Starting phenix.real_space_refine on Wed Mar 4 10:52:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a6c_11670/03_2026/7a6c_11670.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a6c_11670/03_2026/7a6c_11670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a6c_11670/03_2026/7a6c_11670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a6c_11670/03_2026/7a6c_11670.map" model { file = "/net/cci-nas-00/data/ceres_data/7a6c_11670/03_2026/7a6c_11670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a6c_11670/03_2026/7a6c_11670.cif" } resolution = 3.6 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 8251 2.51 5 N 2092 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12717 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9050 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 27, 'TRANS': 1136} Chain breaks: 2 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CYS%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1647 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PRO%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 364 Unusual residues: {'CLR': 10, 'R0Z': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 2.70, per 1000 atoms: 0.21 Number of scatterers: 12717 At special positions: 0 Unit cell: (102.48, 206.64, 98.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2324 8.00 N 2092 7.00 C 8251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 201 " 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: 0.90 Conformation dependent library (CDL) restraints added in 554.5 milliseconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 49.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 44 through 63 removed outlier: 3.543A pdb=" N LYS A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 83 removed outlier: 4.052A pdb=" N GLU A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 157 removed outlier: 4.172A pdb=" N TYR A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 removed outlier: 3.836A pdb=" N VAL A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 166' Processing helix chain 'A' and resid 168 through 211 removed outlier: 5.563A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.718A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 239 through 260 removed outlier: 5.292A pdb=" N LYS A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 267 Processing helix chain 'A' and resid 270 through 324 removed outlier: 3.681A pdb=" N ASN A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 369 removed outlier: 3.582A pdb=" N VAL A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Proline residue: A 350 - end of helix removed outlier: 4.506A pdb=" N TYR A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 3.896A pdb=" N LYS A 405 " --> pdb=" O PRO A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.971A pdb=" N THR A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 525 through 529 removed outlier: 3.583A pdb=" N GLY A 528 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 529 " --> pdb=" O GLU A 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 525 through 529' Processing helix chain 'A' and resid 533 through 547 Processing helix chain 'A' and resid 563 through 575 Processing helix chain 'A' and resid 588 through 592 removed outlier: 3.546A pdb=" N THR A 591 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 619 removed outlier: 3.669A pdb=" N LYS A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 removed outlier: 4.233A pdb=" N LYS A 624 " --> pdb=" O GLY A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 705 removed outlier: 3.820A pdb=" N LEU A 705 " --> pdb=" O LYS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 724 Processing helix chain 'A' and resid 725 through 736 Processing helix chain 'A' and resid 736 through 741 Processing helix chain 'A' and resid 744 through 798 removed outlier: 3.830A pdb=" N LYS A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 798 " --> pdb=" O ARG A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 806 Processing helix chain 'A' and resid 810 through 854 removed outlier: 5.064A pdb=" N ALA A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 830 " --> pdb=" O LYS A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 862 removed outlier: 3.797A pdb=" N LEU A 860 " --> pdb=" O GLN A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 880 Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 913 through 965 removed outlier: 4.148A pdb=" N MET A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 3.637A pdb=" N ASN A 930 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 946 " --> pdb=" O PHE A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 993 Processing helix chain 'A' and resid 998 through 1012 Processing helix chain 'A' and resid 1079 through 1084 removed outlier: 3.650A pdb=" N GLU A1084 " --> pdb=" O VAL A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1113 removed outlier: 3.546A pdb=" N ALA A1111 " --> pdb=" O GLN A1107 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A1113 " --> pdb=" O LEU A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1135 Processing helix chain 'A' and resid 1141 through 1152 removed outlier: 4.269A pdb=" N ARG A1147 " --> pdb=" O GLU A1143 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA A1152 " --> pdb=" O ALA A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1161 removed outlier: 3.608A pdb=" N ILE A1158 " --> pdb=" O ILE A1154 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1174 removed outlier: 3.837A pdb=" N GLY A1173 " --> pdb=" O GLY A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1193 removed outlier: 4.175A pdb=" N ARG A1183 " --> pdb=" O GLY A1179 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A1186 " --> pdb=" O GLN A1182 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A1192 " --> pdb=" O ARG A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1220 removed outlier: 3.645A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1261 Processing helix chain 'A' and resid 1265 through 1271 removed outlier: 3.813A pdb=" N SER A1269 " --> pdb=" O GLY A1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing sheet with id=AA1, first strand: chain 'A' and resid 392 through 393 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 removed outlier: 3.674A pdb=" N PHE A 399 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 410 " --> pdb=" O PHE A 399 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 473 removed outlier: 6.487A pdb=" N GLY A 471 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ASP A 555 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 473 " --> pdb=" O ASP A 555 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL A 423 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA A 424 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A 601 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL A 426 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP A 602 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILE A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 453 removed outlier: 4.001A pdb=" N GLN A 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1053 through 1059 removed outlier: 3.623A pdb=" N GLY A1055 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL A1040 " --> pdb=" O GLY A1055 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER A1057 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLY A1038 " --> pdb=" O SER A1057 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLU A1059 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR A1036 " --> pdb=" O GLU A1059 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL A1040 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA A1091 " --> pdb=" O VAL A1040 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1196 through 1200 removed outlier: 7.583A pdb=" N CYS A1227 " --> pdb=" O LEU A1066 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LEU A1068 " --> pdb=" O CYS A1227 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A1229 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A1245 " --> pdb=" O GLU A1253 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU A1253 " --> pdb=" O VAL A1245 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLN A1247 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A1251 " --> pdb=" O GLN A1247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.189A pdb=" N LEU B 11 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS B 112 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL B 13 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 89 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.645A pdb=" N THR B 119 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 138 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TYR B 178 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 151 through 155 removed outlier: 3.548A pdb=" N TYR B 197 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.181A pdb=" N GLY C 10 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 35 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET C 34 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 17 through 20 Processing sheet with id=AB5, first strand: chain 'C' and resid 126 through 130 removed outlier: 3.666A pdb=" N LEU C 147 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU C 130 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 145 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU C 176 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N THR C 182 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA C 174 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 184 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 159 through 160 641 hydrogen bonds defined for protein. 1851 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: 2.20 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2015 1.29 - 1.42: 3348 1.42 - 1.56: 7501 1.56 - 1.69: 56 1.69 - 1.82: 83 Bond restraints: 13003 Sorted by residual: bond pdb=" C28 R0Z A1301 " pdb=" N29 R0Z A1301 " ideal model delta sigma weight residual 1.451 1.266 0.185 2.00e-02 2.50e+03 8.56e+01 bond pdb=" C28 R0Z A1302 " pdb=" N29 R0Z A1302 " ideal model delta sigma weight residual 1.451 1.286 0.165 2.00e-02 2.50e+03 6.79e+01 bond pdb=" C08 R0Z A1302 " pdb=" N09 R0Z A1302 " ideal model delta sigma weight residual 1.363 1.521 -0.158 2.00e-02 2.50e+03 6.22e+01 bond pdb=" C10 R0Z A1302 " pdb=" N09 R0Z A1302 " ideal model delta sigma weight residual 1.356 1.510 -0.154 2.00e-02 2.50e+03 5.94e+01 bond pdb=" C08 R0Z A1301 " pdb=" N09 R0Z A1301 " ideal model delta sigma weight residual 1.363 1.502 -0.139 2.00e-02 2.50e+03 4.84e+01 ... (remaining 12998 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 16823 2.83 - 5.66: 710 5.66 - 8.49: 99 8.49 - 11.32: 29 11.32 - 14.15: 8 Bond angle restraints: 17669 Sorted by residual: angle pdb=" C ASN A 371 " pdb=" N LYS A 372 " pdb=" CA LYS A 372 " ideal model delta sigma weight residual 121.83 133.04 -11.21 1.56e+00 4.11e-01 5.16e+01 angle pdb=" N ILE B 56 " pdb=" CA ILE B 56 " pdb=" C ILE B 56 " ideal model delta sigma weight residual 109.34 120.05 -10.71 2.08e+00 2.31e-01 2.65e+01 angle pdb=" C LEU A 175 " pdb=" N THR A 176 " pdb=" CA THR A 176 " ideal model delta sigma weight residual 122.17 114.49 7.68 1.54e+00 4.22e-01 2.49e+01 angle pdb=" C18 R0Z A1301 " pdb=" N20 R0Z A1301 " pdb=" C21 R0Z A1301 " ideal model delta sigma weight residual 128.43 114.28 14.15 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C THR C 28 " pdb=" N PHE C 29 " pdb=" CA PHE C 29 " ideal model delta sigma weight residual 120.63 127.91 -7.28 1.61e+00 3.86e-01 2.04e+01 ... (remaining 17664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.48: 7634 26.48 - 52.97: 485 52.97 - 79.45: 54 79.45 - 105.93: 12 105.93 - 132.42: 3 Dihedral angle restraints: 8188 sinusoidal: 3602 harmonic: 4586 Sorted by residual: dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 140.45 -47.45 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" CA VAL A 472 " pdb=" C VAL A 472 " pdb=" N VAL A 473 " pdb=" CA VAL A 473 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA HIS B 98 " pdb=" C HIS B 98 " pdb=" N ALA B 99 " pdb=" CA ALA B 99 " ideal model delta harmonic sigma weight residual -180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 8185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1764 0.101 - 0.201: 238 0.201 - 0.301: 27 0.301 - 0.402: 4 0.402 - 0.502: 5 Chirality restraints: 2038 Sorted by residual: chirality pdb=" C17 CLR A1308 " pdb=" C13 CLR A1308 " pdb=" C16 CLR A1308 " pdb=" C20 CLR A1308 " both_signs ideal model delta sigma weight residual False 2.55 3.06 -0.50 2.00e-01 2.50e+01 6.31e+00 chirality pdb=" CB VAL A 981 " pdb=" CA VAL A 981 " pdb=" CG1 VAL A 981 " pdb=" CG2 VAL A 981 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" C17 CLR A1311 " pdb=" C13 CLR A1311 " pdb=" C16 CLR A1311 " pdb=" C20 CLR A1311 " both_signs ideal model delta sigma weight residual False 2.55 2.99 -0.44 2.00e-01 2.50e+01 4.75e+00 ... (remaining 2035 not shown) Planarity restraints: 2164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 744 " 0.054 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO A 745 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 745 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 745 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 277 " 0.031 2.00e-02 2.50e+03 2.20e-02 9.69e+00 pdb=" CG TYR A 277 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A 277 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 277 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 277 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 277 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 277 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 277 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 852 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C ILE A 852 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A 852 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR A 853 " -0.017 2.00e-02 2.50e+03 ... (remaining 2161 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 935 2.69 - 3.25: 12941 3.25 - 3.80: 19368 3.80 - 4.35: 25132 4.35 - 4.90: 41756 Nonbonded interactions: 100132 Sorted by model distance: nonbonded pdb=" O SER B 176 " pdb=" OG SER B 176 " model vdw 2.143 3.040 nonbonded pdb=" O SER C 85 " pdb=" OG SER C 85 " model vdw 2.199 3.040 nonbonded pdb=" NH1 ARG A 442 " pdb=" O ILE A 461 " model vdw 2.199 3.120 nonbonded pdb=" N ASP B 156 " pdb=" O SER B 196 " model vdw 2.204 3.120 nonbonded pdb=" OH TYR B 41 " pdb=" N PHE C 106 " model vdw 2.213 3.120 ... (remaining 100127 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.960 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.017 0.185 13008 Z= 0.732 Angle : 1.365 14.146 17679 Z= 0.721 Chirality : 0.075 0.502 2038 Planarity : 0.006 0.081 2164 Dihedral : 16.988 132.418 5233 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 25.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.05 % Favored : 88.70 % Rotamer: Outliers : 3.00 % Allowed : 7.94 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -4.28 (0.17), residues: 1584 helix: -2.66 (0.15), residues: 744 sheet: -1.83 (0.29), residues: 257 loop : -3.34 (0.21), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 67 TYR 0.052 0.003 TYR A 277 PHE 0.033 0.004 PHE A 72 TRP 0.033 0.004 TRP A 698 HIS 0.009 0.002 HIS A 166 Details of bonding type rmsd covalent geometry : bond 0.01663 (13003) covalent geometry : angle 1.36562 (17669) SS BOND : bond 0.00186 ( 5) SS BOND : angle 0.68465 ( 10) hydrogen bonds : bond 0.20035 ( 641) hydrogen bonds : angle 7.96624 ( 1851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8116 (tp) REVERT: A 380 LYS cc_start: 0.5430 (OUTLIER) cc_final: 0.4862 (ptpt) REVERT: A 450 MET cc_start: 0.5983 (tmm) cc_final: 0.5147 (tmm) REVERT: A 1015 THR cc_start: 0.5297 (OUTLIER) cc_final: 0.4936 (t) REVERT: B 115 ASP cc_start: 0.5328 (OUTLIER) cc_final: 0.5005 (t0) outliers start: 40 outliers final: 19 residues processed: 164 average time/residue: 0.1344 time to fit residues: 30.8626 Evaluate side-chains 107 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1014 LYS Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 398 HIS A 438 GLN A 508 ASN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 725 GLN A 809 ASN A 839 ASN A 903 ASN A 912 GLN A1054 GLN ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN ** C 161 ASN ** 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 = 0.4422 r_free = 0.4422 target = 0.193875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.148567 restraints weight = 18271.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.142754 restraints weight = 32398.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138278 restraints weight = 23546.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.138333 restraints weight = 22591.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.137624 restraints weight = 18093.184| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13008 Z= 0.185 Angle : 0.729 9.748 17679 Z= 0.370 Chirality : 0.043 0.158 2038 Planarity : 0.005 0.052 2164 Dihedral : 10.572 132.909 2453 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.93 % Favored : 94.00 % Rotamer: Outliers : 1.50 % Allowed : 14.16 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -2.30 (0.19), residues: 1584 helix: -0.69 (0.17), residues: 752 sheet: -1.26 (0.29), residues: 257 loop : -2.68 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 794 TYR 0.014 0.002 TYR C 80 PHE 0.034 0.002 PHE A 904 TRP 0.016 0.002 TRP C 105 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00376 (13003) covalent geometry : angle 0.72909 (17669) SS BOND : bond 0.00336 ( 5) SS BOND : angle 0.82329 ( 10) hydrogen bonds : bond 0.07177 ( 641) hydrogen bonds : angle 5.60480 ( 1851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7403 (tpp) cc_final: 0.6899 (tpp) REVERT: A 78 ILE cc_start: 0.8688 (tt) cc_final: 0.8485 (mt) REVERT: A 380 LYS cc_start: 0.5379 (OUTLIER) cc_final: 0.5122 (ptpt) REVERT: A 450 MET cc_start: 0.6226 (tmm) cc_final: 0.5163 (tmm) REVERT: A 479 LEU cc_start: 0.7677 (mt) cc_final: 0.7422 (mt) REVERT: B 115 ASP cc_start: 0.5715 (OUTLIER) cc_final: 0.5507 (t0) outliers start: 20 outliers final: 9 residues processed: 132 average time/residue: 0.1090 time to fit residues: 21.3199 Evaluate side-chains 108 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 136 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 123 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 110 optimal weight: 20.0000 chunk 141 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 0.0030 chunk 39 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS A 172 ASN ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.194750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.153518 restraints weight = 18377.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.149409 restraints weight = 32786.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.144804 restraints weight = 25357.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.144644 restraints weight = 26146.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.143087 restraints weight = 20756.127| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13008 Z= 0.146 Angle : 0.621 8.372 17679 Z= 0.317 Chirality : 0.041 0.156 2038 Planarity : 0.004 0.072 2164 Dihedral : 9.106 134.394 2411 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 2.47 % Allowed : 15.51 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -1.34 (0.20), residues: 1584 helix: 0.28 (0.19), residues: 758 sheet: -1.00 (0.30), residues: 258 loop : -2.41 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 794 TYR 0.017 0.001 TYR B 197 PHE 0.022 0.002 PHE B 215 TRP 0.014 0.001 TRP C 105 HIS 0.004 0.001 HIS A1254 Details of bonding type rmsd covalent geometry : bond 0.00308 (13003) covalent geometry : angle 0.62087 (17669) SS BOND : bond 0.00299 ( 5) SS BOND : angle 1.03168 ( 10) hydrogen bonds : bond 0.06290 ( 641) hydrogen bonds : angle 5.08022 ( 1851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7686 (tpp) cc_final: 0.7099 (tpp) REVERT: A 156 MET cc_start: 0.8461 (mmt) cc_final: 0.8235 (mmt) REVERT: A 450 MET cc_start: 0.6128 (tmm) cc_final: 0.5132 (tmm) REVERT: A 479 LEU cc_start: 0.7644 (mt) cc_final: 0.7384 (mt) REVERT: A 770 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.7146 (t80) REVERT: B 115 ASP cc_start: 0.5620 (OUTLIER) cc_final: 0.5274 (t0) outliers start: 33 outliers final: 18 residues processed: 132 average time/residue: 0.0965 time to fit residues: 19.4199 Evaluate side-chains 114 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 103 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 HIS ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.194869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.153265 restraints weight = 18273.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.149179 restraints weight = 34655.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.143950 restraints weight = 27987.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.143393 restraints weight = 28953.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142726 restraints weight = 19615.790| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13008 Z= 0.146 Angle : 0.590 7.841 17679 Z= 0.301 Chirality : 0.040 0.156 2038 Planarity : 0.004 0.073 2164 Dihedral : 8.606 133.536 2405 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.49 % Favored : 94.44 % Rotamer: Outliers : 2.47 % Allowed : 18.13 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.83 (0.21), residues: 1584 helix: 0.73 (0.19), residues: 754 sheet: -0.74 (0.31), residues: 244 loop : -2.16 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 262 TYR 0.015 0.001 TYR C 151 PHE 0.016 0.001 PHE A 904 TRP 0.014 0.001 TRP C 105 HIS 0.004 0.001 HIS A1254 Details of bonding type rmsd covalent geometry : bond 0.00313 (13003) covalent geometry : angle 0.59040 (17669) SS BOND : bond 0.00343 ( 5) SS BOND : angle 0.67888 ( 10) hydrogen bonds : bond 0.05988 ( 641) hydrogen bonds : angle 4.83514 ( 1851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.6116 (tmm) cc_final: 0.5207 (tmm) REVERT: A 479 LEU cc_start: 0.7657 (mt) cc_final: 0.7375 (mt) REVERT: A 770 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.7132 (t80) REVERT: A 1159 GLU cc_start: 0.5238 (OUTLIER) cc_final: 0.4980 (mp0) REVERT: B 115 ASP cc_start: 0.5573 (OUTLIER) cc_final: 0.5315 (t0) outliers start: 33 outliers final: 25 residues processed: 126 average time/residue: 0.1054 time to fit residues: 19.6275 Evaluate side-chains 121 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1159 GLU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 153 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 chunk 93 optimal weight: 0.1980 chunk 129 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.195825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.151838 restraints weight = 18391.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.145096 restraints weight = 37555.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135779 restraints weight = 30250.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.136576 restraints weight = 32270.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.137166 restraints weight = 20463.978| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13008 Z= 0.130 Angle : 0.559 7.960 17679 Z= 0.287 Chirality : 0.039 0.162 2038 Planarity : 0.004 0.060 2164 Dihedral : 8.248 132.893 2401 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.56 % Favored : 94.38 % Rotamer: Outliers : 2.55 % Allowed : 19.63 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.45 (0.21), residues: 1584 helix: 1.06 (0.19), residues: 754 sheet: -0.55 (0.32), residues: 237 loop : -2.00 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 794 TYR 0.015 0.001 TYR B 197 PHE 0.010 0.001 PHE B 144 TRP 0.010 0.001 TRP C 105 HIS 0.004 0.001 HIS A1254 Details of bonding type rmsd covalent geometry : bond 0.00274 (13003) covalent geometry : angle 0.55851 (17669) SS BOND : bond 0.00337 ( 5) SS BOND : angle 0.84869 ( 10) hydrogen bonds : bond 0.05624 ( 641) hydrogen bonds : angle 4.64433 ( 1851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 100 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.6075 (tmm) cc_final: 0.5073 (tmm) REVERT: A 479 LEU cc_start: 0.7742 (mt) cc_final: 0.7440 (mt) REVERT: A 770 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.7011 (t80) REVERT: A 948 MET cc_start: 0.7645 (tpt) cc_final: 0.7369 (tpp) REVERT: A 1119 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6482 (pm20) REVERT: B 115 ASP cc_start: 0.5435 (OUTLIER) cc_final: 0.5223 (t0) outliers start: 34 outliers final: 21 residues processed: 127 average time/residue: 0.1067 time to fit residues: 20.5662 Evaluate side-chains 116 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 136 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 43 optimal weight: 8.9990 chunk 103 optimal weight: 0.0570 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 114 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 508 ASN ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.193711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.147359 restraints weight = 18289.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.138836 restraints weight = 35990.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.130389 restraints weight = 27951.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.131424 restraints weight = 27892.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131512 restraints weight = 18717.030| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13008 Z= 0.189 Angle : 0.617 7.729 17679 Z= 0.316 Chirality : 0.042 0.174 2038 Planarity : 0.004 0.052 2164 Dihedral : 8.375 133.904 2401 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.25 % Favored : 93.69 % Rotamer: Outliers : 2.62 % Allowed : 20.75 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.51 (0.21), residues: 1584 helix: 0.94 (0.19), residues: 759 sheet: -0.44 (0.33), residues: 237 loop : -2.01 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 101 TYR 0.016 0.002 TYR C 181 PHE 0.018 0.002 PHE B 94 TRP 0.016 0.001 TRP C 194 HIS 0.005 0.001 HIS A1254 Details of bonding type rmsd covalent geometry : bond 0.00432 (13003) covalent geometry : angle 0.61645 (17669) SS BOND : bond 0.00401 ( 5) SS BOND : angle 0.84292 ( 10) hydrogen bonds : bond 0.06314 ( 641) hydrogen bonds : angle 4.72739 ( 1851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.6098 (tmm) cc_final: 0.4987 (tmm) REVERT: A 770 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.7015 (t80) REVERT: A 912 GLN cc_start: 0.7451 (mm-40) cc_final: 0.6693 (tm-30) REVERT: A 1119 GLU cc_start: 0.7549 (tm-30) cc_final: 0.6672 (mm-30) outliers start: 35 outliers final: 26 residues processed: 122 average time/residue: 0.1017 time to fit residues: 19.0505 Evaluate side-chains 115 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 88 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 30 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 130 optimal weight: 0.0670 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 156 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.196150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.154076 restraints weight = 18207.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.148533 restraints weight = 35113.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.142768 restraints weight = 28715.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.142562 restraints weight = 29101.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.142884 restraints weight = 19391.626| |-----------------------------------------------------------------------------| r_work (final): 0.3857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13008 Z= 0.123 Angle : 0.556 8.008 17679 Z= 0.285 Chirality : 0.039 0.167 2038 Planarity : 0.003 0.050 2164 Dihedral : 8.008 133.679 2399 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 1.95 % Allowed : 21.72 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.11 (0.21), residues: 1584 helix: 1.30 (0.19), residues: 755 sheet: -0.30 (0.33), residues: 237 loop : -1.82 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 794 TYR 0.015 0.001 TYR C 151 PHE 0.012 0.001 PHE B 76 TRP 0.013 0.001 TRP C 194 HIS 0.024 0.001 HIS A1155 Details of bonding type rmsd covalent geometry : bond 0.00246 (13003) covalent geometry : angle 0.55569 (17669) SS BOND : bond 0.00321 ( 5) SS BOND : angle 0.59594 ( 10) hydrogen bonds : bond 0.05581 ( 641) hydrogen bonds : angle 4.55932 ( 1851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 450 MET cc_start: 0.6126 (tmm) cc_final: 0.5244 (tmm) REVERT: A 770 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.7134 (t80) REVERT: A 948 MET cc_start: 0.7635 (tpt) cc_final: 0.7430 (tpp) REVERT: A 1119 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6649 (mm-30) outliers start: 26 outliers final: 18 residues processed: 115 average time/residue: 0.1128 time to fit residues: 19.5485 Evaluate side-chains 106 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 148 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 chunk 10 optimal weight: 0.0970 chunk 127 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.194402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.152502 restraints weight = 18120.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.148808 restraints weight = 34921.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.142361 restraints weight = 30862.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142704 restraints weight = 30787.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.141579 restraints weight = 21045.376| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13008 Z= 0.155 Angle : 0.587 7.755 17679 Z= 0.299 Chirality : 0.040 0.153 2038 Planarity : 0.004 0.052 2164 Dihedral : 8.012 133.023 2399 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 2.25 % Allowed : 21.35 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.08 (0.21), residues: 1584 helix: 1.26 (0.19), residues: 756 sheet: -0.18 (0.33), residues: 239 loop : -1.76 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 101 TYR 0.015 0.001 TYR C 151 PHE 0.015 0.001 PHE B 76 TRP 0.011 0.001 TRP C 194 HIS 0.020 0.001 HIS A1155 Details of bonding type rmsd covalent geometry : bond 0.00345 (13003) covalent geometry : angle 0.58667 (17669) SS BOND : bond 0.00376 ( 5) SS BOND : angle 0.71846 ( 10) hydrogen bonds : bond 0.05885 ( 641) hydrogen bonds : angle 4.56706 ( 1851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 450 MET cc_start: 0.6141 (tmm) cc_final: 0.5300 (tmm) REVERT: A 770 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.7136 (t80) REVERT: A 1119 GLU cc_start: 0.7124 (tm-30) cc_final: 0.6692 (mm-30) outliers start: 30 outliers final: 26 residues processed: 111 average time/residue: 0.1077 time to fit residues: 18.3362 Evaluate side-chains 114 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 48 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.196098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.154773 restraints weight = 18214.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.149323 restraints weight = 35727.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.143713 restraints weight = 32302.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.144380 restraints weight = 28563.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143232 restraints weight = 19764.099| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13008 Z= 0.127 Angle : 0.553 7.998 17679 Z= 0.283 Chirality : 0.039 0.153 2038 Planarity : 0.003 0.050 2164 Dihedral : 7.776 132.582 2399 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.80 % Favored : 95.14 % Rotamer: Outliers : 2.40 % Allowed : 21.12 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.16 (0.21), residues: 1584 helix: 1.45 (0.19), residues: 757 sheet: -0.13 (0.33), residues: 242 loop : -1.61 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 794 TYR 0.016 0.001 TYR C 151 PHE 0.013 0.001 PHE B 76 TRP 0.011 0.001 TRP C 105 HIS 0.015 0.001 HIS A1155 Details of bonding type rmsd covalent geometry : bond 0.00268 (13003) covalent geometry : angle 0.55348 (17669) SS BOND : bond 0.00338 ( 5) SS BOND : angle 0.57473 ( 10) hydrogen bonds : bond 0.05475 ( 641) hydrogen bonds : angle 4.46917 ( 1851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.466 Fit side-chains REVERT: A 450 MET cc_start: 0.6022 (tmm) cc_final: 0.5160 (tmm) REVERT: A 479 LEU cc_start: 0.7615 (mt) cc_final: 0.7408 (mt) REVERT: A 953 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.7175 (t80) REVERT: A 1119 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6744 (mm-30) outliers start: 32 outliers final: 23 residues processed: 123 average time/residue: 0.1116 time to fit residues: 20.7716 Evaluate side-chains 112 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.0270 chunk 125 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.196699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.154438 restraints weight = 18253.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 94)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.147119 restraints weight = 37107.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139966 restraints weight = 32308.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140457 restraints weight = 30101.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.140559 restraints weight = 20570.120| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13008 Z= 0.126 Angle : 0.557 10.119 17679 Z= 0.282 Chirality : 0.039 0.164 2038 Planarity : 0.003 0.049 2164 Dihedral : 7.679 133.361 2399 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.30 % Favored : 94.63 % Rotamer: Outliers : 2.25 % Allowed : 21.87 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.25 (0.21), residues: 1584 helix: 1.48 (0.19), residues: 758 sheet: -0.01 (0.33), residues: 242 loop : -1.54 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 794 TYR 0.015 0.001 TYR C 151 PHE 0.013 0.001 PHE B 76 TRP 0.009 0.001 TRP C 105 HIS 0.014 0.001 HIS A1155 Details of bonding type rmsd covalent geometry : bond 0.00265 (13003) covalent geometry : angle 0.55718 (17669) SS BOND : bond 0.00324 ( 5) SS BOND : angle 0.58063 ( 10) hydrogen bonds : bond 0.05389 ( 641) hydrogen bonds : angle 4.46355 ( 1851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 0.574 Fit side-chains REVERT: A 450 MET cc_start: 0.5964 (tmm) cc_final: 0.5056 (tmm) REVERT: A 479 LEU cc_start: 0.7635 (mt) cc_final: 0.7381 (mt) REVERT: A 953 TYR cc_start: 0.7781 (OUTLIER) cc_final: 0.7272 (t80) REVERT: A 1119 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6847 (mm-30) outliers start: 30 outliers final: 24 residues processed: 115 average time/residue: 0.1087 time to fit residues: 18.9957 Evaluate side-chains 114 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 911 THR Chi-restraints excluded: chain A residue 953 TYR Chi-restraints excluded: chain A residue 988 VAL Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 103 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 144 optimal weight: 0.0470 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 912 GLN ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.195745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.149084 restraints weight = 18299.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.141687 restraints weight = 34183.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.132756 restraints weight = 26211.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.134103 restraints weight = 24474.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.134120 restraints weight = 16961.065| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13008 Z= 0.154 Angle : 0.580 8.925 17679 Z= 0.294 Chirality : 0.040 0.159 2038 Planarity : 0.003 0.050 2164 Dihedral : 7.757 133.174 2399 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.19 % Rotamer: Outliers : 2.10 % Allowed : 22.10 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.18 (0.21), residues: 1584 helix: 1.39 (0.19), residues: 757 sheet: 0.02 (0.32), residues: 242 loop : -1.55 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 101 TYR 0.015 0.001 TYR C 151 PHE 0.017 0.001 PHE B 76 TRP 0.010 0.001 TRP A 855 HIS 0.013 0.001 HIS A1155 Details of bonding type rmsd covalent geometry : bond 0.00344 (13003) covalent geometry : angle 0.57999 (17669) SS BOND : bond 0.00384 ( 5) SS BOND : angle 0.76501 ( 10) hydrogen bonds : bond 0.05795 ( 641) hydrogen bonds : angle 4.51148 ( 1851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2176.31 seconds wall clock time: 38 minutes 29.81 seconds (2309.81 seconds total)