Starting phenix.real_space_refine on Wed Mar 4 11:14:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7niw_12367/03_2026/7niw_12367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7niw_12367/03_2026/7niw_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_12367/03_2026/7niw_12367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7niw_12367/03_2026/7niw_12367.map" model { file = "/net/cci-nas-00/data/ceres_data/7niw_12367/03_2026/7niw_12367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7niw_12367/03_2026/7niw_12367.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.08, per 1000 atoms: 0.25 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: 1.22 Conformation dependent library (CDL) restraints added in 657.9 milliseconds 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: 0.58 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: 2.49 Time building geometry restraints manager: 1.53 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: 6.020 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.950 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.860 ------------------------------------------------------------------------------- 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 : 28.01 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.012 0.001 ARG A1221 TYR 0.044 0.003 TYR A1132 PHE 0.040 0.004 PHE B 99 TRP 0.031 0.004 TRP A 802 HIS 0.017 0.002 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.01519 (12748) covalent geometry : angle 1.28887 (17295) SS BOND : bond 0.00515 ( 4) SS BOND : angle 1.51536 ( 8) hydrogen bonds : bond 0.19862 ( 625) hydrogen bonds : angle 8.41184 ( 1806) *********************** 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 : 0.498 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: 0.8201 (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: 0.3645 (tmm) REVERT: A 884 ARG cc_start: 0.5732 (tpp-160) cc_final: 0.5349 (mtt180) REVERT: A 947 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8581 (t80) REVERT: B 139 ASN cc_start: 0.6873 (m-40) cc_final: 0.5916 (p0) REVERT: C 196 TYR cc_start: 0.7303 (m-80) cc_final: 0.6851 (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: 0.1183 time to fit residues: 32.1288 Evaluate side-chains 130 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4168 r_free = 0.4168 target = 0.168509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.125616 restraints weight = 35380.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123176 restraints weight = 22997.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125717 restraints weight = 16330.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.126484 restraints weight = 11057.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.126812 restraints weight = 9945.093| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 12752 Z= 0.170 Angle : 0.718 8.352 17303 Z= 0.374 Chirality : 0.044 0.218 1974 Planarity : 0.004 0.039 2157 Dihedral : 11.075 130.257 2223 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.13 % Allowed : 17.34 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.18), residues: 1577 helix: -1.12 (0.17), residues: 745 sheet: -2.69 (0.28), residues: 254 loop : -3.29 (0.21), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 109 TYR 0.027 0.002 TYR A 249 PHE 0.031 0.002 PHE A 728 TRP 0.020 0.002 TRP A 234 HIS 0.004 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00367 (12748) covalent geometry : angle 0.71752 (17295) SS BOND : bond 0.00194 ( 4) SS BOND : angle 1.14380 ( 8) hydrogen bonds : bond 0.07007 ( 625) hydrogen bonds : angle 5.68752 ( 1806) *********************** 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 187 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.458 Fit side-chains REVERT: A 119 TYR cc_start: 0.7787 (m-80) cc_final: 0.7477 (m-80) REVERT: A 383 ARG cc_start: 0.7652 (mtp180) cc_final: 0.6482 (ttp-170) REVERT: A 537 GLN cc_start: 0.5723 (mt0) cc_final: 0.5272 (mt0) REVERT: A 553 ILE cc_start: 0.8699 (mp) cc_final: 0.8465 (mp) REVERT: A 875 MET cc_start: 0.3898 (mmm) cc_final: 0.3577 (tmm) REVERT: A 884 ARG cc_start: 0.5588 (tpp-160) cc_final: 0.5203 (mtm180) REVERT: A 947 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8682 (t80) REVERT: B 139 ASN cc_start: 0.6728 (m-40) cc_final: 0.6076 (p0) REVERT: C 196 TYR cc_start: 0.6936 (m-80) cc_final: 0.6325 (m-80) outliers start: 41 outliers final: 25 residues processed: 179 average time/residue: 0.1030 time to fit residues: 27.9558 Evaluate side-chains 144 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 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 556 LEU 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 A residue 1207 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 171 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 154 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.0030 chunk 121 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 106 optimal weight: 0.0970 chunk 79 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.4192 ------------------------------------------------------------------------------- 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** A1214 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 = 0.4165 r_free = 0.4165 target = 0.168067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.123999 restraints weight = 33970.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.123354 restraints weight = 22445.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.125107 restraints weight = 14799.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.125832 restraints weight = 11036.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.126094 restraints weight = 9819.664| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3634 r_free = 0.3634 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12752 Z= 0.166 Angle : 0.648 7.857 17303 Z= 0.338 Chirality : 0.042 0.225 1974 Planarity : 0.004 0.038 2157 Dihedral : 10.222 132.068 2205 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.67 % Allowed : 20.40 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.19), residues: 1577 helix: -0.22 (0.18), residues: 741 sheet: -2.26 (0.29), residues: 246 loop : -2.93 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 109 TYR 0.030 0.002 TYR A 919 PHE 0.019 0.002 PHE B 99 TRP 0.015 0.002 TRP A 234 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00366 (12748) covalent geometry : angle 0.64765 (17295) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.86145 ( 8) hydrogen bonds : bond 0.06514 ( 625) hydrogen bonds : angle 5.26192 ( 1806) *********************** 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 179 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 131 time to evaluate : 0.469 Fit side-chains REVERT: A 383 ARG cc_start: 0.7593 (mtp180) cc_final: 0.6503 (ttp-170) REVERT: A 553 ILE cc_start: 0.8733 (mp) cc_final: 0.8499 (mp) REVERT: A 556 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6477 (mt) REVERT: A 884 ARG cc_start: 0.5491 (tpp-160) cc_final: 0.5146 (mtm180) REVERT: A 947 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8774 (t80) REVERT: A 1036 PHE cc_start: 0.7582 (m-80) cc_final: 0.7368 (m-80) REVERT: B 139 ASN cc_start: 0.6654 (m-40) cc_final: 0.6021 (p0) REVERT: C 196 TYR cc_start: 0.6972 (m-80) cc_final: 0.6522 (m-80) outliers start: 48 outliers final: 36 residues processed: 171 average time/residue: 0.1011 time to fit residues: 26.4128 Evaluate side-chains 157 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 206 PHE 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 523 ASP Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 717 CYS Chi-restraints excluded: chain A residue 761 LEU 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 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 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 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 91 optimal weight: 7.9990 chunk 62 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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** ** 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 = 0.4191 r_free = 0.4191 target = 0.170262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.126123 restraints weight = 35740.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.124461 restraints weight = 23889.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.126399 restraints weight = 17428.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.127087 restraints weight = 12621.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.127614 restraints weight = 10284.321| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12752 Z= 0.153 Angle : 0.607 8.138 17303 Z= 0.317 Chirality : 0.041 0.149 1974 Planarity : 0.004 0.039 2157 Dihedral : 9.840 132.545 2202 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.89 % Allowed : 20.32 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.20), residues: 1577 helix: 0.24 (0.18), residues: 742 sheet: -2.05 (0.29), residues: 246 loop : -2.72 (0.22), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 144 TYR 0.016 0.002 TYR C 53 PHE 0.017 0.001 PHE B 99 TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00336 (12748) covalent geometry : angle 0.60649 (17295) SS BOND : bond 0.00098 ( 4) SS BOND : angle 0.75484 ( 8) hydrogen bonds : bond 0.06158 ( 625) hydrogen bonds : angle 4.99795 ( 1806) *********************** 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 194 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 130 time to evaluate : 0.486 Fit side-chains REVERT: A 119 TYR cc_start: 0.7694 (m-80) cc_final: 0.7415 (m-80) REVERT: A 146 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8137 (tp) REVERT: A 147 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7402 (ttp80) REVERT: A 383 ARG cc_start: 0.7587 (mtp180) cc_final: 0.6390 (ttp80) REVERT: A 444 ARG cc_start: 0.7758 (ttt180) cc_final: 0.6833 (ttt180) REVERT: A 537 GLN cc_start: 0.5570 (mt0) cc_final: 0.5086 (mp10) REVERT: A 553 ILE cc_start: 0.8677 (mp) cc_final: 0.8453 (mp) REVERT: A 556 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6614 (mt) REVERT: A 884 ARG cc_start: 0.5500 (tpp-160) cc_final: 0.5173 (mtm180) REVERT: A 947 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8790 (t80) REVERT: A 1112 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8439 (mt) REVERT: B 139 ASN cc_start: 0.6584 (m-40) cc_final: 0.5989 (p0) REVERT: B 210 PHE cc_start: 0.5338 (p90) cc_final: 0.5070 (p90) REVERT: C 196 TYR cc_start: 0.6914 (m-80) cc_final: 0.6641 (m-10) outliers start: 64 outliers final: 44 residues processed: 185 average time/residue: 0.1011 time to fit residues: 28.5500 Evaluate side-chains 170 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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 146 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 218 LEU 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 523 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 815 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 906 VAL 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 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 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 153 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 120 optimal weight: 0.0030 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 overall best weight: 1.0792 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.171753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.127373 restraints weight = 37194.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126817 restraints weight = 20174.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.128846 restraints weight = 14200.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.129534 restraints weight = 10617.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.129560 restraints weight = 9475.225| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3670 r_free = 0.3670 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12752 Z= 0.136 Angle : 0.588 7.711 17303 Z= 0.305 Chirality : 0.041 0.150 1974 Planarity : 0.003 0.040 2157 Dihedral : 9.523 134.972 2201 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.65 % Allowed : 20.70 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.20), residues: 1577 helix: 0.54 (0.19), residues: 742 sheet: -1.80 (0.30), residues: 243 loop : -2.55 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 109 TYR 0.028 0.001 TYR B 50 PHE 0.020 0.001 PHE A 769 TRP 0.011 0.001 TRP C 112 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00295 (12748) covalent geometry : angle 0.58797 (17295) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.62559 ( 8) hydrogen bonds : bond 0.05849 ( 625) hydrogen bonds : angle 4.76616 ( 1806) *********************** 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 213 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 140 time to evaluate : 0.436 Fit side-chains REVERT: A 132 TYR cc_start: 0.7314 (t80) cc_final: 0.7103 (t80) REVERT: A 146 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8178 (tp) REVERT: A 154 PHE cc_start: 0.7754 (t80) cc_final: 0.7506 (t80) REVERT: A 312 TYR cc_start: 0.7691 (OUTLIER) cc_final: 0.7321 (t80) REVERT: A 383 ARG cc_start: 0.7600 (mtp180) cc_final: 0.6383 (ttp80) REVERT: A 444 ARG cc_start: 0.7699 (ttt180) cc_final: 0.6791 (ttt180) REVERT: A 537 GLN cc_start: 0.5708 (mt0) cc_final: 0.5308 (mt0) REVERT: A 553 ILE cc_start: 0.8606 (mp) cc_final: 0.8387 (mp) REVERT: A 556 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6637 (mt) REVERT: A 724 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8153 (mp) REVERT: A 884 ARG cc_start: 0.5385 (tpp-160) cc_final: 0.5048 (mtm180) REVERT: A 914 LYS cc_start: 0.8028 (pttt) cc_final: 0.7717 (tptt) REVERT: A 947 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8808 (t80) REVERT: A 1112 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8440 (mt) REVERT: B 139 ASN cc_start: 0.6613 (m-40) cc_final: 0.5980 (p0) REVERT: B 210 PHE cc_start: 0.5335 (p90) cc_final: 0.5050 (p90) REVERT: C 196 TYR cc_start: 0.6921 (m-80) cc_final: 0.6626 (m-10) outliers start: 73 outliers final: 52 residues processed: 199 average time/residue: 0.1034 time to fit residues: 30.8270 Evaluate side-chains 182 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 124 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 146 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 218 LEU 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 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 523 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 724 LEU Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 810 THR 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 906 VAL Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 915 PHE 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 1089 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 153 optimal weight: 5.9990 chunk 112 optimal weight: 0.0570 chunk 84 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A1117 GLN C 191 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.171906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.131181 restraints weight = 40255.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128800 restraints weight = 25240.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.131445 restraints weight = 20692.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.131859 restraints weight = 12840.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.136547 restraints weight = 10943.754| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3725 r_free = 0.3725 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12752 Z= 0.138 Angle : 0.590 7.521 17303 Z= 0.307 Chirality : 0.041 0.201 1974 Planarity : 0.004 0.040 2157 Dihedral : 9.338 136.462 2198 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.81 % Allowed : 21.77 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.21), residues: 1577 helix: 0.65 (0.19), residues: 746 sheet: -1.61 (0.31), residues: 241 loop : -2.39 (0.23), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 109 TYR 0.016 0.001 TYR A 467 PHE 0.024 0.001 PHE A 769 TRP 0.011 0.001 TRP C 112 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00300 (12748) covalent geometry : angle 0.58924 (17295) SS BOND : bond 0.00170 ( 4) SS BOND : angle 1.13838 ( 8) hydrogen bonds : bond 0.05773 ( 625) hydrogen bonds : angle 4.71982 ( 1806) *********************** 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 211 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 136 time to evaluate : 0.444 Fit side-chains REVERT: A 63 MET cc_start: 0.7088 (mmm) cc_final: 0.6787 (tpp) REVERT: A 132 TYR cc_start: 0.7399 (t80) cc_final: 0.7159 (t80) REVERT: A 146 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8185 (tp) REVERT: A 154 PHE cc_start: 0.7776 (t80) cc_final: 0.7450 (t80) REVERT: A 312 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7322 (t80) REVERT: A 383 ARG cc_start: 0.7584 (mtp180) cc_final: 0.6375 (ttp80) REVERT: A 444 ARG cc_start: 0.7695 (ttt180) cc_final: 0.6742 (ttt180) REVERT: A 537 GLN cc_start: 0.5764 (mt0) cc_final: 0.5340 (mt0) REVERT: A 556 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6704 (mt) REVERT: A 724 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8167 (mp) REVERT: A 884 ARG cc_start: 0.5224 (tpp-160) cc_final: 0.4975 (mtm180) REVERT: A 886 LYS cc_start: 0.7002 (mtmm) cc_final: 0.6748 (tptt) REVERT: A 914 LYS cc_start: 0.7984 (pttt) cc_final: 0.7680 (tptt) REVERT: A 947 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8886 (t80) REVERT: A 1112 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8467 (mt) REVERT: B 20 VAL cc_start: 0.7345 (t) cc_final: 0.7120 (t) REVERT: B 139 ASN cc_start: 0.6638 (m-40) cc_final: 0.5975 (p0) REVERT: B 210 PHE cc_start: 0.5318 (p90) cc_final: 0.5036 (p90) REVERT: C 196 TYR cc_start: 0.6891 (m-80) cc_final: 0.6634 (m-10) outliers start: 75 outliers final: 60 residues processed: 198 average time/residue: 0.0922 time to fit residues: 28.2011 Evaluate side-chains 193 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 127 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 146 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 218 LEU 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 346 SER 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 452 THR Chi-restraints excluded: chain A residue 523 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 724 LEU Chi-restraints excluded: chain A residue 757 ILE Chi-restraints excluded: chain A residue 761 LEU Chi-restraints excluded: chain A residue 775 THR 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 867 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 930 SER 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 1089 LEU Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1126 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 20 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 7 optimal weight: 0.6980 chunk 145 optimal weight: 0.0570 chunk 87 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 841 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 = 0.4219 r_free = 0.4219 target = 0.172839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.135744 restraints weight = 33608.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.139701 restraints weight = 43260.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.142852 restraints weight = 14182.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143269 restraints weight = 9276.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.144011 restraints weight = 7590.344| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12752 Z= 0.128 Angle : 0.586 11.502 17303 Z= 0.302 Chirality : 0.041 0.206 1974 Planarity : 0.003 0.040 2157 Dihedral : 9.148 136.599 2198 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 4.81 % Allowed : 23.15 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.21), residues: 1577 helix: 0.82 (0.19), residues: 739 sheet: -1.49 (0.31), residues: 241 loop : -2.30 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 109 TYR 0.030 0.001 TYR B 50 PHE 0.020 0.001 PHE A 769 TRP 0.010 0.001 TRP C 112 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00277 (12748) covalent geometry : angle 0.58624 (17295) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.94317 ( 8) hydrogen bonds : bond 0.05553 ( 625) hydrogen bonds : angle 4.62835 ( 1806) *********************** 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 199 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 137 time to evaluate : 0.471 Fit side-chains REVERT: A 132 TYR cc_start: 0.7361 (t80) cc_final: 0.7155 (t80) REVERT: A 154 PHE cc_start: 0.7775 (t80) cc_final: 0.7442 (t80) REVERT: A 312 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.7246 (t80) REVERT: A 383 ARG cc_start: 0.7493 (mtp180) cc_final: 0.6312 (ttp80) REVERT: A 444 ARG cc_start: 0.7616 (ttt180) cc_final: 0.6806 (ttt180) REVERT: A 537 GLN cc_start: 0.5684 (mt0) cc_final: 0.5339 (mt0) REVERT: A 556 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6449 (mt) REVERT: A 593 THR cc_start: 0.4163 (OUTLIER) cc_final: 0.3872 (m) REVERT: A 724 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7888 (mp) REVERT: A 886 LYS cc_start: 0.7131 (mtmm) cc_final: 0.6731 (tptt) REVERT: A 914 LYS cc_start: 0.7914 (pttt) cc_final: 0.7654 (tptt) REVERT: A 947 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8932 (t80) REVERT: B 20 VAL cc_start: 0.7159 (t) cc_final: 0.6953 (t) REVERT: B 139 ASN cc_start: 0.6455 (m-40) cc_final: 0.5958 (p0) REVERT: C 196 TYR cc_start: 0.7053 (m-80) cc_final: 0.6739 (m-10) outliers start: 62 outliers final: 44 residues processed: 189 average time/residue: 0.1005 time to fit residues: 29.0447 Evaluate side-chains 178 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 162 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 314 LEU 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 523 ASP 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 724 LEU Chi-restraints excluded: chain A residue 775 THR Chi-restraints excluded: chain A residue 784 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 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 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 1078 VAL 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 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 51 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 84 optimal weight: 0.6980 chunk 136 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 157 optimal weight: 20.0000 chunk 134 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN C 217 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 = 0.4194 r_free = 0.4194 target = 0.170498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128709 restraints weight = 39167.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127396 restraints weight = 27064.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.130027 restraints weight = 20276.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.130573 restraints weight = 12504.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131219 restraints weight = 11094.533| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12752 Z= 0.163 Angle : 0.614 9.693 17303 Z= 0.317 Chirality : 0.042 0.197 1974 Planarity : 0.004 0.041 2157 Dihedral : 9.175 136.889 2194 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 5.35 % Allowed : 22.92 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.21), residues: 1577 helix: 0.76 (0.19), residues: 739 sheet: -1.46 (0.31), residues: 241 loop : -2.27 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 109 TYR 0.020 0.002 TYR C 53 PHE 0.017 0.001 PHE A 769 TRP 0.012 0.001 TRP C 112 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00367 (12748) covalent geometry : angle 0.61405 (17295) SS BOND : bond 0.00166 ( 4) SS BOND : angle 0.99010 ( 8) hydrogen bonds : bond 0.05885 ( 625) hydrogen bonds : angle 4.74253 ( 1806) *********************** 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 203 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 134 time to evaluate : 0.475 Fit side-chains REVERT: A 132 TYR cc_start: 0.7300 (t80) cc_final: 0.7075 (t80) REVERT: A 154 PHE cc_start: 0.7786 (t80) cc_final: 0.7420 (t80) REVERT: A 312 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.7425 (t80) REVERT: A 383 ARG cc_start: 0.7535 (mtp180) cc_final: 0.6303 (ttp80) REVERT: A 444 ARG cc_start: 0.7650 (ttt180) cc_final: 0.6811 (ttt180) REVERT: A 537 GLN cc_start: 0.5702 (mt0) cc_final: 0.5345 (mt0) REVERT: A 556 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6524 (mt) REVERT: A 593 THR cc_start: 0.4204 (OUTLIER) cc_final: 0.3924 (m) REVERT: A 886 LYS cc_start: 0.7304 (mtmm) cc_final: 0.6854 (tptt) REVERT: A 914 LYS cc_start: 0.7957 (pttt) cc_final: 0.7692 (tptt) REVERT: A 947 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8840 (t80) REVERT: B 20 VAL cc_start: 0.7277 (t) cc_final: 0.7067 (t) REVERT: B 139 ASN cc_start: 0.6532 (m-40) cc_final: 0.5960 (p0) REVERT: C 196 TYR cc_start: 0.7171 (m-80) cc_final: 0.6761 (m-10) outliers start: 69 outliers final: 55 residues processed: 190 average time/residue: 0.1060 time to fit residues: 30.8423 Evaluate side-chains 190 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 131 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 170 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 PHE 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 346 SER Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 369 ASP 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 523 ASP 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 757 ILE 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 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 906 VAL 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 1002 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 1078 VAL 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 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 61 THR 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 40 optimal weight: 0.0060 chunk 109 optimal weight: 9.9990 chunk 89 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.0270 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.3258 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.171615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133400 restraints weight = 31707.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.135680 restraints weight = 37309.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137477 restraints weight = 20540.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138316 restraints weight = 13316.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140530 restraints weight = 10383.338| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12752 Z= 0.145 Angle : 0.605 9.569 17303 Z= 0.310 Chirality : 0.042 0.222 1974 Planarity : 0.003 0.041 2157 Dihedral : 9.088 135.808 2194 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.81 % Allowed : 23.45 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.21), residues: 1577 helix: 0.83 (0.19), residues: 739 sheet: -1.32 (0.31), residues: 241 loop : -2.29 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 109 TYR 0.017 0.001 TYR A 467 PHE 0.015 0.001 PHE A 769 TRP 0.011 0.001 TRP C 112 HIS 0.005 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00322 (12748) covalent geometry : angle 0.60440 (17295) SS BOND : bond 0.00175 ( 4) SS BOND : angle 0.92989 ( 8) hydrogen bonds : bond 0.05775 ( 625) hydrogen bonds : angle 4.70036 ( 1806) *********************** 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 195 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 133 time to evaluate : 0.529 Fit side-chains REVERT: A 132 TYR cc_start: 0.7454 (t80) cc_final: 0.7180 (t80) REVERT: A 154 PHE cc_start: 0.7785 (t80) cc_final: 0.7416 (t80) REVERT: A 312 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.7308 (t80) REVERT: A 383 ARG cc_start: 0.7505 (mtp180) cc_final: 0.6294 (ttp80) REVERT: A 444 ARG cc_start: 0.7675 (ttt180) cc_final: 0.6805 (ttt180) REVERT: A 537 GLN cc_start: 0.5613 (mt0) cc_final: 0.5282 (mt0) REVERT: A 556 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6489 (mt) REVERT: A 593 THR cc_start: 0.4218 (OUTLIER) cc_final: 0.3938 (m) REVERT: A 886 LYS cc_start: 0.7257 (mtmm) cc_final: 0.6773 (tptt) REVERT: A 914 LYS cc_start: 0.7953 (pttt) cc_final: 0.7690 (tptt) REVERT: A 947 PHE cc_start: 0.9174 (OUTLIER) cc_final: 0.8915 (t80) REVERT: A 1112 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8462 (mt) REVERT: B 139 ASN cc_start: 0.6597 (m-40) cc_final: 0.6017 (p0) REVERT: C 196 TYR cc_start: 0.7048 (m-80) cc_final: 0.6590 (m-10) outliers start: 62 outliers final: 56 residues processed: 185 average time/residue: 0.0997 time to fit residues: 28.4340 Evaluate side-chains 190 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 129 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 170 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 PHE 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 346 SER Chi-restraints excluded: chain A residue 347 VAL 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 523 ASP 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 757 ILE Chi-restraints excluded: chain A residue 775 THR 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 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 906 VAL 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 1002 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 1105 VAL Chi-restraints excluded: chain A residue 1112 LEU 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 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 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 88 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 139 optimal weight: 0.3980 chunk 108 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4217 r_free = 0.4217 target = 0.172346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.129488 restraints weight = 39469.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.127658 restraints weight = 26160.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.130294 restraints weight = 18939.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.132274 restraints weight = 11916.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.132380 restraints weight = 10146.027| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12752 Z= 0.124 Angle : 0.584 11.522 17303 Z= 0.299 Chirality : 0.041 0.215 1974 Planarity : 0.003 0.041 2157 Dihedral : 8.868 133.189 2194 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.13 % Allowed : 24.06 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.21), residues: 1577 helix: 1.00 (0.19), residues: 739 sheet: -1.15 (0.32), residues: 240 loop : -2.16 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 109 TYR 0.018 0.001 TYR A 467 PHE 0.014 0.001 PHE A 769 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00264 (12748) covalent geometry : angle 0.58382 (17295) SS BOND : bond 0.00165 ( 4) SS BOND : angle 0.83827 ( 8) hydrogen bonds : bond 0.05412 ( 625) hydrogen bonds : angle 4.54820 ( 1806) ********************** 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 199 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 146 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 154 PHE cc_start: 0.7730 (t80) cc_final: 0.7364 (t80) REVERT: A 312 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.7382 (t80) REVERT: A 383 ARG cc_start: 0.7598 (mtp180) cc_final: 0.6309 (ttp80) REVERT: A 444 ARG cc_start: 0.7730 (ttt180) cc_final: 0.6875 (ttt180) REVERT: A 537 GLN cc_start: 0.5692 (mt0) cc_final: 0.5305 (mt0) REVERT: A 556 LEU cc_start: 0.7045 (OUTLIER) cc_final: 0.6638 (mt) REVERT: A 593 THR cc_start: 0.4185 (OUTLIER) cc_final: 0.3911 (m) REVERT: A 886 LYS cc_start: 0.7380 (mtmm) cc_final: 0.6860 (tptt) REVERT: A 914 LYS cc_start: 0.7935 (pttt) cc_final: 0.7727 (tptt) REVERT: A 947 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8846 (t80) REVERT: A 1112 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8435 (mt) REVERT: B 139 ASN cc_start: 0.6699 (m-40) cc_final: 0.6052 (p0) REVERT: C 195 LEU cc_start: 0.6273 (tp) cc_final: 0.6011 (tp) REVERT: C 196 TYR cc_start: 0.6957 (m-80) cc_final: 0.6501 (m-10) outliers start: 53 outliers final: 45 residues processed: 187 average time/residue: 0.1051 time to fit residues: 29.7946 Evaluate side-chains 186 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 136 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 170 THR 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 347 VAL 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 523 ASP 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 775 THR Chi-restraints excluded: chain A residue 815 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 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 1002 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 50 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 132 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 119 optimal weight: 0.0030 chunk 52 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 overall best weight: 1.1594 ------------------------------------------------------------------------------- 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 = 0.4208 r_free = 0.4208 target = 0.171342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.132419 restraints weight = 27925.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.131328 restraints weight = 31593.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.134081 restraints weight = 23921.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.134472 restraints weight = 14118.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.136472 restraints weight = 12116.233| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12752 Z= 0.137 Angle : 0.604 12.166 17303 Z= 0.307 Chirality : 0.041 0.212 1974 Planarity : 0.003 0.040 2157 Dihedral : 8.881 133.028 2194 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.51 % Allowed : 24.45 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.21), residues: 1577 helix: 0.98 (0.19), residues: 740 sheet: -1.14 (0.32), residues: 239 loop : -2.11 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 109 TYR 0.027 0.002 TYR A 919 PHE 0.024 0.001 PHE A 316 TRP 0.011 0.001 TRP C 112 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00301 (12748) covalent geometry : angle 0.60348 (17295) SS BOND : bond 0.00152 ( 4) SS BOND : angle 1.06088 ( 8) hydrogen bonds : bond 0.05545 ( 625) hydrogen bonds : angle 4.56434 ( 1806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2604.99 seconds wall clock time: 45 minutes 44.67 seconds (2744.67 seconds total)