Starting phenix.real_space_refine on Fri Jul 3 08:09:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7a6c_11670/07_2026/7a6c_11670.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a6c_11670/07_2026/7a6c_11670.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7a6c_11670/07_2026/7a6c_11670.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a6c_11670/07_2026/7a6c_11670.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a6c_11670/07_2026/7a6c_11670.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a6c_11670/07_2026/7a6c_11670.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7a6c_11670/07_2026/7a6c_11670.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7a6c_11670/07_2026/7a6c_11670.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 8251 2.51 5 N 2092 2.21 5 O 2324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12717 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1164, 9050 Classifications: {'peptide': 1164} Link IDs: {'PTRANS': 27, 'TRANS': 1136} Chain breaks: 2 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CYS%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1647 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 205} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PRO%COO:oxt': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 364 Unusual residues: {'CLR': 10, 'R0Z': 2} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 2.69, per 1000 atoms: 0.21 Number of scatterers: 12717 At special positions: 0 Unit cell: (102.48, 206.64, 98.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 2324 8.00 N 2092 7.00 C 8251 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 576.1 milliseconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 49.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 44 through 63 removed outlier: 3.543A pdb=" N LYS A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 83 removed outlier: 4.052A pdb=" N GLU A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASN A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 157 removed outlier: 4.172A pdb=" N TYR A 116 " --> pdb=" O THR A 112 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 157 " --> pdb=" O HIS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 removed outlier: 3.836A pdb=" N VAL A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 166' Processing helix chain 'A' and resid 168 through 211 removed outlier: 5.563A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLY A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.718A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 239 through 260 removed outlier: 5.292A pdb=" N LYS A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 267 Processing helix chain 'A' and resid 270 through 324 removed outlier: 3.681A pdb=" N ASN A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A 319 " --> pdb=" O TRP A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 369 removed outlier: 3.582A pdb=" N VAL A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Proline residue: A 350 - end of helix removed outlier: 4.506A pdb=" N TYR A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 3.896A pdb=" N LYS A 405 " --> pdb=" O PRO A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 441 removed outlier: 3.971A pdb=" N THR A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 525 through 529 removed outlier: 3.583A pdb=" N GLY A 528 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 529 " --> pdb=" O GLU A 526 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 525 through 529' Processing helix chain 'A' and resid 533 through 547 Processing helix chain 'A' and resid 563 through 575 Processing helix chain 'A' and resid 588 through 592 removed outlier: 3.546A pdb=" N THR A 591 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 619 removed outlier: 3.669A pdb=" N LYS A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 removed outlier: 4.233A pdb=" N LYS A 624 " --> pdb=" O GLY A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 705 removed outlier: 3.820A pdb=" N LEU A 705 " --> pdb=" O LYS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 724 Processing helix chain 'A' and resid 725 through 736 Processing helix chain 'A' and resid 736 through 741 Processing helix chain 'A' and resid 744 through 798 removed outlier: 3.830A pdb=" N LYS A 748 " --> pdb=" O ASP A 744 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 798 " --> pdb=" O ARG A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 806 Processing helix chain 'A' and resid 810 through 854 removed outlier: 5.064A pdb=" N ALA A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 830 " --> pdb=" O LYS A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 862 removed outlier: 3.797A pdb=" N LEU A 860 " --> pdb=" O GLN A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 880 Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 913 through 965 removed outlier: 4.148A pdb=" N MET A 919 " --> pdb=" O LYS A 915 " (cutoff:3.500A) Proline residue: A 927 - end of helix removed outlier: 3.637A pdb=" N ASN A 930 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 946 " --> pdb=" O PHE A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 993 Processing helix chain 'A' and resid 998 through 1012 Processing helix chain 'A' and resid 1079 through 1084 removed outlier: 3.650A pdb=" N GLU A1084 " --> pdb=" O VAL A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1113 removed outlier: 3.546A pdb=" N ALA A1111 " --> pdb=" O GLN A1107 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A1113 " --> pdb=" O LEU A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1135 Processing helix chain 'A' and resid 1141 through 1152 removed outlier: 4.269A pdb=" N ARG A1147 " --> pdb=" O GLU A1143 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA A1152 " --> pdb=" O ALA A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1154 through 1161 removed outlier: 3.608A pdb=" N ILE A1158 " --> pdb=" O ILE A1154 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A1160 " --> pdb=" O ALA A1156 " (cutoff:3.500A) Processing helix chain 'A' and resid 1170 through 1174 removed outlier: 3.837A pdb=" N GLY A1173 " --> pdb=" O GLY A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1193 removed outlier: 4.175A pdb=" N ARG A1183 " --> pdb=" O GLY A1179 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A1186 " --> pdb=" O GLN A1182 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A1191 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A1192 " --> pdb=" O ARG A1188 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1220 removed outlier: 3.645A pdb=" N LYS A1212 " --> pdb=" O THR A1208 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1257 through 1261 Processing helix chain 'A' and resid 1265 through 1271 removed outlier: 3.813A pdb=" N SER A1269 " --> pdb=" O GLY A1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing sheet with id=AA1, first strand: chain 'A' and resid 392 through 393 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399 removed outlier: 3.674A pdb=" N PHE A 399 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 410 " --> pdb=" O PHE A 399 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 470 through 473 removed outlier: 6.487A pdb=" N GLY A 471 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ASP A 555 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 473 " --> pdb=" O ASP A 555 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL A 423 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA A 424 " --> pdb=" O ALA A 599 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A 601 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N VAL A 426 " --> pdb=" O PHE A 601 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP A 602 " --> pdb=" O ILE A 606 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ILE A 606 " --> pdb=" O ASP A 602 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 452 through 453 removed outlier: 4.001A pdb=" N GLN A 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1053 through 1059 removed outlier: 3.623A pdb=" N GLY A1055 " --> pdb=" O VAL A1040 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL A1040 " --> pdb=" O GLY A1055 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N SER A1057 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLY A1038 " --> pdb=" O SER A1057 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLU A1059 " --> pdb=" O THR A1036 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N THR A1036 " --> pdb=" O GLU A1059 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL A1040 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA A1091 " --> pdb=" O VAL A1040 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1196 through 1200 removed outlier: 7.583A pdb=" N CYS A1227 " --> pdb=" O LEU A1066 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N LEU A1068 " --> pdb=" O CYS A1227 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A1229 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A1245 " --> pdb=" O GLU A1253 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLU A1253 " --> pdb=" O VAL A1245 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLN A1247 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL A1251 " --> pdb=" O GLN A1247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 14 removed outlier: 6.189A pdb=" N LEU B 11 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS B 112 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL B 13 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 89 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 119 through 123 removed outlier: 3.645A pdb=" N THR B 119 " --> pdb=" O ASN B 142 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL B 138 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TYR B 178 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 151 through 155 removed outlier: 3.548A pdb=" N TYR B 197 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.181A pdb=" N GLY C 10 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER C 35 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET C 34 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL C 48 " --> pdb=" O TRP C 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 17 through 20 Processing sheet with id=AB5, first strand: chain 'C' and resid 126 through 130 removed outlier: 3.666A pdb=" N LEU C 147 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU C 130 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 145 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR C 181 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU C 176 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N THR C 182 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA C 174 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 184 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 159 through 160 641 hydrogen bonds defined for protein. 1851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.51 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: 7136 26.48 - 52.97: 428 52.97 - 79.45: 43 79.45 - 105.93: 8 105.93 - 132.42: 1 Dihedral angle restraints: 7616 sinusoidal: 3030 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 7613 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: 3.700 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.210 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 16.361 132.418 4661 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 25.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.05 % Favored : 88.70 % Rotamer: Outliers : 3.00 % Allowed : 7.94 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.17), residues: 1584 helix: -2.66 (0.15), residues: 744 sheet: -1.83 (0.29), residues: 257 loop : -3.34 (0.21), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 67 TYR 0.052 0.003 TYR A 277 PHE 0.033 0.004 PHE A 72 TRP 0.033 0.004 TRP A 698 HIS 0.009 0.002 HIS A 166 Details of bonding type rmsd/Z covalent geometry : bond 0.01663 / 0.73 (13003) covalent geometry : angle 1.36562 / 0.72 (17669) SS BOND : bond 0.00186 / 0.12 ( 5) SS BOND : angle 0.68465 / 0.44 ( 10) hydrogen bonds : bond 0.20035 / 12.99 ( 641) hydrogen bonds : angle 7.96624 / 5.58 ( 1851) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 236 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8116 (tp) REVERT: A 380 LYS cc_start: 0.5430 (OUTLIER) cc_final: 0.4862 (ptpt) REVERT: A 450 MET cc_start: 0.5983 (tmm) cc_final: 0.5147 (tmm) REVERT: A 1015 THR cc_start: 0.5297 (OUTLIER) cc_final: 0.4936 (t) REVERT: B 115 ASP cc_start: 0.5328 (OUTLIER) cc_final: 0.5005 (t0) outliers start: 40 outliers final: 19 residues processed: 164 average time/residue: 0.1322 time to fit residues: 30.4776 Evaluate side-chains 107 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 381 SER Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 878 MET Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 924 LEU Chi-restraints excluded: chain A residue 1014 LYS Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 HIS A 438 GLN A 508 ASN A 594 ASN A 611 ASN A 725 GLN A 809 ASN A 839 ASN A 903 ASN A 912 GLN A1054 GLN ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 ASN C 39 GLN ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.194697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.148773 restraints weight = 18291.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138101 restraints weight = 33640.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131341 restraints weight = 30472.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133190 restraints weight = 23390.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132887 restraints weight = 16635.097| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13008 Z= 0.178 Angle : 0.725 9.762 17679 Z= 0.366 Chirality : 0.043 0.156 2038 Planarity : 0.005 0.052 2164 Dihedral : 10.079 133.328 1881 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.74 % Favored : 94.19 % Rotamer: Outliers : 1.72 % Allowed : 14.61 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.19), residues: 1584 helix: -0.63 (0.17), residues: 755 sheet: -1.21 (0.30), residues: 257 loop : -2.66 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 794 TYR 0.016 0.002 TYR A 928 PHE 0.035 0.002 PHE A 904 TRP 0.017 0.002 TRP C 105 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (13003) covalent geometry : angle 0.72469 / 0.37 (17669) SS BOND : bond 0.00456 / 0.30 ( 5) SS BOND : angle 0.93849 / 0.52 ( 10) hydrogen bonds : bond 0.06987 / 4.54 ( 641) hydrogen bonds : angle 5.54864 / 3.93 ( 1851) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6951 (mpp) REVERT: A 380 LYS cc_start: 0.5726 (OUTLIER) cc_final: 0.5270 (ptpt) REVERT: A 450 MET cc_start: 0.6094 (tmm) cc_final: 0.4949 (tmm) REVERT: A 479 LEU cc_start: 0.7712 (mt) cc_final: 0.7426 (mt) outliers start: 23 outliers final: 9 residues processed: 135 average time/residue: 0.1166 time to fit residues: 23.2591 Evaluate side-chains 108 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 192 MET 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 C residue 136 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 123 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 110 optimal weight: 20.0000 chunk 141 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 93 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 143 GLN A 145 HIS A 172 ASN ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1105 ASN ** A1254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.194060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.153585 restraints weight = 18431.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.148485 restraints weight = 31616.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.142924 restraints weight = 32650.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.141756 restraints weight = 32560.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.139305 restraints weight = 26043.279| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13008 Z= 0.156 Angle : 0.627 8.470 17679 Z= 0.319 Chirality : 0.041 0.159 2038 Planarity : 0.004 0.071 2164 Dihedral : 8.904 130.947 1840 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.93 % Favored : 94.00 % Rotamer: Outliers : 2.40 % Allowed : 16.85 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.20), residues: 1584 helix: 0.24 (0.18), residues: 761 sheet: -0.98 (0.30), residues: 258 loop : -2.41 (0.23), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 101 TYR 0.015 0.002 TYR B 197 PHE 0.020 0.002 PHE B 215 TRP 0.013 0.001 TRP C 105 HIS 0.004 0.001 HIS A1254 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (13003) covalent geometry : angle 0.62643 / 0.32 (17669) SS BOND : bond 0.00814 / 0.58 ( 5) SS BOND : angle 1.16425 / 0.65 ( 10) hydrogen bonds : bond 0.06411 / 4.20 ( 641) hydrogen bonds : angle 5.06351 / 3.58 ( 1851) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8419 (mmt) cc_final: 0.8206 (mmt) REVERT: A 450 MET cc_start: 0.6130 (tmm) cc_final: 0.5111 (tmm) REVERT: A 479 LEU cc_start: 0.7673 (mt) cc_final: 0.7387 (mt) REVERT: A 770 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.7102 (t80) outliers start: 32 outliers final: 19 residues processed: 130 average time/residue: 0.1119 time to fit residues: 21.7890 Evaluate side-chains 111 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 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 91 THR Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 142 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 50 optimal weight: 30.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.192392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.145753 restraints weight = 18383.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137830 restraints weight = 36261.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.129653 restraints weight = 27914.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130378 restraints weight = 27865.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130209 restraints weight = 20709.681| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13008 Z= 0.216 Angle : 0.665 8.527 17679 Z= 0.338 Chirality : 0.042 0.161 2038 Planarity : 0.004 0.069 2164 Dihedral : 8.644 132.120 1831 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.38 % Favored : 93.56 % Rotamer: Outliers : 2.70 % Allowed : 18.95 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.20), residues: 1584 helix: 0.41 (0.18), residues: 754 sheet: -0.81 (0.31), residues: 244 loop : -2.22 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 794 TYR 0.018 0.002 TYR B 145 PHE 0.019 0.002 PHE B 94 TRP 0.015 0.002 TRP A 708 HIS 0.005 0.001 HIS A1254 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (13003) covalent geometry : angle 0.66451 / 0.34 (17669) SS BOND : bond 0.00433 / 0.29 ( 5) SS BOND : angle 0.98277 / 0.71 ( 10) hydrogen bonds : bond 0.06791 / 4.44 ( 641) hydrogen bonds : angle 5.02517 / 3.56 ( 1851) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 111 MET cc_start: 0.8056 (mmm) cc_final: 0.7687 (mmm) REVERT: A 156 MET cc_start: 0.8591 (mmt) cc_final: 0.8204 (mmt) REVERT: A 380 LYS cc_start: 0.5720 (OUTLIER) cc_final: 0.5400 (ptpt) REVERT: A 448 GLU cc_start: 0.5287 (OUTLIER) cc_final: 0.5081 (mt-10) REVERT: A 450 MET cc_start: 0.6023 (tmm) cc_final: 0.4876 (tmm) REVERT: A 479 LEU cc_start: 0.7699 (mt) cc_final: 0.7364 (mt) REVERT: A 770 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7172 (t80) REVERT: A 1159 GLU cc_start: 0.5127 (OUTLIER) cc_final: 0.4883 (mp0) outliers start: 36 outliers final: 23 residues processed: 123 average time/residue: 0.1069 time to fit residues: 20.0411 Evaluate side-chains 111 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain A residue 448 GLU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN A 441 GLN A 508 ASN ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.192794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.144624 restraints weight = 18452.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136307 restraints weight = 32080.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126838 restraints weight = 23574.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127773 restraints weight = 28035.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128367 restraints weight = 18620.646| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2778 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= 0.187 Angle : 0.629 8.258 17679 Z= 0.320 Chirality : 0.041 0.156 2038 Planarity : 0.004 0.057 2164 Dihedral : 8.456 132.135 1827 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.44 % Favored : 93.50 % Rotamer: Outliers : 3.07 % Allowed : 20.90 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.21), residues: 1584 helix: 0.66 (0.19), residues: 754 sheet: -0.69 (0.31), residues: 244 loop : -2.14 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 101 TYR 0.016 0.002 TYR B 145 PHE 0.032 0.002 PHE A 904 TRP 0.012 0.001 TRP C 105 HIS 0.005 0.001 HIS A1254 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (13003) covalent geometry : angle 0.62858 / 0.32 (17669) SS BOND : bond 0.00406 / 0.27 ( 5) SS BOND : angle 0.89241 / 0.63 ( 10) hydrogen bonds : bond 0.06548 / 4.29 ( 641) hydrogen bonds : angle 4.90858 / 3.48 ( 1851) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 86 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8573 (mmt) cc_final: 0.8320 (mmt) REVERT: A 183 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8631 (t0) REVERT: A 380 LYS cc_start: 0.5662 (OUTLIER) cc_final: 0.5145 (ttpt) REVERT: A 450 MET cc_start: 0.6088 (tmm) cc_final: 0.4941 (tmm) REVERT: A 770 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.7148 (t80) REVERT: A 912 GLN cc_start: 0.7479 (mm110) cc_final: 0.6778 (tm-30) REVERT: A 1119 GLU cc_start: 0.6984 (tm-30) cc_final: 0.5754 (pm20) outliers start: 41 outliers final: 28 residues processed: 122 average time/residue: 0.1037 time to fit residues: 19.4805 Evaluate side-chains 117 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 183 ASN 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 380 LYS Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 606 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 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 1191 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 43 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 55 optimal weight: 30.0000 chunk 114 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN A 936 HIS ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.195152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.151404 restraints weight = 18256.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.147416 restraints weight = 31961.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.141882 restraints weight = 21369.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.141312 restraints weight = 22428.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.141122 restraints weight = 16138.100| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3024 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= 0.133 Angle : 0.575 7.859 17679 Z= 0.293 Chirality : 0.040 0.167 2038 Planarity : 0.004 0.059 2164 Dihedral : 8.218 131.649 1827 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 2.62 % Allowed : 21.80 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.21), residues: 1584 helix: 0.98 (0.19), residues: 753 sheet: -0.52 (0.32), residues: 237 loop : -1.99 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 794 TYR 0.015 0.001 TYR C 151 PHE 0.023 0.001 PHE A 904 TRP 0.016 0.001 TRP C 194 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (13003) covalent geometry : angle 0.57501 / 0.29 (17669) SS BOND : bond 0.00358 / 0.24 ( 5) SS BOND : angle 0.66902 / 0.47 ( 10) hydrogen bonds : bond 0.05934 / 3.88 ( 641) hydrogen bonds : angle 4.72586 / 3.35 ( 1851) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.465 Fit side-chains REVERT: A 172 ASN cc_start: 0.7250 (m110) cc_final: 0.7042 (m110) REVERT: A 380 LYS cc_start: 0.5245 (tppt) cc_final: 0.5006 (ttpt) REVERT: A 450 MET cc_start: 0.6216 (tmm) cc_final: 0.5185 (tmm) REVERT: A 1119 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6303 (pm20) outliers start: 35 outliers final: 26 residues processed: 124 average time/residue: 0.1013 time to fit residues: 19.4171 Evaluate side-chains 115 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 606 ILE Chi-restraints excluded: chain A residue 744 ASP Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 811 THR Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1041 VAL Chi-restraints excluded: chain A residue 1113 LEU Chi-restraints excluded: chain A residue 1191 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 30 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 130 optimal weight: 0.0010 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN ** 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 = 0.4429 r_free = 0.4429 target = 0.194395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.147699 restraints weight = 18247.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.141746 restraints weight = 36391.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.134180 restraints weight = 24387.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134386 restraints weight = 25709.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134079 restraints weight = 20242.282| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13008 Z= 0.156 Angle : 0.596 7.497 17679 Z= 0.305 Chirality : 0.040 0.186 2038 Planarity : 0.004 0.055 2164 Dihedral : 8.146 132.612 1827 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.93 % Favored : 94.00 % Rotamer: Outliers : 3.15 % Allowed : 22.02 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.21), residues: 1584 helix: 1.03 (0.19), residues: 753 sheet: -0.39 (0.32), residues: 237 loop : -1.92 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 101 TYR 0.018 0.001 TYR C 181 PHE 0.020 0.001 PHE A 904 TRP 0.012 0.001 TRP C 194 HIS 0.022 0.001 HIS A1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (13003) covalent geometry : angle 0.59641 / 0.30 (17669) SS BOND : bond 0.00362 / 0.24 ( 5) SS BOND : angle 0.72506 / 0.48 ( 10) hydrogen bonds : bond 0.06042 / 3.96 ( 641) hydrogen bonds : angle 4.71420 / 3.35 ( 1851) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 88 time to evaluate : 0.457 Fit side-chains REVERT: A 380 LYS cc_start: 0.5354 (OUTLIER) cc_final: 0.4969 (ttpt) REVERT: A 450 MET cc_start: 0.6159 (tmm) cc_final: 0.4998 (tmm) REVERT: A 628 MET cc_start: 0.1032 (mtp) cc_final: 0.0624 (tmm) REVERT: A 1119 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6716 (mm-30) outliers start: 42 outliers final: 27 residues processed: 122 average time/residue: 0.1035 time to fit residues: 19.5878 Evaluate side-chains 113 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 380 LYS 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 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 1010 MET 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 102 THR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 148 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 148 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 32 optimal weight: 0.0870 chunk 157 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 ASN ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN ** 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 = 0.4438 r_free = 0.4438 target = 0.195834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.150881 restraints weight = 18083.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.145403 restraints weight = 36249.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.140129 restraints weight = 29861.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.139343 restraints weight = 23654.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139914 restraints weight = 20275.234| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13008 Z= 0.126 Angle : 0.555 7.572 17679 Z= 0.284 Chirality : 0.039 0.171 2038 Planarity : 0.003 0.052 2164 Dihedral : 7.902 131.464 1827 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.82 % Rotamer: Outliers : 2.32 % Allowed : 22.77 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.21), residues: 1584 helix: 1.33 (0.19), residues: 757 sheet: -0.22 (0.33), residues: 239 loop : -1.79 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 794 TYR 0.014 0.001 TYR C 151 PHE 0.017 0.001 PHE A 904 TRP 0.012 0.001 TRP C 194 HIS 0.016 0.001 HIS A1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (13003) covalent geometry : angle 0.55547 / 0.28 (17669) SS BOND : bond 0.00334 / 0.22 ( 5) SS BOND : angle 0.57492 / 0.41 ( 10) hydrogen bonds : bond 0.05430 / 3.56 ( 641) hydrogen bonds : angle 4.54679 / 3.23 ( 1851) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.488 Fit side-chains REVERT: A 380 LYS cc_start: 0.5202 (tppt) cc_final: 0.4979 (ttpt) REVERT: A 450 MET cc_start: 0.6103 (tmm) cc_final: 0.5030 (tmm) REVERT: A 912 GLN cc_start: 0.7364 (mm-40) cc_final: 0.6721 (tm-30) REVERT: A 1119 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6777 (mm-30) outliers start: 31 outliers final: 24 residues processed: 120 average time/residue: 0.1064 time to fit residues: 19.5047 Evaluate side-chains 111 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 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 1113 LEU Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 48 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 139 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN ** 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 = 0.4437 r_free = 0.4437 target = 0.195665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.154347 restraints weight = 18201.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.150353 restraints weight = 35638.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144349 restraints weight = 27193.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.143878 restraints weight = 28542.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.143973 restraints weight = 18846.787| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13008 Z= 0.128 Angle : 0.571 8.916 17679 Z= 0.290 Chirality : 0.039 0.159 2038 Planarity : 0.003 0.051 2164 Dihedral : 7.854 132.446 1827 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.30 % Favored : 94.63 % Rotamer: Outliers : 2.32 % Allowed : 23.00 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1584 helix: 1.43 (0.19), residues: 757 sheet: -0.19 (0.32), residues: 242 loop : -1.66 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 794 TYR 0.017 0.001 TYR B 197 PHE 0.014 0.001 PHE B 76 TRP 0.010 0.001 TRP C 105 HIS 0.014 0.001 HIS A1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (13003) covalent geometry : angle 0.57116 / 0.29 (17669) SS BOND : bond 0.00338 / 0.23 ( 5) SS BOND : angle 0.60899 / 0.40 ( 10) hydrogen bonds : bond 0.05420 / 3.56 ( 641) hydrogen bonds : angle 4.50334 / 3.20 ( 1851) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.468 Fit side-chains REVERT: A 380 LYS cc_start: 0.5168 (tppt) cc_final: 0.4960 (ttpt) REVERT: A 450 MET cc_start: 0.6023 (tmm) cc_final: 0.5031 (tmm) REVERT: A 479 LEU cc_start: 0.7494 (mt) cc_final: 0.7118 (mt) REVERT: A 628 MET cc_start: 0.0988 (mtp) cc_final: -0.0274 (ptt) REVERT: A 912 GLN cc_start: 0.7304 (mm-40) cc_final: 0.6666 (tm-30) REVERT: A 953 TYR cc_start: 0.7774 (OUTLIER) cc_final: 0.7267 (t80) REVERT: A 1119 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6788 (mm-30) outliers start: 31 outliers final: 26 residues processed: 118 average time/residue: 0.1052 time to fit residues: 19.2116 Evaluate side-chains 116 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 213 LYS Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 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 953 TYR 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 78 LEU Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 40 optimal weight: 0.0970 chunk 27 optimal weight: 0.0010 chunk 13 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 145 optimal weight: 0.8980 chunk 102 optimal weight: 0.3980 chunk 112 optimal weight: 10.0000 chunk 121 optimal weight: 0.0170 chunk 59 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 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 = 0.4475 r_free = 0.4475 target = 0.199447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.160801 restraints weight = 18251.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.162470 restraints weight = 47475.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.159598 restraints weight = 21439.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159460 restraints weight = 17589.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.159730 restraints weight = 12049.023| |-----------------------------------------------------------------------------| r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13008 Z= 0.110 Angle : 0.549 8.734 17679 Z= 0.278 Chirality : 0.038 0.169 2038 Planarity : 0.003 0.048 2164 Dihedral : 7.620 130.681 1827 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.23 % Favored : 95.71 % Rotamer: Outliers : 1.65 % Allowed : 23.37 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.22), residues: 1584 helix: 1.74 (0.19), residues: 753 sheet: 0.07 (0.33), residues: 242 loop : -1.55 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 794 TYR 0.014 0.001 TYR C 151 PHE 0.013 0.001 PHE A 983 TRP 0.009 0.001 TRP C 105 HIS 0.012 0.001 HIS A1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.11 (13003) covalent geometry : angle 0.54934 / 0.28 (17669) SS BOND : bond 0.00245 / 0.16 ( 5) SS BOND : angle 0.45366 / 0.31 ( 10) hydrogen bonds : bond 0.04692 / 3.09 ( 641) hydrogen bonds : angle 4.35247 / 3.09 ( 1851) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 MET cc_start: 0.5881 (tmm) cc_final: 0.5171 (tmm) REVERT: A 479 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7045 (mt) REVERT: A 628 MET cc_start: 0.0909 (mtp) cc_final: 0.0381 (tmm) REVERT: A 1087 TYR cc_start: 0.7449 (m-80) cc_final: 0.7238 (m-80) outliers start: 22 outliers final: 17 residues processed: 115 average time/residue: 0.1079 time to fit residues: 18.8140 Evaluate side-chains 110 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 TRP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 353 GLU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 770 PHE Chi-restraints excluded: chain A residue 785 THR 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 103 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 40 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 0.3980 chunk 48 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 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 = 0.4452 r_free = 0.4452 target = 0.197037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.158159 restraints weight = 18260.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.152895 restraints weight = 33636.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.149223 restraints weight = 31551.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.148103 restraints weight = 30436.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.146303 restraints weight = 22973.657| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13008 Z= 0.124 Angle : 0.552 9.219 17679 Z= 0.279 Chirality : 0.039 0.172 2038 Planarity : 0.003 0.049 2164 Dihedral : 7.617 131.858 1827 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.18 % Favored : 94.76 % Rotamer: Outliers : 1.42 % Allowed : 23.82 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.22), residues: 1584 helix: 1.69 (0.19), residues: 757 sheet: 0.08 (0.32), residues: 243 loop : -1.51 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 794 TYR 0.016 0.001 TYR C 181 PHE 0.015 0.001 PHE B 76 TRP 0.017 0.001 TRP C 194 HIS 0.012 0.001 HIS A1155 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13003) covalent geometry : angle 0.55173 / 0.28 (17669) SS BOND : bond 0.00331 / 0.22 ( 5) SS BOND : angle 0.61637 / 0.38 ( 10) hydrogen bonds : bond 0.05087 / 3.35 ( 641) hydrogen bonds : angle 4.35538 / 3.10 ( 1851) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2214.63 seconds wall clock time: 39 minutes 20.59 seconds (2360.59 seconds total)