.00173 ( 4) SS BOND : angle 0.79688 ( 8) covalent geometry : bond 0.00256 (12748) covalent geometry : angle 0.59026 (17295) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 1.266 Fit side-chains REVERT: A 119 TYR cc_start: 0.7627 (m-80) cc_final: 0.7390 (m-80) REVERT: A 154 PHE cc_start: 0.7773 (t80) cc_final: 0.7355 (t80) REVERT: A 312 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.7298 (t80) REVERT: A 383 ARG cc_start: 0.7557 (mtp180) cc_final: 0.6309 (ttp80) REVERT: A 444 ARG cc_start: 0.7723 (ttt180) cc_final: 0.6813 (ttt180) REVERT: A 537 GLN cc_start: 0.5749 (mt0) cc_final: 0.5339 (mt0) REVERT: A 553 ILE cc_start: 0.8629 (mp) cc_final: 0.8413 (mp) REVERT: A 556 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6484 (mt) REVERT: A 590 ARG cc_start: 0.3542 (OUTLIER) cc_final: 0.3259 (mpt180) REVERT: A 884 ARG cc_start: 0.5249 (tpp-160) cc_final: 0.4940 (mtm180) REVERT: A 886 LYS cc_start: 0.7365 (mtmm) cc_final: 0.6841 (tptt) REVERT: A 914 LYS cc_start: 0.7956 (pttt) cc_final: 0.7693 (tptt) REVERT: A 947 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8756 (t80) REVERT: B 20 VAL cc_start: 0.7379 (t) cc_final: 0.7168 (t) REVERT: B 139 ASN cc_start: 0.6545 (m-40) cc_final: 0.5960 (p0) REVERT: C 196 TYR cc_start: 0.7049 (m-80) cc_final: 0.6760 (m-10) outliers start: 53 outliers final: 43 residues processed: 185 average time/residue: 0.2284 time to fit residues: 62.9625 Evaluate side-chains 177 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 130 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 590 ARG Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1125 SER Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 103 optimal weight: 0.0980 chunk 61 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 91 optimal weight: 0.0970 chunk 31 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 902 ASN A1117 GLN C 217 ASN ** C 220 HIS ** 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 = 0.4244 r_free = 0.4244 target = 0.175099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.138473 restraints weight = 33983.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.140866 restraints weight = 42171.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.144229 restraints weight = 18418.556| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3854 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3854 r_free = 0.3854 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3854 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12752 Z= 0.117 Angle : 0.583 11.811 17303 Z= 0.296 Chirality : 0.040 0.194 1974 Planarity : 0.003 0.041 2157 Dihedral : 8.822 136.248 2195 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.20 % Allowed : 24.14 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.21), residues: 1577 helix: 1.02 (0.19), residues: 739 sheet: -1.35 (0.31), residues: 248 loop : -2.17 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.000 HIS C 38 PHE 0.016 0.001 PHE A 769 TYR 0.023 0.001 TYR A 919 ARG 0.007 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.05234 ( 625) hydrogen bonds : angle 4.46139 ( 1806) SS BOND : bond 0.00195 ( 4) SS BOND : angle 0.66170 ( 8) covalent geometry : bond 0.00240 (12748) covalent geometry : angle 0.58265 (17295) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8174 (mm) REVERT: A 312 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.7310 (t80) REVERT: A 374 ASN cc_start: 0.7407 (m-40) cc_final: 0.6996 (t0) REVERT: A 383 ARG cc_start: 0.7445 (mtp180) cc_final: 0.6312 (ttp80) REVERT: A 444 ARG cc_start: 0.7613 (ttt180) cc_final: 0.6800 (ttt180) REVERT: A 537 GLN cc_start: 0.5677 (mt0) cc_final: 0.5367 (mt0) REVERT: A 553 ILE cc_start: 0.8730 (mp) cc_final: 0.8501 (mp) REVERT: A 556 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6279 (mt) REVERT: A 593 THR cc_start: 0.4233 (OUTLIER) cc_final: 0.3974 (m) REVERT: A 886 LYS cc_start: 0.7359 (mtmm) cc_final: 0.6754 (tptt) REVERT: A 947 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8849 (t80) REVERT: B 139 ASN cc_start: 0.6433 (m-40) cc_final: 0.5979 (p0) REVERT: C 196 TYR cc_start: 0.7107 (m-80) cc_final: 0.6795 (m-10) outliers start: 54 outliers final: 38 residues processed: 196 average time/residue: 0.2219 time to fit residues: 65.6121 Evaluate side-chains 182 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1125 SER Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 86 optimal weight: 0.5980 chunk 90 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.174112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.136396 restraints weight = 33232.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.138599 restraints weight = 40404.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141810 restraints weight = 18669.673| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3819 r_free = 0.3819 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12752 Z= 0.124 Angle : 0.583 9.888 17303 Z= 0.295 Chirality : 0.040 0.185 1974 Planarity : 0.003 0.041 2157 Dihedral : 8.785 135.125 2194 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.67 % Allowed : 24.90 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1577 helix: 1.10 (0.19), residues: 742 sheet: -1.27 (0.31), residues: 248 loop : -2.10 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 112 HIS 0.003 0.001 HIS C 38 PHE 0.020 0.001 PHE A 770 TYR 0.030 0.001 TYR B 50 ARG 0.007 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.05268 ( 625) hydrogen bonds : angle 4.42001 ( 1806) SS BOND : bond 0.00163 ( 4) SS BOND : angle 0.70245 ( 8) covalent geometry : bond 0.00269 (12748) covalent geometry : angle 0.58249 (17295) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 312 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.7380 (t80) REVERT: A 374 ASN cc_start: 0.7386 (m-40) cc_final: 0.6947 (t0) REVERT: A 383 ARG cc_start: 0.7496 (mtp180) cc_final: 0.6320 (ttp80) REVERT: A 444 ARG cc_start: 0.7661 (ttt180) cc_final: 0.6847 (ttt180) REVERT: A 537 GLN cc_start: 0.5685 (mt0) cc_final: 0.5365 (mt0) REVERT: A 553 ILE cc_start: 0.8665 (mp) cc_final: 0.8444 (mp) REVERT: A 556 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6411 (mt) REVERT: A 593 THR cc_start: 0.4285 (OUTLIER) cc_final: 0.4050 (m) REVERT: A 886 LYS cc_start: 0.7347 (mtmm) cc_final: 0.6766 (tptt) REVERT: A 947 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8919 (t80) REVERT: B 139 ASN cc_start: 0.6505 (m-40) cc_final: 0.5997 (p0) REVERT: C 196 TYR cc_start: 0.7138 (m-80) cc_final: 0.6833 (m-10) outliers start: 47 outliers final: 41 residues processed: 185 average time/residue: 0.2240 time to fit residues: 62.6848 Evaluate side-chains 186 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1125 SER Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.170438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128215 restraints weight = 39123.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.125936 restraints weight = 24852.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.128023 restraints weight = 20217.593| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 12752 Z= 0.185 Angle : 0.647 10.104 17303 Z= 0.332 Chirality : 0.043 0.231 1974 Planarity : 0.004 0.040 2157 Dihedral : 9.044 136.404 2191 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.13 % Allowed : 24.60 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.21), residues: 1577 helix: 0.88 (0.19), residues: 741 sheet: -1.39 (0.31), residues: 249 loop : -2.13 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 112 HIS 0.005 0.001 HIS A 67 PHE 0.022 0.002 PHE A 316 TYR 0.026 0.002 TYR A 919 ARG 0.007 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.05984 ( 625) hydrogen bonds : angle 4.62841 ( 1806) SS BOND : bond 0.00133 ( 4) SS BOND : angle 1.06613 ( 8) covalent geometry : bond 0.00425 (12748) covalent geometry : angle 0.64638 (17295) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3154 Ramachandran restraints generated. 1577 Oldfield, 0 Emsley, 1577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 142 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 383 ARG cc_start: 0.7562 (mtp180) cc_final: 0.6341 (ttp80) REVERT: A 444 ARG cc_start: 0.7721 (ttt180) cc_final: 0.6852 (ttt180) REVERT: A 537 GLN cc_start: 0.5653 (mt0) cc_final: 0.5285 (mt0) REVERT: A 553 ILE cc_start: 0.8606 (mp) cc_final: 0.8401 (mp) REVERT: A 556 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6546 (mt) REVERT: A 593 THR cc_start: 0.4313 (OUTLIER) cc_final: 0.4080 (m) REVERT: A 947 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8825 (t80) REVERT: A 1057 LEU cc_start: 0.7725 (mt) cc_final: 0.7504 (mt) REVERT: B 139 ASN cc_start: 0.6641 (m-40) cc_final: 0.6001 (p0) REVERT: C 196 TYR cc_start: 0.7180 (m-80) cc_final: 0.6713 (m-10) outliers start: 53 outliers final: 46 residues processed: 185 average time/residue: 0.2231 time to fit residues: 63.3083 Evaluate side-chains 181 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1002 LEU Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1125 SER Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 40 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 46 optimal weight: 30.0000 chunk 102 optimal weight: 0.0010 chunk 24 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 152 optimal weight: 0.0470 overall best weight: 0.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.173309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.131171 restraints weight = 39504.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.129371 restraints weight = 25862.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.131921 restraints weight = 19218.585| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12752 Z= 0.122 Angle : 0.597 10.387 17303 Z= 0.302 Chirality : 0.041 0.282 1974 Planarity : 0.003 0.041 2157 Dihedral : 8.722 133.669 2191 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.44 % Allowed : 25.67 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.21), residues: 1577 helix: 1.09 (0.19), residues: 741 sheet: -1.09 (0.32), residues: 243 loop : -2.04 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS C 38 PHE 0.023 0.001 PHE A 316 TYR 0.026 0.001 TYR A 919 ARG 0.007 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.05334 ( 625) hydrogen bonds : angle 4.46125 ( 1806) SS BOND : bond 0.00157 ( 4) SS BOND : angle 0.71149 ( 8) covalent geometry : bond 0.00260 (12748) covalent geometry : angle 0.59726 (17295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4879.78 seconds wall clock time: 84 minutes 58.74 seconds (5098.74 seconds total)