Starting phenix.real_space_refine on Sat Sep 12 02:42:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7niw_12367/09_2026/7niw_12367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7niw_12367/09_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_12367/09_2026/7niw_12367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7niw_12367/09_2026/7niw_12367.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7niw_12367/09_2026/7niw_12367.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7niw_12367/09_2026/7niw_12367.cif" model { file = "/net/cci-nas-00/data/ceres_data/7niw_12367/09_2026/7niw_12367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7niw_12367/09_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): 0.12s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 2.49, per 1000 atoms: 0.20 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: 0.73 Conformation dependent library (CDL) restraints added in 574.7 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: 0.32 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: 2.06 Time building geometry restraints manager: 0.99 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: 7008 25.83 - 51.65: 449 51.65 - 77.48: 38 77.48 - 103.31: 11 103.31 - 129.14: 2 Dihedral angle restraints: 7508 sinusoidal: 2943 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 7505 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: 7.580 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.980 Find NCS groups from input model: 0.060 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 16.721 129.137 4574 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/Z covalent geometry : bond 0.01519 / 0.68 (12748) covalent geometry : angle 1.28887 / 0.69 (17295) SS BOND : bond 0.00515 / 0.22 ( 4) SS BOND : angle 1.51536 / 0.86 ( 8) hydrogen bonds : bond 0.19862 / 12.89 ( 625) hydrogen bonds : angle 8.41184 / 6.06 ( 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 : 0.335 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: 0.1076 time to fit residues: 29.5387 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 : 0.453 ------------------------------------------------------------------------------- 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... 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.168257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125256 restraints weight = 35373.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122649 restraints weight = 22652.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.125040 restraints weight = 16106.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.125665 restraints weight = 11291.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.125996 restraints weight = 10409.583| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12752 Z= 0.166 Angle : 0.719 8.496 17303 Z= 0.374 Chirality : 0.044 0.224 1974 Planarity : 0.004 0.039 2157 Dihedral : 10.383 128.127 1840 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.06 % Allowed : 17.42 % 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: -3.33 (0.18), residues: 1577 helix: -1.14 (0.17), residues: 745 sheet: -2.70 (0.28), residues: 254 loop : -3.30 (0.21), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 109 TYR 0.027 0.002 TYR A 249 PHE 0.030 0.002 PHE A 728 TRP 0.021 0.002 TRP A 234 HIS 0.004 0.001 HIS A1154 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (12748) covalent geometry : angle 0.71871 / 0.37 (17295) SS BOND : bond 0.00213 / 0.10 ( 4) SS BOND : angle 1.20202 / 0.67 ( 8) hydrogen bonds : bond 0.07108 / 4.66 ( 625) hydrogen bonds : angle 5.70302 / 4.12 ( 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 186 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.354 Fit side-chains REVERT: A 119 TYR cc_start: 0.7829 (m-80) cc_final: 0.7526 (m-80) REVERT: A 218 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8437 (mm) REVERT: A 383 ARG cc_start: 0.7670 (mtp180) cc_final: 0.6377 (ttp80) REVERT: A 537 GLN cc_start: 0.5714 (mt0) cc_final: 0.5248 (mt0) REVERT: A 553 ILE cc_start: 0.8669 (mp) cc_final: 0.8441 (mp) REVERT: A 875 MET cc_start: 0.3914 (mmm) cc_final: 0.3577 (tmm) REVERT: A 884 ARG cc_start: 0.5706 (tpp-160) cc_final: 0.5266 (mtm180) REVERT: A 901 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7660 (mt-10) REVERT: A 947 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8687 (t80) REVERT: B 139 ASN cc_start: 0.6771 (m-40) cc_final: 0.6070 (p0) REVERT: C 196 TYR cc_start: 0.6867 (m-80) cc_final: 0.6337 (m-80) outliers start: 40 outliers final: 25 residues processed: 179 average time/residue: 0.0871 time to fit residues: 23.8502 Evaluate side-chains 146 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 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: 0.8980 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 121 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 332 ASN A 349 GLN A 841 ASN ** A 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.170660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134273 restraints weight = 33721.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136820 restraints weight = 42722.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.139185 restraints weight = 16787.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140961 restraints weight = 10349.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.141628 restraints weight = 7957.259| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3804 r_free = 0.3804 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12752 Z= 0.149 Angle : 0.624 7.219 17303 Z= 0.325 Chirality : 0.041 0.242 1974 Planarity : 0.004 0.038 2157 Dihedral : 9.467 124.612 1822 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.51 % Allowed : 20.17 % Favored : 76.32 % 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: -2.16 (0.20), residues: 1577 helix: -0.05 (0.18), residues: 741 sheet: -2.19 (0.29), residues: 246 loop : -2.87 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 109 TYR 0.028 0.002 TYR A 919 PHE 0.020 0.002 PHE C 142 TRP 0.015 0.002 TRP A 234 HIS 0.002 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (12748) covalent geometry : angle 0.62374 / 0.33 (17295) SS BOND : bond 0.00129 / 0.06 ( 4) SS BOND : angle 0.78255 / 0.45 ( 8) hydrogen bonds : bond 0.06211 / 4.04 ( 625) hydrogen bonds : angle 5.11101 / 3.71 ( 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 185 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 0.431 Fit side-chains REVERT: A 383 ARG cc_start: 0.7519 (mtp180) cc_final: 0.6512 (ttp-170) REVERT: A 553 ILE cc_start: 0.8813 (mp) cc_final: 0.8566 (mp) REVERT: A 556 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6370 (mt) REVERT: A 769 PHE cc_start: 0.8805 (m-80) cc_final: 0.8584 (m-80) REVERT: A 884 ARG cc_start: 0.5292 (tpp-160) cc_final: 0.5076 (mtm180) REVERT: A 914 LYS cc_start: 0.8077 (pttt) cc_final: 0.7674 (tptt) REVERT: A 947 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8821 (t80) REVERT: A 1036 PHE cc_start: 0.7461 (m-80) cc_final: 0.7224 (m-80) REVERT: A 1129 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8424 (t0) REVERT: B 139 ASN cc_start: 0.6549 (m-40) cc_final: 0.6010 (p0) REVERT: C 196 TYR cc_start: 0.7002 (m-80) cc_final: 0.6551 (m-80) outliers start: 46 outliers final: 36 residues processed: 176 average time/residue: 0.0965 time to fit residues: 25.6325 Evaluate side-chains 158 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASP 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 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 846 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 915 PHE 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 1129 ASN Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 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 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 118 optimal weight: 0.0570 chunk 90 optimal weight: 0.4980 chunk 86 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 49 optimal weight: 0.0010 chunk 102 optimal weight: 0.0770 chunk 88 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 64.648 > 50:) overall best weight: 0.2662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 GLN A 929 ASN A1129 ASN A1214 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.174401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.130980 restraints weight = 35605.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.130034 restraints weight = 22703.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.132353 restraints weight = 14536.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.132984 restraints weight = 10670.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.133220 restraints weight = 9525.514| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 12752 Z= 0.122 Angle : 0.577 7.050 17303 Z= 0.301 Chirality : 0.040 0.140 1974 Planarity : 0.003 0.039 2157 Dihedral : 8.866 120.182 1818 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.05 % Allowed : 20.40 % Favored : 75.55 % 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: -1.49 (0.20), residues: 1577 helix: 0.54 (0.19), residues: 739 sheet: -1.83 (0.30), residues: 246 loop : -2.60 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 144 TYR 0.017 0.001 TYR A 120 PHE 0.016 0.001 PHE A1041 TRP 0.013 0.001 TRP A 234 HIS 0.005 0.001 HIS A 614 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (12748) covalent geometry : angle 0.57747 / 0.30 (17295) SS BOND : bond 0.00144 / 0.07 ( 4) SS BOND : angle 0.55464 / 0.33 ( 8) hydrogen bonds : bond 0.05525 / 3.56 ( 625) hydrogen bonds : angle 4.77010 / 3.46 ( 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 196 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 143 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 119 TYR cc_start: 0.7536 (m-80) cc_final: 0.7289 (m-80) REVERT: A 132 TYR cc_start: 0.7247 (t80) cc_final: 0.7022 (t80) REVERT: A 154 PHE cc_start: 0.7762 (t80) cc_final: 0.7555 (t80) REVERT: A 218 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8134 (mm) REVERT: A 383 ARG cc_start: 0.7584 (mtp180) cc_final: 0.6407 (ttp80) REVERT: A 444 ARG cc_start: 0.7726 (ttt180) cc_final: 0.6780 (ttt180) REVERT: A 522 PHE cc_start: 0.5955 (m-80) cc_final: 0.5532 (m-10) REVERT: A 553 ILE cc_start: 0.8649 (mp) cc_final: 0.8425 (mp) REVERT: A 556 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6629 (mt) REVERT: A 769 PHE cc_start: 0.8857 (m-80) cc_final: 0.8644 (m-80) REVERT: A 884 ARG cc_start: 0.5383 (tpp-160) cc_final: 0.5054 (mtm180) REVERT: A 914 LYS cc_start: 0.8013 (pttt) cc_final: 0.7698 (tptt) REVERT: A 947 PHE cc_start: 0.9012 (OUTLIER) cc_final: 0.8780 (t80) REVERT: B 139 ASN cc_start: 0.6527 (m-40) cc_final: 0.5958 (p0) REVERT: B 210 PHE cc_start: 0.5290 (p90) cc_final: 0.4982 (p90) REVERT: C 196 TYR cc_start: 0.6936 (m-80) cc_final: 0.6715 (m-10) outliers start: 53 outliers final: 34 residues processed: 186 average time/residue: 0.0912 time to fit residues: 25.8427 Evaluate side-chains 163 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 126 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 314 LEU 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 846 ILE Chi-restraints excluded: chain A residue 851 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 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 107 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 94 THR Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 153 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 332 ASN A 349 GLN A1141 GLN A1214 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.169132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.127140 restraints weight = 37574.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.124198 restraints weight = 24973.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126294 restraints weight = 20475.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.128613 restraints weight = 12865.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.128746 restraints weight = 10493.306| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12752 Z= 0.193 Angle : 0.643 7.882 17303 Z= 0.334 Chirality : 0.042 0.208 1974 Planarity : 0.004 0.039 2157 Dihedral : 8.999 121.234 1816 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 5.65 % Allowed : 21.24 % Favored : 73.11 % 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: -1.55 (0.20), residues: 1577 helix: 0.42 (0.19), residues: 745 sheet: -1.92 (0.30), residues: 245 loop : -2.51 (0.23), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 109 TYR 0.026 0.002 TYR C 53 PHE 0.017 0.002 PHE B 99 TRP 0.013 0.002 TRP C 112 HIS 0.005 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.19 (12748) covalent geometry : angle 0.64246 / 0.33 (17295) SS BOND : bond 0.00286 / 0.15 ( 4) SS BOND : angle 1.24003 / 0.71 ( 8) hydrogen bonds : bond 0.06297 / 4.10 ( 625) hydrogen bonds : angle 4.90169 / 3.56 ( 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 203 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 129 time to evaluate : 0.464 Fit side-chains REVERT: A 146 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8223 (tp) REVERT: A 154 PHE cc_start: 0.7862 (t80) cc_final: 0.7610 (t80) REVERT: A 312 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7391 (t80) REVERT: A 383 ARG cc_start: 0.7549 (mtp180) cc_final: 0.6370 (ttp80) REVERT: A 444 ARG cc_start: 0.7720 (ttt180) cc_final: 0.6834 (ttt180) REVERT: A 537 GLN cc_start: 0.5720 (mt0) cc_final: 0.5319 (mt0) REVERT: A 553 ILE cc_start: 0.8671 (mp) cc_final: 0.8450 (mp) REVERT: A 556 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6558 (mt) REVERT: A 724 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8159 (mp) REVERT: A 884 ARG cc_start: 0.5291 (tpp-160) cc_final: 0.5011 (mtm180) REVERT: A 914 LYS cc_start: 0.8074 (pttt) cc_final: 0.7725 (tptt) REVERT: A 947 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8858 (t80) REVERT: A 948 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7969 (ttm) REVERT: A 1112 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8476 (mt) REVERT: B 139 ASN cc_start: 0.6560 (m-40) cc_final: 0.5964 (p0) REVERT: B 210 PHE cc_start: 0.5336 (p90) cc_final: 0.5070 (p90) REVERT: C 196 TYR cc_start: 0.7083 (m-80) cc_final: 0.6762 (m-10) outliers start: 74 outliers final: 49 residues processed: 190 average time/residue: 0.0843 time to fit residues: 25.0302 Evaluate side-chains 179 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 123 time to evaluate : 0.388 ------------------------------------------------------------------------------- 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 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 713 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 784 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 948 MET Chi-restraints excluded: chain A residue 987 LEU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 153 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 GLN A1214 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 = 0.4213 r_free = 0.4213 target = 0.172333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131885 restraints weight = 40410.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.129620 restraints weight = 26050.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132213 restraints weight = 21203.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.133295 restraints weight = 12306.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.135316 restraints weight = 10610.179| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3717 r_free = 0.3717 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12752 Z= 0.130 Angle : 0.582 7.305 17303 Z= 0.302 Chirality : 0.040 0.211 1974 Planarity : 0.003 0.040 2157 Dihedral : 8.659 119.501 1814 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.81 % Allowed : 22.46 % Favored : 72.73 % 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: -1.18 (0.21), residues: 1577 helix: 0.72 (0.19), residues: 745 sheet: -1.62 (0.31), residues: 241 loop : -2.37 (0.23), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 109 TYR 0.016 0.001 TYR A 120 PHE 0.017 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/Z covalent geometry : bond 0.00275 / 0.13 (12748) covalent geometry : angle 0.58173 / 0.30 (17295) SS BOND : bond 0.00120 / 0.06 ( 4) SS BOND : angle 0.84641 / 0.49 ( 8) hydrogen bonds : bond 0.05690 / 3.68 ( 625) hydrogen bonds : angle 4.65928 / 3.38 ( 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 202 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 139 time to evaluate : 0.388 Fit side-chains REVERT: A 132 TYR cc_start: 0.7347 (t80) cc_final: 0.7127 (t80) REVERT: A 146 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8106 (tp) REVERT: A 154 PHE cc_start: 0.7790 (t80) cc_final: 0.7515 (t80) REVERT: A 218 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8218 (mm) REVERT: A 312 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7345 (t80) REVERT: A 383 ARG cc_start: 0.7558 (mtp180) cc_final: 0.6298 (ttp80) REVERT: A 444 ARG cc_start: 0.7683 (ttt180) cc_final: 0.6770 (ttt180) REVERT: A 537 GLN cc_start: 0.5760 (mt0) cc_final: 0.5345 (mt0) REVERT: A 553 ILE cc_start: 0.8591 (mp) cc_final: 0.8382 (mp) REVERT: A 556 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6688 (mt) REVERT: A 724 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8156 (mp) REVERT: A 884 ARG cc_start: 0.5306 (tpp-160) cc_final: 0.5038 (mtm180) REVERT: A 914 LYS cc_start: 0.7975 (pttt) cc_final: 0.7701 (tptt) REVERT: A 947 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8866 (t80) REVERT: A 1112 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8427 (mt) REVERT: B 139 ASN cc_start: 0.6575 (m-40) cc_final: 0.5997 (p0) REVERT: B 210 PHE cc_start: 0.5311 (p90) cc_final: 0.5038 (p90) REVERT: C 196 TYR cc_start: 0.6931 (m-80) cc_final: 0.6633 (m-10) outliers start: 63 outliers final: 44 residues processed: 191 average time/residue: 0.0882 time to fit residues: 25.9958 Evaluate side-chains 178 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain A residue 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 719 ILE 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 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 947 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1112 LEU Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1173 THR Chi-restraints excluded: chain A residue 1195 ILE Chi-restraints excluded: chain A residue 1202 THR Chi-restraints excluded: chain A residue 1226 CYS Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 20 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 145 optimal weight: 0.0870 chunk 87 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 GLN 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 = 0.4222 r_free = 0.4222 target = 0.173185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.136679 restraints weight = 33533.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138558 restraints weight = 45422.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.141987 restraints weight = 18103.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.145121 restraints weight = 10180.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145428 restraints weight = 6743.969| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12752 Z= 0.125 Angle : 0.591 11.639 17303 Z= 0.301 Chirality : 0.040 0.217 1974 Planarity : 0.004 0.058 2157 Dihedral : 8.489 118.088 1814 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.35 % Allowed : 23.15 % Favored : 72.50 % 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: -0.97 (0.21), residues: 1577 helix: 0.89 (0.19), residues: 738 sheet: -1.45 (0.32), residues: 242 loop : -2.26 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 109 TYR 0.018 0.001 TYR B 141 PHE 0.023 0.001 PHE A 769 TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (12748) covalent geometry : angle 0.59073 / 0.30 (17295) SS BOND : bond 0.00125 / 0.06 ( 4) SS BOND : angle 0.80019 / 0.47 ( 8) hydrogen bonds : bond 0.05548 / 3.58 ( 625) hydrogen bonds : angle 4.55740 / 3.31 ( 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 196 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 139 time to evaluate : 0.312 Fit side-chains REVERT: A 132 TYR cc_start: 0.7338 (t80) cc_final: 0.7108 (t80) REVERT: A 154 PHE cc_start: 0.7775 (t80) cc_final: 0.7406 (t80) REVERT: A 218 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8225 (mm) REVERT: A 312 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.7226 (t80) REVERT: A 383 ARG cc_start: 0.7446 (mtp180) cc_final: 0.6329 (ttp80) REVERT: A 444 ARG cc_start: 0.7644 (ttt180) cc_final: 0.6790 (ttt180) REVERT: A 537 GLN cc_start: 0.5690 (mt0) cc_final: 0.5346 (mt0) REVERT: A 553 ILE cc_start: 0.8669 (mp) cc_final: 0.8449 (mp) REVERT: A 556 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6402 (mt) REVERT: A 593 THR cc_start: 0.4168 (OUTLIER) cc_final: 0.3853 (m) REVERT: A 724 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7915 (mp) REVERT: A 914 LYS cc_start: 0.7923 (pttt) cc_final: 0.7665 (tptt) REVERT: A 947 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8919 (t80) REVERT: B 20 VAL cc_start: 0.7073 (t) cc_final: 0.6852 (t) REVERT: B 139 ASN cc_start: 0.6434 (m-40) cc_final: 0.5978 (p0) REVERT: B 210 PHE cc_start: 0.5283 (p90) cc_final: 0.5055 (p90) REVERT: C 196 TYR cc_start: 0.7041 (m-80) cc_final: 0.6721 (m-10) outliers start: 57 outliers final: 45 residues processed: 187 average time/residue: 0.0894 time to fit residues: 25.6287 Evaluate side-chains 181 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 130 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 THR 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 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 719 ILE Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 775 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 947 PHE Chi-restraints excluded: chain A residue 987 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 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: 2.9990 chunk 136 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 134 optimal weight: 0.0370 chunk 23 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4208 r_free = 0.4208 target = 0.171901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130304 restraints weight = 38632.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129094 restraints weight = 26042.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.131145 restraints weight = 19281.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.133607 restraints weight = 11884.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.133633 restraints weight = 9843.813| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (5 function evaluations) r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12752 Z= 0.147 Angle : 0.597 9.696 17303 Z= 0.308 Chirality : 0.041 0.217 1974 Planarity : 0.004 0.039 2157 Dihedral : 8.415 116.187 1811 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.74 % Allowed : 23.07 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.95 (0.21), residues: 1577 helix: 0.88 (0.19), residues: 738 sheet: -1.43 (0.31), residues: 240 loop : -2.22 (0.24), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 109 TYR 0.021 0.002 TYR A 919 PHE 0.019 0.001 PHE A 769 TRP 0.012 0.001 TRP C 112 HIS 0.005 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (12748) covalent geometry : angle 0.59674 / 0.31 (17295) SS BOND : bond 0.00137 / 0.07 ( 4) SS BOND : angle 0.80132 / 0.47 ( 8) hydrogen bonds : bond 0.05715 / 3.71 ( 625) hydrogen bonds : angle 4.62716 / 3.36 ( 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 197 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 136 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 154 PHE cc_start: 0.7808 (t80) cc_final: 0.7474 (t80) REVERT: A 218 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8229 (mm) REVERT: A 312 TYR cc_start: 0.7844 (OUTLIER) cc_final: 0.7410 (t80) REVERT: A 383 ARG cc_start: 0.7488 (mtp180) cc_final: 0.6318 (ttp80) REVERT: A 444 ARG cc_start: 0.7669 (ttt180) cc_final: 0.6820 (ttt180) REVERT: A 537 GLN cc_start: 0.5710 (mt0) cc_final: 0.5364 (mt0) REVERT: A 553 ILE cc_start: 0.8699 (mp) cc_final: 0.8489 (mp) REVERT: A 556 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6481 (mt) REVERT: A 593 THR cc_start: 0.4151 (OUTLIER) cc_final: 0.3841 (m) REVERT: A 914 LYS cc_start: 0.7945 (pttt) cc_final: 0.7674 (tptt) REVERT: A 947 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8838 (t80) REVERT: A 1112 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8417 (mt) REVERT: B 20 VAL cc_start: 0.7188 (t) cc_final: 0.6977 (t) REVERT: B 139 ASN cc_start: 0.6456 (m-40) cc_final: 0.5925 (p0) REVERT: C 196 TYR cc_start: 0.7104 (m-80) cc_final: 0.6777 (m-10) outliers start: 61 outliers final: 49 residues processed: 185 average time/residue: 0.0903 time to fit residues: 25.7804 Evaluate side-chains 185 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 130 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 170 THR 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 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 719 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 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 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 B residue 186 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 40 optimal weight: 5.9990 chunk 109 optimal weight: 0.0020 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 0.0770 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 overall best weight: 0.3946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 GLN A1117 GLN A1214 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 = 0.4242 r_free = 0.4242 target = 0.174911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.138089 restraints weight = 31540.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141466 restraints weight = 38681.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143359 restraints weight = 17508.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.144877 restraints weight = 11115.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.145914 restraints weight = 8894.532| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3869 r_free = 0.3869 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.3869 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 12752 Z= 0.116 Angle : 0.578 11.067 17303 Z= 0.293 Chirality : 0.039 0.218 1974 Planarity : 0.003 0.040 2157 Dihedral : 8.061 111.646 1811 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.59 % Allowed : 24.75 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.69 (0.21), residues: 1577 helix: 1.10 (0.19), residues: 735 sheet: -1.19 (0.32), residues: 241 loop : -2.14 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 109 TYR 0.020 0.001 TYR A 132 PHE 0.017 0.001 PHE A 316 TRP 0.013 0.001 TRP A 234 HIS 0.003 0.000 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (12748) covalent geometry : angle 0.57803 / 0.29 (17295) SS BOND : bond 0.00205 / 0.10 ( 4) SS BOND : angle 0.61733 / 0.36 ( 8) hydrogen bonds : bond 0.05224 / 3.35 ( 625) hydrogen bonds : angle 4.42221 / 3.22 ( 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 201 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.496 Fit side-chains revert: symmetry clash REVERT: A 154 PHE cc_start: 0.7702 (t80) cc_final: 0.7377 (t80) REVERT: A 218 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8233 (mm) REVERT: A 312 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.7336 (t80) REVERT: A 374 ASN cc_start: 0.7294 (m-40) cc_final: 0.6905 (t0) REVERT: A 383 ARG cc_start: 0.7410 (mtp180) cc_final: 0.6290 (ttp80) REVERT: A 444 ARG cc_start: 0.7612 (ttt180) cc_final: 0.6829 (ttt180) REVERT: A 537 GLN cc_start: 0.5626 (mt0) cc_final: 0.5371 (mt0) REVERT: A 553 ILE cc_start: 0.8716 (mp) cc_final: 0.8487 (mp) REVERT: A 556 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6345 (mt) REVERT: A 593 THR cc_start: 0.3994 (OUTLIER) cc_final: 0.3691 (m) REVERT: A 947 PHE cc_start: 0.9144 (OUTLIER) cc_final: 0.8908 (t80) REVERT: A 1112 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8480 (mt) REVERT: B 139 ASN cc_start: 0.6349 (m-40) cc_final: 0.5943 (p0) REVERT: C 196 TYR cc_start: 0.7110 (m-80) cc_final: 0.6778 (m-10) outliers start: 46 outliers final: 37 residues processed: 192 average time/residue: 0.1030 time to fit residues: 30.3688 Evaluate side-chains 184 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 141 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 PHE Chi-restraints excluded: chain A residue 87 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 206 PHE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 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 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 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 186 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 88 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 97 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 GLN ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4226 r_free = 0.4226 target = 0.172913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.130298 restraints weight = 39431.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.128217 restraints weight = 24098.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.131210 restraints weight = 18997.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.131860 restraints weight = 12007.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.133560 restraints weight = 10603.987| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3718 r_free = 0.3718 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3719 r_free = 0.3719 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.3719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12752 Z= 0.128 Angle : 0.596 10.539 17303 Z= 0.304 Chirality : 0.040 0.219 1974 Planarity : 0.003 0.040 2157 Dihedral : 7.944 109.645 1811 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.44 % Allowed : 25.13 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.61 (0.21), residues: 1577 helix: 1.13 (0.19), residues: 738 sheet: -1.16 (0.32), residues: 242 loop : -2.07 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 109 TYR 0.026 0.001 TYR A 919 PHE 0.025 0.001 PHE A 316 TRP 0.010 0.001 TRP C 112 HIS 0.003 0.000 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (12748) covalent geometry : angle 0.59585 / 0.30 (17295) SS BOND : bond 0.00158 / 0.08 ( 4) SS BOND : angle 1.04599 / 0.61 ( 8) hydrogen bonds : bond 0.05285 / 3.42 ( 625) hydrogen bonds : angle 4.42902 / 3.23 ( 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 186 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 142 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 154 PHE cc_start: 0.7717 (t80) cc_final: 0.7384 (t80) REVERT: A 218 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8211 (mm) REVERT: A 312 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7498 (t80) REVERT: A 374 ASN cc_start: 0.7402 (m-40) cc_final: 0.6922 (t0) REVERT: A 383 ARG cc_start: 0.7573 (mtp180) cc_final: 0.6322 (ttp80) REVERT: A 444 ARG cc_start: 0.7699 (ttt180) cc_final: 0.6846 (ttt180) REVERT: A 537 GLN cc_start: 0.5720 (mt0) cc_final: 0.5359 (mt0) REVERT: A 556 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6656 (mt) REVERT: A 593 THR cc_start: 0.4071 (OUTLIER) cc_final: 0.3756 (m) REVERT: A 947 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8841 (t80) REVERT: B 139 ASN cc_start: 0.6554 (m-40) cc_final: 0.5980 (p0) REVERT: C 196 TYR cc_start: 0.6911 (m-80) cc_final: 0.6398 (m-10) outliers start: 44 outliers final: 34 residues processed: 175 average time/residue: 0.1004 time to fit residues: 27.3122 Evaluate side-chains 176 residues out of total 1305 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 218 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 312 TYR Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 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 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 1002 LEU Chi-restraints excluded: chain A residue 1022 GLU Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1049 VAL Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1078 VAL Chi-restraints excluded: chain A residue 1105 VAL Chi-restraints excluded: chain A residue 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 186 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 50 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 119 optimal weight: 0.0050 chunk 52 optimal weight: 0.0010 chunk 144 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 GLN 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 = 0.4223 r_free = 0.4223 target = 0.172507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.134046 restraints weight = 27913.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.134127 restraints weight = 29364.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.136071 restraints weight = 23248.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.137072 restraints weight = 13781.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.138645 restraints weight = 11644.172| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (6 function evaluations) r_final: 0.3797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12752 Z= 0.130 Angle : 0.600 10.612 17303 Z= 0.306 Chirality : 0.041 0.223 1974 Planarity : 0.003 0.040 2157 Dihedral : 7.736 107.539 1808 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.74 % Allowed : 24.90 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.57 (0.21), residues: 1577 helix: 1.16 (0.19), residues: 741 sheet: -1.05 (0.32), residues: 238 loop : -2.08 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 109 TYR 0.023 0.002 TYR A 919 PHE 0.023 0.001 PHE A 316 TRP 0.010 0.001 TRP C 112 HIS 0.003 0.000 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (12748) covalent geometry : angle 0.59942 / 0.31 (17295) SS BOND : bond 0.00151 / 0.07 ( 4) SS BOND : angle 1.24480 / 0.64 ( 8) hydrogen bonds : bond 0.05346 / 3.46 ( 625) hydrogen bonds : angle 4.41867 / 3.22 ( 1806) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.11 seconds wall clock time: 41 minutes 34.05 seconds (2494.05 seconds total)