Starting phenix.real_space_refine on Thu Jul 31 02:49:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a6c_11670/07_2025/7a6c_11670.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a6c_11670/07_2025/7a6c_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_11670/07_2025/7a6c_11670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a6c_11670/07_2025/7a6c_11670.map" model { file = "/net/cci-nas-00/data/ceres_data/7a6c_11670/07_2025/7a6c_11670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a6c_11670/07_2025/7a6c_11670.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.06, per 1000 atoms: 0.63 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: 5.30 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.51 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: 4.39 Time building geometry restraints manager: 4.06 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 32.200 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.970 ------------------------------------------------------------------------------- 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 : 25.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.033 0.004 TRP A 698 HIS 0.009 0.002 HIS A 166 PHE 0.033 0.004 PHE A 72 TYR 0.052 0.003 TYR A 277 ARG 0.009 0.001 ARG C 67 Details of bonding type rmsd hydrogen bonds : bond 0.20035 ( 641) hydrogen bonds : angle 7.96624 ( 1851) SS BOND : bond 0.00186 ( 5) SS BOND : angle 0.68465 ( 10) covalent geometry : bond 0.01663 (13003) covalent geometry : angle 1.36562 (17669) *********************** 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 : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash 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: 0.5149 (tmm) REVERT: A 1015 THR cc_start: 0.5297 (OUTLIER) cc_final: 0.4934 (t) REVERT: B 115 ASP cc_start: 0.5328 (OUTLIER) cc_final: 0.5005 (t0) outliers start: 40 outliers final: 20 residues processed: 164 average time/residue: 0.2821 time to fit residues: 64.6018 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 : 1.244 ------------------------------------------------------------------------------- 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 133 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 80 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 143 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 GLN A 508 ASN A 611 ASN A 725 GLN A 809 ASN A 839 ASN A 903 ASN A 912 GLN A 966 HIS 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 = 0.4434 r_free = 0.4434 target = 0.194938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.146607 restraints weight = 18136.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.141718 restraints weight = 30984.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.130520 restraints weight = 19870.903| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13008 Z= 0.166 Angle : 0.719 9.654 17679 Z= 0.364 Chirality : 0.042 0.154 2038 Planarity : 0.005 0.052 2164 Dihedral : 10.577 133.477 2453 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 1.50 % Allowed : 13.71 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.19), residues: 1584 helix: -0.61 (0.18), residues: 752 sheet: -1.25 (0.29), residues: 257 loop : -2.68 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 708 HIS 0.006 0.001 HIS A 61 PHE 0.039 0.002 PHE A 904 TYR 0.014 0.002 TYR A 622 ARG 0.007 0.001 ARG A 794 Details of bonding type rmsd hydrogen bonds : bond 0.07072 ( 641) hydrogen bonds : angle 5.56123 ( 1851) SS BOND : bond 0.00321 ( 5) SS BOND : angle 0.72305 ( 10) covalent geometry : bond 0.00340 (13003) covalent geometry : angle 0.71861 (17669) *********************** 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 136 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7539 (tpp) cc_final: 0.6895 (tpp) REVERT: A 78 ILE cc_start: 0.8493 (tt) cc_final: 0.8272 (mt) REVERT: A 380 LYS cc_start: 0.5762 (OUTLIER) cc_final: 0.5219 (ptpt) REVERT: A 450 MET cc_start: 0.5960 (tmm) cc_final: 0.4810 (tmm) REVERT: A 479 LEU cc_start: 0.7740 (mt) cc_final: 0.7442 (mt) REVERT: B 115 ASP cc_start: 0.5634 (OUTLIER) cc_final: 0.5419 (t0) outliers start: 20 outliers final: 9 residues processed: 134 average time/residue: 0.2411 time to fit residues: 47.7331 Evaluate side-chains 110 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 1.411 ------------------------------------------------------------------------------- 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 120 optimal weight: 0.2980 chunk 52 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 131 optimal weight: 0.0980 chunk 93 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 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 143 GLN A 145 HIS A 172 ASN ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.193253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.151054 restraints weight = 18308.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.146542 restraints weight = 32370.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.141861 restraints weight = 26665.564| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13008 Z= 0.169 Angle : 0.637 8.775 17679 Z= 0.325 Chirality : 0.042 0.175 2038 Planarity : 0.004 0.072 2164 Dihedral : 9.048 133.903 2411 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.19 % Favored : 93.75 % Rotamer: Outliers : 2.62 % Allowed : 16.03 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.20), residues: 1584 helix: 0.23 (0.18), residues: 761 sheet: -0.99 (0.30), residues: 258 loop : -2.42 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 105 HIS 0.004 0.001 HIS A 61 PHE 0.020 0.002 PHE B 215 TYR 0.014 0.002 TYR C 151 ARG 0.004 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.06569 ( 641) hydrogen bonds : angle 5.08250 ( 1851) SS BOND : bond 0.00313 ( 5) SS BOND : angle 1.24570 ( 10) covalent geometry : bond 0.00375 (13003) covalent geometry : angle 0.63602 (17669) *********************** 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 139 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 104 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8418 (mmt) cc_final: 0.8129 (mmt) REVERT: A 450 MET cc_start: 0.6149 (tmm) cc_final: 0.5185 (tmm) REVERT: A 479 LEU cc_start: 0.7649 (mt) cc_final: 0.7378 (mt) REVERT: A 770 PHE cc_start: 0.7471 (OUTLIER) cc_final: 0.7189 (t80) REVERT: B 115 ASP cc_start: 0.5589 (OUTLIER) cc_final: 0.5233 (t0) outliers start: 35 outliers final: 21 residues processed: 135 average time/residue: 0.2416 time to fit residues: 49.0363 Evaluate side-chains 115 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.263 ------------------------------------------------------------------------------- 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 365 ILE 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 A residue 1081 GLN 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 89 GLU 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 0 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 79 optimal weight: 0.0870 chunk 64 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 936 HIS ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.196711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.156093 restraints weight = 18066.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.151693 restraints weight = 34665.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.145740 restraints weight = 28447.518| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13008 Z= 0.128 Angle : 0.567 7.431 17679 Z= 0.290 Chirality : 0.039 0.149 2038 Planarity : 0.004 0.070 2164 Dihedral : 8.430 133.556 2405 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 2.17 % Allowed : 18.73 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.21), residues: 1584 helix: 0.92 (0.19), residues: 753 sheet: -0.70 (0.31), residues: 238 loop : -2.10 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 105 HIS 0.004 0.001 HIS A 61 PHE 0.016 0.001 PHE A 904 TYR 0.016 0.001 TYR C 151 ARG 0.007 0.000 ARG A 794 Details of bonding type rmsd hydrogen bonds : bond 0.05592 ( 641) hydrogen bonds : angle 4.74136 ( 1851) SS BOND : bond 0.00529 ( 5) SS BOND : angle 0.53634 ( 10) covalent geometry : bond 0.00257 (13003) covalent geometry : angle 0.56713 (17669) *********************** 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 137 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.362 Fit side-chains revert: symmetry clash REVERT: A 450 MET cc_start: 0.6139 (tmm) cc_final: 0.5267 (tmm) REVERT: A 479 LEU cc_start: 0.7624 (mt) cc_final: 0.7342 (mt) REVERT: A 814 LEU cc_start: 0.8451 (mt) cc_final: 0.8240 (mt) REVERT: A 1119 GLU cc_start: 0.6733 (tm-30) cc_final: 0.6233 (pm20) REVERT: A 1159 GLU cc_start: 0.5293 (OUTLIER) cc_final: 0.5059 (mp0) REVERT: B 115 ASP cc_start: 0.5490 (OUTLIER) cc_final: 0.5244 (t0) outliers start: 29 outliers final: 15 residues processed: 129 average time/residue: 0.2612 time to fit residues: 49.8893 Evaluate side-chains 114 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 437 VAL Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 115 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN A 508 ASN ** A1064 GLN ** 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 = 0.4396 r_free = 0.4396 target = 0.191158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.146176 restraints weight = 18359.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.140206 restraints weight = 33073.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.134579 restraints weight = 24989.150| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13008 Z= 0.256 Angle : 0.693 8.704 17679 Z= 0.353 Chirality : 0.044 0.177 2038 Planarity : 0.004 0.058 2164 Dihedral : 8.767 134.687 2401 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.01 % Favored : 92.93 % Rotamer: Outliers : 2.85 % Allowed : 19.85 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.20), residues: 1584 helix: 0.54 (0.18), residues: 757 sheet: -0.60 (0.32), residues: 235 loop : -2.09 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 855 HIS 0.006 0.001 HIS A1254 PHE 0.024 0.002 PHE B 94 TYR 0.018 0.002 TYR B 54 ARG 0.009 0.001 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.07118 ( 641) hydrogen bonds : angle 4.97536 ( 1851) SS BOND : bond 0.00479 ( 5) SS BOND : angle 1.14296 ( 10) covalent geometry : bond 0.00595 (13003) covalent geometry : angle 0.69284 (17669) *********************** 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 127 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: A 68 MET cc_start: 0.7618 (tpp) cc_final: 0.7011 (tpp) REVERT: A 450 MET cc_start: 0.6147 (tmm) cc_final: 0.5154 (tmm) REVERT: A 855 TRP cc_start: 0.6653 (t60) cc_final: 0.6084 (t60) REVERT: A 1119 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6945 (tt0) outliers start: 38 outliers final: 25 residues processed: 124 average time/residue: 0.2358 time to fit residues: 44.2518 Evaluate side-chains 110 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 7 optimal weight: 0.4980 chunk 75 optimal weight: 0.0060 chunk 84 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.195951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.148184 restraints weight = 18323.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.142465 restraints weight = 29256.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.130484 restraints weight = 21087.258| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13008 Z= 0.125 Angle : 0.569 7.828 17679 Z= 0.290 Chirality : 0.039 0.164 2038 Planarity : 0.004 0.054 2164 Dihedral : 8.138 133.143 2399 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.67 % Favored : 95.27 % Rotamer: Outliers : 2.25 % Allowed : 21.65 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.21), residues: 1584 helix: 1.11 (0.19), residues: 754 sheet: -0.42 (0.32), residues: 237 loop : -1.92 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 194 HIS 0.005 0.001 HIS A 61 PHE 0.030 0.001 PHE A 904 TYR 0.016 0.001 TYR C 181 ARG 0.005 0.000 ARG A 794 Details of bonding type rmsd hydrogen bonds : bond 0.05761 ( 641) hydrogen bonds : angle 4.65278 ( 1851) SS BOND : bond 0.00335 ( 5) SS BOND : angle 0.63468 ( 10) covalent geometry : bond 0.00251 (13003) covalent geometry : angle 0.56872 (17669) *********************** 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 122 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 92 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 68 MET cc_start: 0.7536 (tpp) cc_final: 0.6740 (tpp) REVERT: A 450 MET cc_start: 0.5931 (tmm) cc_final: 0.4745 (tmm) REVERT: A 814 LEU cc_start: 0.8502 (mt) cc_final: 0.8299 (mt) REVERT: A 1119 GLU cc_start: 0.7495 (tm-30) cc_final: 0.6863 (mm-30) outliers start: 30 outliers final: 22 residues processed: 117 average time/residue: 0.2400 time to fit residues: 42.4001 Evaluate side-chains 111 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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 297 ILE 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 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 103 PHE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 136 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 41 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 80 optimal weight: 0.0980 chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 398 HIS ** 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 = 0.4420 r_free = 0.4420 target = 0.193794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.151710 restraints weight = 18333.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.146407 restraints weight = 36743.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.139395 restraints weight = 31543.646| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13008 Z= 0.157 Angle : 0.594 8.144 17679 Z= 0.303 Chirality : 0.040 0.161 2038 Planarity : 0.004 0.055 2164 Dihedral : 8.124 132.986 2399 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.81 % Rotamer: Outliers : 2.55 % Allowed : 22.02 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1584 helix: 1.14 (0.19), residues: 753 sheet: -0.31 (0.33), residues: 237 loop : -1.86 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 194 HIS 0.021 0.001 HIS A1155 PHE 0.023 0.001 PHE A 904 TYR 0.016 0.001 TYR C 151 ARG 0.005 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.06046 ( 641) hydrogen bonds : angle 4.63536 ( 1851) SS BOND : bond 0.00387 ( 5) SS BOND : angle 0.73342 ( 10) covalent geometry : bond 0.00351 (13003) covalent geometry : angle 0.59383 (17669) *********************** 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 126 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: A 68 MET cc_start: 0.7769 (tpp) cc_final: 0.6836 (tpp) REVERT: A 450 MET cc_start: 0.6212 (tmm) cc_final: 0.5285 (tmm) REVERT: A 628 MET cc_start: 0.1168 (mtp) cc_final: 0.0555 (tmm) outliers start: 34 outliers final: 27 residues processed: 121 average time/residue: 0.2693 time to fit residues: 49.2988 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 : 1.412 ------------------------------------------------------------------------------- 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 297 ILE 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 461 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 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 136 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 189 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 103 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 137 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 143 optimal weight: 0.3980 chunk 19 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.191875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.143978 restraints weight = 18417.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.140779 restraints weight = 36064.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.134211 restraints weight = 24606.460| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13008 Z= 0.220 Angle : 0.654 8.287 17679 Z= 0.333 Chirality : 0.043 0.156 2038 Planarity : 0.004 0.058 2164 Dihedral : 8.350 134.077 2399 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.44 % Favored : 93.50 % Rotamer: Outliers : 2.47 % Allowed : 22.17 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.21), residues: 1584 helix: 0.86 (0.19), residues: 761 sheet: -0.31 (0.32), residues: 243 loop : -1.91 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 855 HIS 0.017 0.001 HIS A1155 PHE 0.025 0.002 PHE B 76 TYR 0.016 0.002 TYR B 54 ARG 0.009 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.06781 ( 641) hydrogen bonds : angle 4.78860 ( 1851) SS BOND : bond 0.00484 ( 5) SS BOND : angle 0.95800 ( 10) covalent geometry : bond 0.00510 (13003) covalent geometry : angle 0.65388 (17669) *********************** 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 119 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 1.535 Fit side-chains REVERT: A 68 MET cc_start: 0.7622 (tpp) cc_final: 0.6654 (tpp) REVERT: A 450 MET cc_start: 0.6221 (tmm) cc_final: 0.5208 (tmm) REVERT: A 628 MET cc_start: 0.0986 (mtp) cc_final: 0.0437 (tmm) REVERT: A 808 LYS cc_start: 0.6852 (tptt) cc_final: 0.6320 (pttt) outliers start: 33 outliers final: 28 residues processed: 115 average time/residue: 0.2320 time to fit residues: 40.6879 Evaluate side-chains 112 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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 297 ILE 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 461 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 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 103 PHE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 50 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 398 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.194025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.151775 restraints weight = 18245.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.154045 restraints weight = 50840.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.153212 restraints weight = 18323.993| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13008 Z= 0.158 Angle : 0.590 8.049 17679 Z= 0.301 Chirality : 0.040 0.158 2038 Planarity : 0.004 0.055 2164 Dihedral : 8.031 133.268 2399 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 2.10 % Allowed : 22.62 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1584 helix: 1.15 (0.19), residues: 757 sheet: -0.30 (0.33), residues: 241 loop : -1.75 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 105 HIS 0.014 0.001 HIS A1155 PHE 0.019 0.001 PHE A 904 TYR 0.014 0.001 TYR C 151 ARG 0.006 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.06105 ( 641) hydrogen bonds : angle 4.66227 ( 1851) SS BOND : bond 0.00402 ( 5) SS BOND : angle 0.72358 ( 10) covalent geometry : bond 0.00353 (13003) covalent geometry : angle 0.59040 (17669) *********************** 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 119 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.470 Fit side-chains REVERT: A 68 MET cc_start: 0.7877 (tpp) cc_final: 0.7129 (tpp) REVERT: A 450 MET cc_start: 0.6179 (tmm) cc_final: 0.5278 (tmm) outliers start: 28 outliers final: 25 residues processed: 114 average time/residue: 0.2328 time to fit residues: 40.4323 Evaluate side-chains 110 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 297 ILE 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 461 ILE 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 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 1078 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 103 PHE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 22 optimal weight: 0.6980 chunk 147 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 155 optimal weight: 8.9990 chunk 99 optimal weight: 0.0570 chunk 148 optimal weight: 0.8980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 398 HIS ** 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 = 0.4454 r_free = 0.4454 target = 0.196948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.153531 restraints weight = 18241.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.145263 restraints weight = 34638.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.139015 restraints weight = 29128.287| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13008 Z= 0.121 Angle : 0.551 9.211 17679 Z= 0.282 Chirality : 0.039 0.161 2038 Planarity : 0.003 0.053 2164 Dihedral : 7.692 132.477 2399 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Rotamer: Outliers : 2.10 % Allowed : 22.47 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1584 helix: 1.46 (0.19), residues: 757 sheet: -0.09 (0.33), residues: 242 loop : -1.64 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 105 HIS 0.013 0.001 HIS A1155 PHE 0.013 0.001 PHE B 76 TYR 0.015 0.001 TYR C 151 ARG 0.003 0.000 ARG A 794 Details of bonding type rmsd hydrogen bonds : bond 0.05368 ( 641) hydrogen bonds : angle 4.48353 ( 1851) SS BOND : bond 0.00324 ( 5) SS BOND : angle 0.56961 ( 10) covalent geometry : bond 0.00248 (13003) covalent geometry : angle 0.55106 (17669) ********************** 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 119 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 1.498 Fit side-chains REVERT: A 68 MET cc_start: 0.7707 (tpp) cc_final: 0.6873 (tpp) REVERT: A 450 MET cc_start: 0.6012 (tmm) cc_final: 0.5040 (tmm) REVERT: A 479 LEU cc_start: 0.7599 (mt) cc_final: 0.7356 (mt) REVERT: A 628 MET cc_start: 0.0810 (mtp) cc_final: -0.0330 (ptt) outliers start: 28 outliers final: 23 residues processed: 113 average time/residue: 0.3105 time to fit residues: 55.6783 Evaluate side-chains 111 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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 461 ILE Chi-restraints excluded: chain A residue 695 VAL 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 C residue 38 ARG Chi-restraints excluded: chain C residue 91 THR 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 17 optimal weight: 0.0020 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- 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 398 HIS ** 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 = 0.4443 r_free = 0.4443 target = 0.195817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.149718 restraints weight = 18161.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.145238 restraints weight = 33689.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.135875 restraints weight = 22537.500| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13008 Z= 0.138 Angle : 0.569 8.540 17679 Z= 0.289 Chirality : 0.040 0.170 2038 Planarity : 0.003 0.054 2164 Dihedral : 7.686 133.080 2399 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.56 % Favored : 94.38 % Rotamer: Outliers : 1.80 % Allowed : 22.77 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1584 helix: 1.43 (0.19), residues: 758 sheet: -0.03 (0.33), residues: 242 loop : -1.60 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 194 HIS 0.012 0.001 HIS A1155 PHE 0.017 0.001 PHE B 76 TYR 0.015 0.001 TYR C 151 ARG 0.004 0.000 ARG B 101 Details of bonding type rmsd hydrogen bonds : bond 0.05566 ( 641) hydrogen bonds : angle 4.51355 ( 1851) SS BOND : bond 0.00372 ( 5) SS BOND : angle 0.70316 ( 10) covalent geometry : bond 0.00302 (13003) covalent geometry : angle 0.56880 (17669) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4363.19 seconds wall clock time: 79 minutes 12.22 seconds (4752.22 seconds total)