Starting phenix.real_space_refine on Sun Aug 24 00:27:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bx7_16311/08_2025/8bx7_16311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bx7_16311/08_2025/8bx7_16311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bx7_16311/08_2025/8bx7_16311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bx7_16311/08_2025/8bx7_16311.map" model { file = "/net/cci-nas-00/data/ceres_data/8bx7_16311/08_2025/8bx7_16311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bx7_16311/08_2025/8bx7_16311.cif" } resolution = 2.76 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= 0.018 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 80 5.16 5 C 10046 2.51 5 N 2644 2.21 5 O 2867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15637 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 3561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3561 Classifications: {'peptide': 465} Incomplete info: {'backbone_only': 26, 'truncation_to_alanine': 35} Link IDs: {'PTRANS': 14, 'TRANS': 450} Chain breaks: 2 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 3, 'TRP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 125 Chain: "A" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 3916 Classifications: {'peptide': 511} Incomplete info: {'backbone_only': 48, 'truncation_to_alanine': 12} Link IDs: {'PTRANS': 15, 'TRANS': 495} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 6, 'GLN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 117 Chain: "B" Number of atoms: 3954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3954 Classifications: {'peptide': 505} Incomplete info: {'backbone_only': 41, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 490} Chain breaks: 1 Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "C" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3946 Classifications: {'peptide': 513} Incomplete info: {'backbone_only': 53, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 496} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 4, 'GLN:plan1': 4, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "E" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 260 Classifications: {'peptide': 65} Incomplete info: {'backbone_only': 60} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 166 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 4, 'PHE:plan': 3, 'ASP:plan': 7, 'ASN:plan1': 3, 'TYR:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 151 Time building chain proxies: 3.46, per 1000 atoms: 0.22 Number of scatterers: 15637 At special positions: 0 Unit cell: (94.86, 122.4, 176.46, 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 80 16.00 O 2867 8.00 N 2644 7.00 C 10046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.26 Conformation dependent library (CDL) restraints added in 625.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 11 sheets defined 66.0% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'D' and resid 769 through 794 Proline residue: D 789 - end of helix Processing helix chain 'D' and resid 798 through 819 removed outlier: 4.694A pdb=" N HIS D 803 " --> pdb=" O PRO D 799 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU D 804 " --> pdb=" O ASP D 800 " (cutoff:3.500A) Processing helix chain 'D' and resid 841 through 848 removed outlier: 4.176A pdb=" N VAL D 847 " --> pdb=" O ARG D 843 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS D 848 " --> pdb=" O ASN D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 855 Processing helix chain 'D' and resid 872 through 877 removed outlier: 3.953A pdb=" N ARG D 876 " --> pdb=" O ASN D 872 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 877 " --> pdb=" O PRO D 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 872 through 877' Processing helix chain 'D' and resid 882 through 897 removed outlier: 3.985A pdb=" N PHE D 886 " --> pdb=" O LYS D 882 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 887 " --> pdb=" O TYR D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 931 removed outlier: 3.862A pdb=" N ARG D 904 " --> pdb=" O ALA D 900 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL D 905 " --> pdb=" O TYR D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 957 removed outlier: 3.693A pdb=" N ARG D 948 " --> pdb=" O ASN D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 971 through 1021 removed outlier: 4.225A pdb=" N GLY D 976 " --> pdb=" O ILE D 972 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU D 977 " --> pdb=" O VAL D 973 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLY D1003 " --> pdb=" O ALA D 999 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN D1004 " --> pdb=" O ALA D1000 " (cutoff:3.500A) Processing helix chain 'D' and resid 1024 through 1040 Processing helix chain 'D' and resid 1047 through 1053 removed outlier: 4.033A pdb=" N GLN D1053 " --> pdb=" O GLU D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1067 Processing helix chain 'D' and resid 1067 through 1073 removed outlier: 4.071A pdb=" N VAL D1071 " --> pdb=" O ASN D1067 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1091 removed outlier: 4.075A pdb=" N ILE D1085 " --> pdb=" O ASP D1081 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1149 removed outlier: 3.784A pdb=" N LEU D1148 " --> pdb=" O ILE D1145 " (cutoff:3.500A) Processing helix chain 'D' and resid 1172 through 1182 removed outlier: 4.085A pdb=" N HIS D1182 " --> pdb=" O GLU D1178 " (cutoff:3.500A) Processing helix chain 'D' and resid 1183 through 1203 removed outlier: 3.856A pdb=" N LEU D1189 " --> pdb=" O GLU D1185 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN D1201 " --> pdb=" O MET D1197 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN D1202 " --> pdb=" O LEU D1198 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS D1203 " --> pdb=" O ARG D1199 " (cutoff:3.500A) Processing helix chain 'D' and resid 1238 through 1265 Processing helix chain 'A' and resid 160 through 180 removed outlier: 3.722A pdb=" N LEU A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Proline residue: A 173 - end of helix Processing helix chain 'A' and resid 181 through 187 removed outlier: 3.512A pdb=" N PHE A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.850A pdb=" N GLN A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 244 through 249 Processing helix chain 'A' and resid 255 through 261 removed outlier: 3.950A pdb=" N ILE A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 3.508A pdb=" N ILE A 268 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN A 271 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.581A pdb=" N PHE A 282 " --> pdb=" O ARG A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.924A pdb=" N SER A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 402 removed outlier: 3.644A pdb=" N PHE A 374 " --> pdb=" O ASP A 370 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 421 Processing helix chain 'A' and resid 425 through 442 Processing helix chain 'A' and resid 447 through 452 removed outlier: 3.507A pdb=" N LEU A 452 " --> pdb=" O GLU A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 482 through 491 Processing helix chain 'A' and resid 576 through 583 Processing helix chain 'A' and resid 586 through 604 Processing helix chain 'A' and resid 619 through 665 Processing helix chain 'B' and resid 160 through 180 Proline residue: B 173 - end of helix Processing helix chain 'B' and resid 181 through 187 Processing helix chain 'B' and resid 194 through 216 removed outlier: 3.616A pdb=" N ASP B 202 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.525A pdb=" N LEU B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 259 removed outlier: 3.828A pdb=" N ILE B 259 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 274 removed outlier: 3.612A pdb=" N ILE B 268 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASN B 271 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG B 272 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 290 removed outlier: 4.255A pdb=" N MET B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 324 removed outlier: 3.784A pdb=" N ILE B 323 " --> pdb=" O ILE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 358 removed outlier: 3.932A pdb=" N SER B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 402 removed outlier: 3.605A pdb=" N PHE B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 422 Processing helix chain 'B' and resid 425 through 442 Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 470 through 474 Processing helix chain 'B' and resid 482 through 492 removed outlier: 3.546A pdb=" N GLU B 488 " --> pdb=" O GLY B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 548 removed outlier: 3.894A pdb=" N ILE B 547 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU B 548 " --> pdb=" O GLU B 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 543 through 548' Processing helix chain 'B' and resid 576 through 584 Processing helix chain 'B' and resid 586 through 605 removed outlier: 3.601A pdb=" N GLY B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 664 Processing helix chain 'C' and resid 161 through 187 Proline residue: C 173 - end of helix removed outlier: 5.129A pdb=" N ILE C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA C 183 " --> pdb=" O THR C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 194 Processing helix chain 'C' and resid 196 through 218 Processing helix chain 'C' and resid 230 through 239 Processing helix chain 'C' and resid 241 through 252 removed outlier: 3.762A pdb=" N LYS C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 256 No H-bonds generated for 'chain 'C' and resid 254 through 256' Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.210A pdb=" N ASN C 271 " --> pdb=" O ILE C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 290 removed outlier: 3.582A pdb=" N MET C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU C 287 " --> pdb=" O PHE C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 324 removed outlier: 3.722A pdb=" N PHE C 296 " --> pdb=" O TYR C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 359 Processing helix chain 'C' and resid 369 through 422 removed outlier: 4.856A pdb=" N ALA C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ARG C 405 " --> pdb=" O MET C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 442 Processing helix chain 'C' and resid 447 through 454 removed outlier: 3.789A pdb=" N TYR C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 468 Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.508A pdb=" N ALA C 479 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ASP C 480 " --> pdb=" O ILE C 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 476 through 480' Processing helix chain 'C' and resid 482 through 491 Processing helix chain 'C' and resid 576 through 584 Processing helix chain 'C' and resid 586 through 604 removed outlier: 3.964A pdb=" N LYS C 590 " --> pdb=" O TYR C 586 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY C 591 " --> pdb=" O PRO C 587 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP C 604 " --> pdb=" O ILE C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 670 removed outlier: 3.523A pdb=" N ARG C 641 " --> pdb=" O THR C 637 " (cutoff:3.500A) Proline residue: C 666 - end of helix Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.957A pdb=" N HIS E 108 " --> pdb=" O ALA E 104 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR E 111 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASN E 112 " --> pdb=" O HIS E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 139 through 148 Processing sheet with id=AA1, first strand: chain 'D' and resid 829 through 831 removed outlier: 3.685A pdb=" N PHE D 829 " --> pdb=" O ILE D 836 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 1093 through 1097 removed outlier: 6.835A pdb=" N ASN D1167 " --> pdb=" O GLN D1117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 1101 through 1104 removed outlier: 6.513A pdb=" N TYR D1102 " --> pdb=" O ALA D1162 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA D1162 " --> pdb=" O TYR D1102 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN D1159 " --> pdb=" O LEU D1124 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL D1121 " --> pdb=" O THR D1135 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR D1135 " --> pdb=" O VAL D1121 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL D1123 " --> pdb=" O LEU D1133 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 494 through 496 Processing sheet with id=AA5, first strand: chain 'A' and resid 503 through 505 removed outlier: 6.490A pdb=" N TYR A 503 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER A 565 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASN A 562 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 534 " --> pdb=" O VAL A 524 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 494 through 496 Processing sheet with id=AA7, first strand: chain 'B' and resid 532 through 534 removed outlier: 3.832A pdb=" N VAL B 534 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN B 562 " --> pdb=" O VAL B 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 222 through 223 Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AB1, first strand: chain 'C' and resid 503 through 505 removed outlier: 6.128A pdb=" N TYR C 503 " --> pdb=" O SER C 565 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N SER C 565 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS C 505 " --> pdb=" O ILE C 563 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL C 534 " --> pdb=" O VAL C 524 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 100 through 102 1018 hydrogen bonds defined for protein. 2967 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: 2.45 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5070 1.34 - 1.46: 3867 1.46 - 1.58: 6904 1.58 - 1.70: 0 1.70 - 1.82: 134 Bond restraints: 15975 Sorted by residual: bond pdb=" N ILE D1109 " pdb=" CA ILE D1109 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.19e-02 7.06e+03 9.68e+00 bond pdb=" N GLU D1108 " pdb=" CA GLU D1108 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.18e-02 7.18e+03 9.40e+00 bond pdb=" N GLU D1112 " pdb=" CA GLU D1112 " ideal model delta sigma weight residual 1.454 1.492 -0.039 1.34e-02 5.57e+03 8.29e+00 bond pdb=" N ARG D1111 " pdb=" CA ARG D1111 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.21e-02 6.83e+03 5.54e+00 bond pdb=" N ARG D1156 " pdb=" CA ARG D1156 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.25e-02 6.40e+03 5.39e+00 ... (remaining 15970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 21147 2.05 - 4.11: 332 4.11 - 6.16: 58 6.16 - 8.21: 8 8.21 - 10.27: 7 Bond angle restraints: 21552 Sorted by residual: angle pdb=" C LYS B 506 " pdb=" CA LYS B 506 " pdb=" CB LYS B 506 " ideal model delta sigma weight residual 116.63 110.22 6.41 1.16e+00 7.43e-01 3.05e+01 angle pdb=" N GLU D1112 " pdb=" CA GLU D1112 " pdb=" C GLU D1112 " ideal model delta sigma weight residual 110.19 115.77 -5.58 1.24e+00 6.50e-01 2.03e+01 angle pdb=" CB LYS C 453 " pdb=" CG LYS C 453 " pdb=" CD LYS C 453 " ideal model delta sigma weight residual 111.30 121.57 -10.27 2.30e+00 1.89e-01 1.99e+01 angle pdb=" N ILE D 958 " pdb=" CA ILE D 958 " pdb=" C ILE D 958 " ideal model delta sigma weight residual 113.53 109.75 3.78 9.80e-01 1.04e+00 1.49e+01 angle pdb=" N THR C 359 " pdb=" CA THR C 359 " pdb=" C THR C 359 " ideal model delta sigma weight residual 110.35 105.79 4.56 1.38e+00 5.25e-01 1.09e+01 ... (remaining 21547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 7992 17.33 - 34.67: 878 34.67 - 52.00: 202 52.00 - 69.34: 50 69.34 - 86.67: 13 Dihedral angle restraints: 9135 sinusoidal: 3536 harmonic: 5599 Sorted by residual: dihedral pdb=" CA TYR B 568 " pdb=" C TYR B 568 " pdb=" N SER B 569 " pdb=" CA SER B 569 " ideal model delta harmonic sigma weight residual 180.00 156.67 23.33 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ILE C 516 " pdb=" C ILE C 516 " pdb=" N ILE C 517 " pdb=" CA ILE C 517 " ideal model delta harmonic sigma weight residual 180.00 -157.17 -22.83 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TRP C 198 " pdb=" C TRP C 198 " pdb=" N LEU C 199 " pdb=" CA LEU C 199 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 9132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1507 0.036 - 0.072: 583 0.072 - 0.108: 150 0.108 - 0.144: 31 0.144 - 0.179: 4 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CA MET B 592 " pdb=" N MET B 592 " pdb=" C MET B 592 " pdb=" CB MET B 592 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CA ILE C 517 " pdb=" N ILE C 517 " pdb=" C ILE C 517 " pdb=" CB ILE C 517 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 6.00e-01 chirality pdb=" CB ILE B 309 " pdb=" CA ILE B 309 " pdb=" CG1 ILE B 309 " pdb=" CG2 ILE B 309 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 2272 not shown) Planarity restraints: 2780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 773 " 0.022 2.00e-02 2.50e+03 1.97e-02 9.74e+00 pdb=" CG TRP D 773 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 773 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP D 773 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 773 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 773 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 773 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 773 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 773 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 773 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 364 " -0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO A 365 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY D1107 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C GLY D1107 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY D1107 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU D1108 " 0.012 2.00e-02 2.50e+03 ... (remaining 2777 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1749 2.75 - 3.29: 15908 3.29 - 3.82: 26481 3.82 - 4.36: 29402 4.36 - 4.90: 50676 Nonbonded interactions: 124216 Sorted by model distance: nonbonded pdb=" OD2 ASP B 370 " pdb=" NH2 ARG C 342 " model vdw 2.209 3.120 nonbonded pdb=" O PHE B 214 " pdb=" OG1 THR B 217 " model vdw 2.210 3.040 nonbonded pdb=" OD2 ASP C 188 " pdb=" NZ LYS C 321 " model vdw 2.215 3.120 nonbonded pdb=" NH2 ARG D1025 " pdb=" OD1 ASN D1029 " model vdw 2.221 3.120 nonbonded pdb=" OH TYR A 209 " pdb=" O ARG A 272 " model vdw 2.223 3.040 ... (remaining 124211 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 154 through 359 or (resid 360 and (name N or name CA or na \ me C or name O or name CB )) or resid 361 through 362 or (resid 363 and (name N \ or name CA or name C or name O or name CB )) or resid 364 through 572 or (resid \ 573 and (name N or name CA or name C or name O or name CB )) or resid 574 throug \ h 601 or (resid 602 through 604 and (name N or name CA or name C or name O or na \ me CB )) or (resid 605 through 613 and (name N or name CA or name C or name O or \ name CB )) or resid 624 through 664)) selection = (chain 'B' and (resid 154 through 215 or (resid 216 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 217 through 277 or (resid 278 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 279 \ through 359 or (resid 360 and (name N or name CA or name C or name O or name CB \ )) or resid 361 through 442 or (resid 443 and (name N or name CA or name C or na \ me O or name CB )) or resid 444 through 457 or (resid 458 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 459 through 511 or (resid \ 512 and (name N or name CA or name C or name O or name CB )) or resid 513 throu \ gh 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) or \ resid 550 through 553 or (resid 554 through 555 and (name N or name CA or name \ C or name O or name CB )) or resid 556 through 561 or (resid 562 and (name N or \ name CA or name C or name O or name CB )) or resid 563 through 575 or (resid 576 \ and (name N or name CA or name C or name O or name CB or name CG or name CD )) \ or resid 577 through 601 or (resid 602 through 604 and (name N or name CA or nam \ e C or name O or name CB )) or resid 605 or (resid 606 through 613 and (name N o \ r name CA or name C or name O or name CB )) or resid 624 through 664)) selection = (chain 'C' and (resid 154 through 215 or (resid 216 and (name N or name CA or na \ me C or name O or name CB or name CG )) or resid 217 through 277 or (resid 278 a \ nd (name N or name CA or name C or name O or name CB or name CG )) or resid 279 \ through 362 or (resid 363 and (name N or name CA or name C or name O or name CB \ )) or resid 364 through 442 or (resid 443 and (name N or name CA or name C or na \ me O or name CB )) or resid 444 through 457 or (resid 458 and (name N or name CA \ or name C or name O or name CB or name CG )) or resid 459 through 511 or (resid \ 512 and (name N or name CA or name C or name O or name CB )) or resid 513 throu \ gh 548 or (resid 549 and (name N or name CA or name C or name O or name CB )) or \ resid 550 through 561 or (resid 562 and (name N or name CA or name C or name O \ or name CB )) or resid 563 through 572 or (resid 573 and (name N or name CA or n \ ame C or name O or name CB )) or resid 574 through 575 or (resid 576 and (name N \ or name CA or name C or name O or name CB or name CG or name CD )) or resid 577 \ through 603 or (resid 604 and (name N or name CA or name C or name O or name CB \ )) or (resid 605 through 613 and (name N or name CA or name C or name O or name \ CB )) or resid 624 through 664)) } 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 individual isotropic 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: 1.890 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: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.140 Find NCS groups from input model: 0.290 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:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.003 0.062 15975 Z= 0.156 Angle : 0.659 10.266 21552 Z= 0.377 Chirality : 0.040 0.179 2275 Planarity : 0.004 0.060 2780 Dihedral : 15.281 86.671 5695 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.61 % Rotamer: Outliers : 1.92 % Allowed : 19.51 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.20), residues: 2039 helix: 1.46 (0.15), residues: 1316 sheet: -0.91 (0.67), residues: 68 loop : -1.54 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 269 TYR 0.017 0.001 TYR D 810 PHE 0.014 0.001 PHE A 421 TRP 0.054 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00306 (15975) covalent geometry : angle 0.65949 (21552) hydrogen bonds : bond 0.12247 ( 1018) hydrogen bonds : angle 5.03167 ( 2967) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7455 (tmt) cc_final: 0.6753 (ttp) REVERT: B 449 ARG cc_start: 0.8194 (mtt90) cc_final: 0.7927 (mpt-90) REVERT: B 595 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8526 (mp0) REVERT: C 513 GLU cc_start: 0.8375 (mp0) cc_final: 0.7906 (mp0) outliers start: 30 outliers final: 13 residues processed: 203 average time/residue: 0.4464 time to fit residues: 102.5847 Evaluate side-chains 174 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 595 GLU Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.0670 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 891 ASN D1167 ASN A 442 ASN B 224 GLN B 284 GLN B 417 GLN B 494 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.137669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.103274 restraints weight = 27655.915| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.79 r_work: 0.3474 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15975 Z= 0.162 Angle : 0.575 8.119 21552 Z= 0.307 Chirality : 0.042 0.153 2275 Planarity : 0.004 0.055 2780 Dihedral : 5.313 56.491 2278 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.49 % Favored : 94.46 % Rotamer: Outliers : 3.90 % Allowed : 17.59 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.19), residues: 2039 helix: 1.67 (0.15), residues: 1323 sheet: -0.96 (0.65), residues: 68 loop : -1.60 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 269 TYR 0.014 0.001 TYR D 810 PHE 0.016 0.002 PHE A 421 TRP 0.027 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00377 (15975) covalent geometry : angle 0.57492 (21552) hydrogen bonds : bond 0.04151 ( 1018) hydrogen bonds : angle 4.01244 ( 2967) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 171 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6100 (OUTLIER) cc_final: 0.5664 (pt0) REVERT: D 1049 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: A 355 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8552 (m) REVERT: A 428 MET cc_start: 0.7661 (tpp) cc_final: 0.7452 (tpp) REVERT: B 258 TYR cc_start: 0.5605 (OUTLIER) cc_final: 0.4909 (t80) REVERT: B 270 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6657 (mp) REVERT: B 407 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7480 (mm-30) REVERT: B 415 ILE cc_start: 0.8138 (tp) cc_final: 0.7868 (tp) REVERT: C 297 ARG cc_start: 0.8353 (ttp-170) cc_final: 0.8072 (ttp-170) outliers start: 61 outliers final: 21 residues processed: 217 average time/residue: 0.4412 time to fit residues: 108.1595 Evaluate side-chains 181 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 1049 GLU Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 512 ARG Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 187 optimal weight: 8.9990 chunk 200 optimal weight: 8.9990 chunk 53 optimal weight: 0.4980 chunk 1 optimal weight: 6.9990 chunk 144 optimal weight: 40.0000 chunk 70 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN B 284 GLN C 191 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.136377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.101974 restraints weight = 27962.500| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.79 r_work: 0.3455 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15975 Z= 0.163 Angle : 0.566 9.123 21552 Z= 0.300 Chirality : 0.042 0.161 2275 Planarity : 0.004 0.055 2780 Dihedral : 4.798 58.824 2266 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.25 % Favored : 94.70 % Rotamer: Outliers : 4.80 % Allowed : 17.53 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.19), residues: 2039 helix: 1.75 (0.15), residues: 1317 sheet: -0.88 (0.66), residues: 68 loop : -1.56 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 449 TYR 0.013 0.001 TYR D 810 PHE 0.018 0.001 PHE A 421 TRP 0.024 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00383 (15975) covalent geometry : angle 0.56612 (21552) hydrogen bonds : bond 0.04051 ( 1018) hydrogen bonds : angle 3.90689 ( 2967) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 171 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6111 (OUTLIER) cc_final: 0.5710 (pt0) REVERT: D 1049 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: A 213 MET cc_start: 0.8400 (mmm) cc_final: 0.7719 (mmt) REVERT: A 355 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8555 (m) REVERT: A 428 MET cc_start: 0.7641 (tpp) cc_final: 0.7431 (tpp) REVERT: B 258 TYR cc_start: 0.5676 (OUTLIER) cc_final: 0.4987 (t80) REVERT: B 407 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7431 (mm-30) REVERT: B 415 ILE cc_start: 0.8146 (tp) cc_final: 0.7899 (tp) outliers start: 75 outliers final: 30 residues processed: 226 average time/residue: 0.4430 time to fit residues: 113.4194 Evaluate side-chains 193 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 980 PHE Chi-restraints excluded: chain D residue 1049 GLU Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 44 optimal weight: 50.0000 chunk 31 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.137608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.103223 restraints weight = 27698.798| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.80 r_work: 0.3470 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15975 Z= 0.129 Angle : 0.541 9.325 21552 Z= 0.287 Chirality : 0.041 0.155 2275 Planarity : 0.004 0.055 2780 Dihedral : 4.713 59.887 2266 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.61 % Rotamer: Outliers : 4.73 % Allowed : 18.49 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.20), residues: 2039 helix: 1.88 (0.15), residues: 1316 sheet: -0.81 (0.64), residues: 68 loop : -1.47 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 269 TYR 0.028 0.001 TYR D 810 PHE 0.018 0.001 PHE A 421 TRP 0.026 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00297 (15975) covalent geometry : angle 0.54119 (21552) hydrogen bonds : bond 0.03731 ( 1018) hydrogen bonds : angle 3.75657 ( 2967) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 179 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6057 (OUTLIER) cc_final: 0.5657 (pt0) REVERT: D 893 LEU cc_start: 0.8975 (tp) cc_final: 0.8741 (tt) REVERT: A 213 MET cc_start: 0.8309 (mmm) cc_final: 0.7794 (mmt) REVERT: A 355 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8530 (m) REVERT: B 222 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7138 (pp) REVERT: B 258 TYR cc_start: 0.5698 (OUTLIER) cc_final: 0.5003 (t80) REVERT: B 407 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7387 (mm-30) REVERT: B 415 ILE cc_start: 0.8149 (tp) cc_final: 0.7890 (tp) REVERT: C 297 ARG cc_start: 0.8290 (ttt180) cc_final: 0.7787 (mtp-110) REVERT: C 397 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8147 (mtm) outliers start: 74 outliers final: 40 residues processed: 229 average time/residue: 0.3663 time to fit residues: 96.2353 Evaluate side-chains 203 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 980 PHE Chi-restraints excluded: chain D residue 1012 ASP Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1054 LEU Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 76 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.0370 chunk 188 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN B 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.136210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.101746 restraints weight = 27747.521| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.78 r_work: 0.3445 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 15975 Z= 0.169 Angle : 0.581 9.664 21552 Z= 0.307 Chirality : 0.043 0.190 2275 Planarity : 0.004 0.055 2780 Dihedral : 4.732 59.978 2266 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.54 % Favored : 94.41 % Rotamer: Outliers : 5.05 % Allowed : 19.45 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.19), residues: 2039 helix: 1.80 (0.15), residues: 1321 sheet: -0.67 (0.69), residues: 61 loop : -1.44 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 269 TYR 0.026 0.001 TYR D 810 PHE 0.019 0.001 PHE A 421 TRP 0.035 0.002 TRP D 783 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00401 (15975) covalent geometry : angle 0.58080 (21552) hydrogen bonds : bond 0.03955 ( 1018) hydrogen bonds : angle 3.79963 ( 2967) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 178 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6124 (OUTLIER) cc_final: 0.5726 (pt0) REVERT: D 893 LEU cc_start: 0.9033 (tp) cc_final: 0.8813 (tt) REVERT: D 993 MET cc_start: 0.8929 (tpp) cc_final: 0.8221 (mpp) REVERT: A 213 MET cc_start: 0.8355 (mmm) cc_final: 0.7691 (mmt) REVERT: B 222 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7210 (pp) REVERT: B 258 TYR cc_start: 0.5840 (OUTLIER) cc_final: 0.5017 (t80) REVERT: B 407 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7400 (mm-30) REVERT: B 415 ILE cc_start: 0.8192 (tp) cc_final: 0.7939 (tp) REVERT: B 419 MET cc_start: 0.7195 (mtm) cc_final: 0.6860 (mtm) REVERT: B 450 GLU cc_start: 0.8436 (tp30) cc_final: 0.8199 (tp30) REVERT: C 303 MET cc_start: 0.8320 (ttm) cc_final: 0.8088 (ttt) REVERT: C 397 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8207 (mtm) outliers start: 79 outliers final: 41 residues processed: 233 average time/residue: 0.4405 time to fit residues: 117.4994 Evaluate side-chains 206 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 812 CYS Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 980 PHE Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 298 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 199 optimal weight: 40.0000 chunk 178 optimal weight: 0.4980 chunk 119 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.135782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.101373 restraints weight = 27809.255| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.78 r_work: 0.3438 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15975 Z= 0.178 Angle : 0.590 9.709 21552 Z= 0.310 Chirality : 0.043 0.177 2275 Planarity : 0.004 0.055 2780 Dihedral : 4.726 57.899 2266 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 4.73 % Allowed : 20.47 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.19), residues: 2039 helix: 1.78 (0.15), residues: 1321 sheet: -0.64 (0.69), residues: 61 loop : -1.41 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 269 TYR 0.021 0.001 TYR D 810 PHE 0.024 0.001 PHE A 374 TRP 0.033 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00424 (15975) covalent geometry : angle 0.58984 (21552) hydrogen bonds : bond 0.04000 ( 1018) hydrogen bonds : angle 3.80989 ( 2967) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 174 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6143 (OUTLIER) cc_final: 0.5767 (pt0) REVERT: D 893 LEU cc_start: 0.8993 (tp) cc_final: 0.8763 (tt) REVERT: D 894 GLU cc_start: 0.8208 (mp0) cc_final: 0.7991 (mp0) REVERT: D 1117 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6263 (tm-30) REVERT: A 474 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.8042 (tptt) REVERT: B 222 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7183 (pp) REVERT: B 258 TYR cc_start: 0.5926 (OUTLIER) cc_final: 0.5041 (t80) REVERT: B 407 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7385 (mm-30) REVERT: B 412 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7723 (tt) REVERT: B 450 GLU cc_start: 0.8291 (tp30) cc_final: 0.8027 (tp30) REVERT: C 303 MET cc_start: 0.8310 (ttm) cc_final: 0.8072 (ttt) outliers start: 74 outliers final: 39 residues processed: 223 average time/residue: 0.4040 time to fit residues: 102.9056 Evaluate side-chains 206 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 906 ILE Chi-restraints excluded: chain D residue 1012 ASP Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1117 GLN Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 503 TYR Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 106 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 140 optimal weight: 0.2980 chunk 147 optimal weight: 0.7980 chunk 187 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 201 optimal weight: 40.0000 chunk 18 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN B 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.137114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.102981 restraints weight = 27281.448| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.76 r_work: 0.3466 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15975 Z= 0.129 Angle : 0.563 9.703 21552 Z= 0.294 Chirality : 0.041 0.174 2275 Planarity : 0.003 0.055 2780 Dihedral : 4.611 56.222 2265 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.10 % Favored : 94.85 % Rotamer: Outliers : 4.41 % Allowed : 20.99 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.19), residues: 2039 helix: 1.89 (0.15), residues: 1317 sheet: 0.00 (0.73), residues: 51 loop : -1.42 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 269 TYR 0.020 0.001 TYR D 810 PHE 0.020 0.001 PHE A 421 TRP 0.037 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00296 (15975) covalent geometry : angle 0.56277 (21552) hydrogen bonds : bond 0.03701 ( 1018) hydrogen bonds : angle 3.71849 ( 2967) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 172 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6138 (OUTLIER) cc_final: 0.5758 (pt0) REVERT: D 893 LEU cc_start: 0.9002 (tp) cc_final: 0.8790 (tt) REVERT: D 1117 GLN cc_start: 0.7450 (OUTLIER) cc_final: 0.6194 (tm-30) REVERT: A 213 MET cc_start: 0.8331 (mmm) cc_final: 0.7709 (mmt) REVERT: B 222 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7157 (pp) REVERT: B 258 TYR cc_start: 0.5854 (OUTLIER) cc_final: 0.5016 (t80) REVERT: B 279 MET cc_start: 0.7814 (ptm) cc_final: 0.7078 (ptm) REVERT: B 407 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7409 (mm-30) REVERT: B 412 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7611 (tt) REVERT: B 450 GLU cc_start: 0.8254 (tp30) cc_final: 0.7971 (tp30) REVERT: B 499 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8484 (m) outliers start: 69 outliers final: 40 residues processed: 220 average time/residue: 0.4342 time to fit residues: 109.6513 Evaluate side-chains 203 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 811 LEU Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1117 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 445 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 263 TRP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 599 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 58 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 103 optimal weight: 0.0170 chunk 187 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 114 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.137865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103553 restraints weight = 27572.174| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.79 r_work: 0.3477 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 15975 Z= 0.124 Angle : 0.565 9.769 21552 Z= 0.295 Chirality : 0.041 0.177 2275 Planarity : 0.003 0.054 2780 Dihedral : 4.531 54.554 2265 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 3.90 % Allowed : 21.75 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.19), residues: 2039 helix: 1.92 (0.15), residues: 1318 sheet: -0.12 (0.75), residues: 48 loop : -1.37 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 269 TYR 0.020 0.001 TYR D 810 PHE 0.028 0.001 PHE A 374 TRP 0.044 0.002 TRP D 783 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00286 (15975) covalent geometry : angle 0.56474 (21552) hydrogen bonds : bond 0.03592 ( 1018) hydrogen bonds : angle 3.70859 ( 2967) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6099 (OUTLIER) cc_final: 0.5747 (pt0) REVERT: D 893 LEU cc_start: 0.8998 (tp) cc_final: 0.8784 (tt) REVERT: A 213 MET cc_start: 0.8304 (mmm) cc_final: 0.7716 (mmt) REVERT: A 474 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8085 (tptt) REVERT: A 548 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.7047 (pp) REVERT: B 222 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7138 (pp) REVERT: B 258 TYR cc_start: 0.5857 (OUTLIER) cc_final: 0.5076 (t80) REVERT: B 263 TRP cc_start: 0.7634 (t-100) cc_final: 0.7089 (t-100) REVERT: B 407 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7392 (mm-30) REVERT: B 412 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7631 (tt) REVERT: B 450 GLU cc_start: 0.8235 (tp30) cc_final: 0.7949 (tp30) REVERT: B 499 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8518 (m) REVERT: B 532 GLN cc_start: 0.6073 (mm-40) cc_final: 0.5751 (mm-40) outliers start: 61 outliers final: 35 residues processed: 217 average time/residue: 0.4821 time to fit residues: 119.5024 Evaluate side-chains 204 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 828 GLN Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 263 TRP Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 599 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 129 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 197 optimal weight: 30.0000 chunk 144 optimal weight: 30.0000 chunk 8 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN B 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.137607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.103505 restraints weight = 27538.706| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.77 r_work: 0.3474 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15975 Z= 0.131 Angle : 0.584 11.922 21552 Z= 0.302 Chirality : 0.041 0.195 2275 Planarity : 0.003 0.054 2780 Dihedral : 4.498 53.906 2265 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.10 % Favored : 94.85 % Rotamer: Outliers : 3.84 % Allowed : 21.94 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.19), residues: 2039 helix: 1.96 (0.15), residues: 1312 sheet: -0.04 (0.76), residues: 48 loop : -1.35 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 269 TYR 0.021 0.001 TYR D 810 PHE 0.020 0.001 PHE A 421 TRP 0.055 0.002 TRP D 783 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00305 (15975) covalent geometry : angle 0.58417 (21552) hydrogen bonds : bond 0.03587 ( 1018) hydrogen bonds : angle 3.70562 ( 2967) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 893 LEU cc_start: 0.9004 (tp) cc_final: 0.8801 (tt) REVERT: D 1117 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6103 (tm-30) REVERT: A 213 MET cc_start: 0.8309 (mmm) cc_final: 0.7717 (mmt) REVERT: A 474 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8059 (tptt) REVERT: A 548 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7096 (pp) REVERT: B 222 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7130 (pp) REVERT: B 258 TYR cc_start: 0.5880 (OUTLIER) cc_final: 0.5080 (t80) REVERT: B 263 TRP cc_start: 0.7644 (t-100) cc_final: 0.7072 (t-100) REVERT: B 407 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7400 (mm-30) REVERT: B 412 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7631 (tt) REVERT: B 450 GLU cc_start: 0.8217 (tp30) cc_final: 0.7906 (tp30) REVERT: B 499 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8515 (m) REVERT: B 532 GLN cc_start: 0.6188 (mm-40) cc_final: 0.5856 (mm-40) REVERT: C 303 MET cc_start: 0.8367 (ttm) cc_final: 0.8128 (ttt) outliers start: 60 outliers final: 36 residues processed: 212 average time/residue: 0.4093 time to fit residues: 99.5902 Evaluate side-chains 205 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1117 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 474 LYS Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 599 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 17 optimal weight: 8.9990 chunk 150 optimal weight: 0.5980 chunk 131 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.138215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.104138 restraints weight = 27342.899| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.77 r_work: 0.3484 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 15975 Z= 0.127 Angle : 0.599 12.025 21552 Z= 0.309 Chirality : 0.042 0.202 2275 Planarity : 0.003 0.054 2780 Dihedral : 4.458 53.254 2265 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.95 % Favored : 95.00 % Rotamer: Outliers : 3.26 % Allowed : 22.65 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.19), residues: 2039 helix: 1.95 (0.15), residues: 1315 sheet: 0.03 (0.76), residues: 48 loop : -1.29 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 269 TYR 0.042 0.001 TYR D 810 PHE 0.028 0.001 PHE A 374 TRP 0.063 0.002 TRP D 783 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00296 (15975) covalent geometry : angle 0.59911 (21552) hydrogen bonds : bond 0.03560 ( 1018) hydrogen bonds : angle 3.69091 ( 2967) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4078 Ramachandran restraints generated. 2039 Oldfield, 0 Emsley, 2039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 170 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 893 LEU cc_start: 0.9003 (tp) cc_final: 0.8800 (tt) REVERT: D 1117 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.5979 (tm-30) REVERT: A 213 MET cc_start: 0.8291 (mmm) cc_final: 0.7715 (mmt) REVERT: A 548 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7107 (pp) REVERT: B 222 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7114 (pp) REVERT: B 258 TYR cc_start: 0.5906 (OUTLIER) cc_final: 0.5115 (t80) REVERT: B 263 TRP cc_start: 0.7738 (t-100) cc_final: 0.7168 (t-100) REVERT: B 412 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7536 (tt) REVERT: B 450 GLU cc_start: 0.8221 (tp30) cc_final: 0.7847 (tp30) REVERT: B 499 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8512 (m) REVERT: B 532 GLN cc_start: 0.6214 (mm-40) cc_final: 0.5968 (mm-40) REVERT: C 303 MET cc_start: 0.8347 (ttm) cc_final: 0.8108 (ttt) outliers start: 51 outliers final: 34 residues processed: 207 average time/residue: 0.3713 time to fit residues: 87.5895 Evaluate side-chains 204 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1117 GLN Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 258 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 318 SER Chi-restraints excluded: chain B residue 412 ILE Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 428 MET Chi-restraints excluded: chain C residue 449 ARG Chi-restraints excluded: chain C residue 504 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 73 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 84 optimal weight: 0.1980 chunk 145 optimal weight: 10.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN B 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.137942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103774 restraints weight = 27300.846| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.76 r_work: 0.3480 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15975 Z= 0.134 Angle : 0.606 12.278 21552 Z= 0.313 Chirality : 0.042 0.199 2275 Planarity : 0.003 0.054 2780 Dihedral : 4.460 53.029 2265 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.95 % Rotamer: Outliers : 3.20 % Allowed : 22.71 % Favored : 74.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.19), residues: 2039 helix: 1.97 (0.15), residues: 1314 sheet: 0.08 (0.76), residues: 48 loop : -1.26 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 269 TYR 0.016 0.001 TYR B 292 PHE 0.020 0.001 PHE A 421 TRP 0.077 0.002 TRP D 783 HIS 0.005 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00313 (15975) covalent geometry : angle 0.60580 (21552) hydrogen bonds : bond 0.03598 ( 1018) hydrogen bonds : angle 3.69433 ( 2967) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4962.96 seconds wall clock time: 85 minutes 15.70 seconds (5115.70 seconds total)