Starting phenix.real_space_refine on Sat Jun 14 03:21:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bx7_16311/06_2025/8bx7_16311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bx7_16311/06_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_16311/06_2025/8bx7_16311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bx7_16311/06_2025/8bx7_16311.map" model { file = "/net/cci-nas-00/data/ceres_data/8bx7_16311/06_2025/8bx7_16311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bx7_16311/06_2025/8bx7_16311.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} 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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7} 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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} 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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 151 Time building chain proxies: 9.07, per 1000 atoms: 0.58 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: 3.71 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.69 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: 5.01 Time building geometry restraints manager: 4.44 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: 21.350 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 35.780 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 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:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.040 ------------------------------------------------------------------------------- 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 : 10.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (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 TRP 0.054 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.014 0.001 PHE A 421 TYR 0.017 0.001 TYR D 810 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.12247 ( 1018) hydrogen bonds : angle 5.03167 ( 2967) covalent geometry : bond 0.00306 (15975) covalent geometry : angle 0.65949 (21552) *********************** 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 : 1.725 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: 1.2180 time to fit residues: 279.0343 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 : 2.352 ------------------------------------------------------------------------------- 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 172 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 0.0040 chunk 119 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 442 ASN B 224 GLN B 284 GLN B 417 GLN B 494 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.139872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.105529 restraints weight = 27533.071| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.80 r_work: 0.3512 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15975 Z= 0.126 Angle : 0.550 8.201 21552 Z= 0.294 Chirality : 0.041 0.147 2275 Planarity : 0.004 0.055 2780 Dihedral : 5.181 55.228 2278 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.30 % Favored : 94.65 % Rotamer: Outliers : 3.58 % Allowed : 17.47 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.20), residues: 2039 helix: 1.73 (0.15), residues: 1323 sheet: -0.98 (0.68), residues: 63 loop : -1.55 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.017 0.001 PHE A 421 TYR 0.014 0.001 TYR D 810 ARG 0.007 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 1018) hydrogen bonds : angle 3.99930 ( 2967) covalent geometry : bond 0.00281 (15975) covalent geometry : angle 0.54991 (21552) *********************** 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 236 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 180 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6119 (OUTLIER) cc_final: 0.5696 (pt0) REVERT: D 1049 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: B 258 TYR cc_start: 0.5570 (OUTLIER) cc_final: 0.4838 (t80) REVERT: B 279 MET cc_start: 0.7639 (ppp) cc_final: 0.7353 (ptm) REVERT: B 407 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7454 (mm-30) REVERT: B 415 ILE cc_start: 0.8055 (tp) cc_final: 0.7805 (tp) outliers start: 56 outliers final: 20 residues processed: 219 average time/residue: 1.0279 time to fit residues: 255.2920 Evaluate side-chains 183 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 1.775 ------------------------------------------------------------------------------- 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 1027 VAL 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 273 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 439 LEU 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 301 LEU Chi-restraints excluded: chain B residue 318 SER 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 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 571 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 156 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 171 optimal weight: 0.0770 chunk 147 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1167 ASN B 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.138772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.104893 restraints weight = 27344.211| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.77 r_work: 0.3502 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15975 Z= 0.126 Angle : 0.535 9.384 21552 Z= 0.285 Chirality : 0.041 0.158 2275 Planarity : 0.004 0.054 2780 Dihedral : 4.841 57.189 2270 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.95 % Favored : 95.00 % Rotamer: Outliers : 3.90 % Allowed : 17.85 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.20), residues: 2039 helix: 1.86 (0.15), residues: 1323 sheet: -0.69 (0.69), residues: 61 loop : -1.47 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.018 0.001 PHE A 421 TYR 0.036 0.001 TYR C 503 ARG 0.005 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03732 ( 1018) hydrogen bonds : angle 3.79951 ( 2967) covalent geometry : bond 0.00285 (15975) covalent geometry : angle 0.53499 (21552) *********************** 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 240 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 179 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6084 (OUTLIER) cc_final: 0.5688 (pt0) REVERT: D 1049 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: A 548 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7190 (pp) REVERT: B 222 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7111 (pp) REVERT: B 258 TYR cc_start: 0.5679 (OUTLIER) cc_final: 0.4935 (t80) REVERT: B 407 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7383 (mm-30) REVERT: B 415 ILE cc_start: 0.8054 (tp) cc_final: 0.7777 (tp) REVERT: C 297 ARG cc_start: 0.8076 (ttt180) cc_final: 0.7754 (ptt180) outliers start: 61 outliers final: 27 residues processed: 220 average time/residue: 1.2116 time to fit residues: 305.3878 Evaluate side-chains 193 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 2.004 ------------------------------------------------------------------------------- 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 219 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 497 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain B residue 171 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 530 ILE Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 331 VAL 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 571 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 110 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 198 optimal weight: 30.0000 chunk 133 optimal weight: 0.4980 chunk 148 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 GLN B 284 GLN B 494 GLN C 191 GLN C 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.138945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.104925 restraints weight = 27402.272| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.78 r_work: 0.3496 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 15975 Z= 0.119 Angle : 0.524 9.800 21552 Z= 0.277 Chirality : 0.040 0.153 2275 Planarity : 0.003 0.054 2780 Dihedral : 4.752 58.553 2268 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.90 % Rotamer: Outliers : 4.03 % Allowed : 17.85 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 2039 helix: 1.93 (0.15), residues: 1324 sheet: -0.09 (0.72), residues: 51 loop : -1.43 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.018 0.001 PHE A 421 TYR 0.024 0.001 TYR D 810 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 1018) hydrogen bonds : angle 3.71260 ( 2967) covalent geometry : bond 0.00273 (15975) covalent geometry : angle 0.52411 (21552) *********************** 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 240 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 177 time to evaluate : 3.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6029 (OUTLIER) cc_final: 0.5641 (pt0) REVERT: A 548 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7167 (pp) REVERT: B 222 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7176 (pp) REVERT: B 258 TYR cc_start: 0.5689 (OUTLIER) cc_final: 0.4937 (t80) REVERT: B 407 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7319 (mm-30) REVERT: B 415 ILE cc_start: 0.8147 (tp) cc_final: 0.7878 (tp) REVERT: C 503 TYR cc_start: 0.8790 (m-80) cc_final: 0.8566 (m-80) outliers start: 63 outliers final: 30 residues processed: 221 average time/residue: 1.2774 time to fit residues: 326.4712 Evaluate side-chains 196 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 3.337 ------------------------------------------------------------------------------- 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 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 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 548 LEU Chi-restraints excluded: chain B residue 171 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 530 ILE Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR 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 571 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 93 optimal weight: 20.0000 chunk 185 optimal weight: 0.3980 chunk 139 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.135335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.100886 restraints weight = 28034.351| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.78 r_work: 0.3427 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.119 15975 Z= 0.212 Angle : 0.599 9.181 21552 Z= 0.317 Chirality : 0.044 0.197 2275 Planarity : 0.004 0.054 2780 Dihedral : 4.948 59.965 2268 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.31 % Rotamer: Outliers : 4.35 % Allowed : 18.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.19), residues: 2039 helix: 1.80 (0.15), residues: 1317 sheet: -0.48 (0.69), residues: 56 loop : -1.45 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 773 HIS 0.004 0.001 HIS A 468 PHE 0.020 0.002 PHE A 421 TYR 0.021 0.001 TYR D 810 ARG 0.006 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 1018) hydrogen bonds : angle 3.84823 ( 2967) covalent geometry : bond 0.00508 (15975) covalent geometry : angle 0.59945 (21552) *********************** 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 244 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 176 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6123 (OUTLIER) cc_final: 0.5740 (pt0) REVERT: D 893 LEU cc_start: 0.8962 (tp) cc_final: 0.8717 (tt) REVERT: D 894 GLU cc_start: 0.8273 (mp0) cc_final: 0.7924 (mp0) REVERT: D 907 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7734 (ttm-80) REVERT: B 222 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7225 (pp) REVERT: B 258 TYR cc_start: 0.5905 (OUTLIER) cc_final: 0.5033 (t80) REVERT: B 407 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7390 (mm-30) REVERT: B 415 ILE cc_start: 0.8173 (tp) cc_final: 0.7954 (tp) REVERT: B 450 GLU cc_start: 0.8407 (tp30) cc_final: 0.8151 (tp30) REVERT: C 297 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7752 (ptm160) outliers start: 68 outliers final: 34 residues processed: 220 average time/residue: 1.0110 time to fit residues: 252.3682 Evaluate side-chains 200 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.903 ------------------------------------------------------------------------------- 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 906 ILE Chi-restraints excluded: chain D residue 907 ARG Chi-restraints excluded: chain D residue 980 PHE 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 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 577 ASP 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 297 ARG 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 512 ARG Chi-restraints excluded: chain C residue 531 THR 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 139 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 30 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 78 optimal weight: 0.0060 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.4088 r_free = 0.4088 target = 0.137968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.103684 restraints weight = 27648.924| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.78 r_work: 0.3478 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15975 Z= 0.118 Angle : 0.542 9.092 21552 Z= 0.285 Chirality : 0.041 0.183 2275 Planarity : 0.003 0.054 2780 Dihedral : 4.779 58.847 2268 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.90 % Rotamer: Outliers : 3.45 % Allowed : 21.24 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.19), residues: 2039 helix: 1.93 (0.15), residues: 1318 sheet: -0.01 (0.75), residues: 46 loop : -1.39 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.018 0.001 PHE A 421 TYR 0.020 0.001 TYR D 810 ARG 0.004 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 1018) hydrogen bonds : angle 3.68363 ( 2967) covalent geometry : bond 0.00267 (15975) covalent geometry : angle 0.54222 (21552) *********************** 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 228 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 174 time to evaluate : 1.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6085 (OUTLIER) cc_final: 0.5707 (pt0) REVERT: D 893 LEU cc_start: 0.8977 (tp) cc_final: 0.8757 (tt) REVERT: B 222 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7165 (pp) REVERT: B 258 TYR cc_start: 0.5778 (OUTLIER) cc_final: 0.5009 (t80) REVERT: B 407 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7407 (mm-30) REVERT: B 415 ILE cc_start: 0.8111 (tp) cc_final: 0.7876 (tp) REVERT: B 450 GLU cc_start: 0.8296 (tp30) cc_final: 0.8039 (tp30) REVERT: C 297 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7861 (ptm160) REVERT: C 303 MET cc_start: 0.8325 (ttm) cc_final: 0.8096 (ttt) outliers start: 54 outliers final: 29 residues processed: 205 average time/residue: 0.9993 time to fit residues: 232.4778 Evaluate side-chains 195 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 1.933 ------------------------------------------------------------------------------- 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 1012 ASP Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 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 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 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 530 ILE Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 297 ARG 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 571 LEU Chi-restraints excluded: chain C residue 599 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 194 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 161 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 192 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 GLN C 294 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.135713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.101254 restraints weight = 27996.069| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.79 r_work: 0.3437 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15975 Z= 0.191 Angle : 0.588 9.771 21552 Z= 0.309 Chirality : 0.043 0.173 2275 Planarity : 0.004 0.054 2780 Dihedral : 4.805 57.358 2267 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.59 % Favored : 94.36 % Rotamer: Outliers : 4.48 % Allowed : 20.60 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 2039 helix: 1.88 (0.15), residues: 1314 sheet: -0.08 (0.70), residues: 51 loop : -1.39 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.021 0.002 PHE A 374 TYR 0.018 0.001 TYR D 810 ARG 0.006 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 1018) hydrogen bonds : angle 3.77744 ( 2967) covalent geometry : bond 0.00454 (15975) covalent geometry : angle 0.58797 (21552) *********************** 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: 70 poor density : 171 time to evaluate : 1.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6140 (OUTLIER) cc_final: 0.5776 (pt0) REVERT: D 893 LEU cc_start: 0.8991 (tp) cc_final: 0.8770 (tt) REVERT: D 894 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7894 (mp0) REVERT: D 1117 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6246 (tm-30) REVERT: D 1144 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8213 (pt0) REVERT: B 222 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7239 (pp) REVERT: B 258 TYR cc_start: 0.5946 (OUTLIER) cc_final: 0.5096 (t80) REVERT: B 263 TRP cc_start: 0.7680 (t-100) cc_final: 0.7376 (t-100) REVERT: B 279 MET cc_start: 0.7899 (ptm) cc_final: 0.7105 (ptm) REVERT: B 407 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7402 (mm-30) REVERT: B 415 ILE cc_start: 0.8173 (tp) cc_final: 0.7950 (tp) REVERT: B 450 GLU cc_start: 0.8290 (tp30) cc_final: 0.8026 (tp30) REVERT: B 532 GLN cc_start: 0.6078 (mm-40) cc_final: 0.5796 (mm-40) REVERT: C 297 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7841 (ptm160) REVERT: C 303 MET cc_start: 0.8328 (ttm) cc_final: 0.8091 (ttt) outliers start: 70 outliers final: 34 residues processed: 217 average time/residue: 0.9523 time to fit residues: 234.7309 Evaluate side-chains 202 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 779 LEU Chi-restraints excluded: chain D residue 817 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 D residue 1144 GLU 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 577 ASP Chi-restraints excluded: chain B residue 599 GLN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 297 ARG 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 512 ARG Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 149 optimal weight: 0.9990 chunk 197 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 202 optimal weight: 50.0000 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 30.0000 chunk 194 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 891 ASN A 599 GLN B 284 GLN B 494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.135083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.100667 restraints weight = 27814.053| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.76 r_work: 0.3433 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 15975 Z= 0.205 Angle : 0.617 9.521 21552 Z= 0.325 Chirality : 0.044 0.176 2275 Planarity : 0.004 0.054 2780 Dihedral : 4.877 55.349 2267 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.31 % Rotamer: Outliers : 4.41 % Allowed : 21.05 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.19), residues: 2039 helix: 1.78 (0.15), residues: 1315 sheet: -0.74 (0.67), residues: 61 loop : -1.39 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 773 HIS 0.004 0.001 HIS A 310 PHE 0.020 0.002 PHE A 421 TYR 0.019 0.001 TYR D 810 ARG 0.006 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.04141 ( 1018) hydrogen bonds : angle 3.85692 ( 2967) covalent geometry : bond 0.00490 (15975) covalent geometry : angle 0.61723 (21552) *********************** 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 241 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 172 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6227 (OUTLIER) cc_final: 0.5852 (pt0) REVERT: D 893 LEU cc_start: 0.9019 (tp) cc_final: 0.8802 (tt) REVERT: D 894 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7975 (mp0) REVERT: D 1117 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6176 (tm-30) REVERT: D 1144 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8218 (pt0) REVERT: A 428 MET cc_start: 0.7736 (tpp) cc_final: 0.7478 (tpp) REVERT: B 222 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7184 (pp) REVERT: B 258 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.5064 (t80) REVERT: B 263 TRP cc_start: 0.7715 (t-100) cc_final: 0.7434 (t-100) REVERT: B 407 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7415 (mm-30) REVERT: B 412 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7719 (tt) REVERT: B 450 GLU cc_start: 0.8279 (tp30) cc_final: 0.7950 (tp30) REVERT: B 532 GLN cc_start: 0.6223 (mm-40) cc_final: 0.5942 (mm-40) REVERT: C 297 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7842 (ptm160) REVERT: C 303 MET cc_start: 0.8302 (ttm) cc_final: 0.8067 (ttt) outliers start: 69 outliers final: 36 residues processed: 220 average time/residue: 1.0091 time to fit residues: 255.9295 Evaluate side-chains 208 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 906 ILE Chi-restraints excluded: chain D residue 980 PHE Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1117 GLN Chi-restraints excluded: chain D residue 1144 GLU 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 412 ILE Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 577 ASP 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 297 ARG 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 512 ARG Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 571 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 158 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4049 r_free = 0.4049 target = 0.135178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.100317 restraints weight = 27551.183| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.78 r_work: 0.3437 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15975 Z= 0.173 Angle : 0.607 9.874 21552 Z= 0.318 Chirality : 0.043 0.186 2275 Planarity : 0.004 0.055 2780 Dihedral : 4.841 54.919 2267 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.31 % Rotamer: Outliers : 3.65 % Allowed : 21.94 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 2039 helix: 1.78 (0.15), residues: 1320 sheet: -0.77 (0.67), residues: 61 loop : -1.29 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 773 HIS 0.005 0.001 HIS A 310 PHE 0.030 0.001 PHE A 374 TYR 0.020 0.001 TYR D 810 ARG 0.006 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 1018) hydrogen bonds : angle 3.83823 ( 2967) covalent geometry : bond 0.00413 (15975) covalent geometry : angle 0.60733 (21552) *********************** 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 229 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 172 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6208 (OUTLIER) cc_final: 0.5855 (pt0) REVERT: D 1087 ASP cc_start: 0.7648 (t0) cc_final: 0.7420 (t0) REVERT: D 1144 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8210 (pt0) REVERT: A 548 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7156 (pp) REVERT: B 222 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7215 (pp) REVERT: B 258 TYR cc_start: 0.5985 (OUTLIER) cc_final: 0.5053 (t80) REVERT: B 407 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7408 (mm-30) REVERT: B 450 GLU cc_start: 0.8234 (tp30) cc_final: 0.7900 (tp30) REVERT: B 532 GLN cc_start: 0.6248 (mm-40) cc_final: 0.5983 (mm-40) REVERT: C 297 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7827 (ptm160) REVERT: C 303 MET cc_start: 0.8337 (ttm) cc_final: 0.8104 (ttt) outliers start: 57 outliers final: 38 residues processed: 208 average time/residue: 0.9649 time to fit residues: 228.1593 Evaluate side-chains 203 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 906 ILE Chi-restraints excluded: chain D residue 980 PHE Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1141 VAL Chi-restraints excluded: chain D residue 1144 GLU 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 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 548 LEU Chi-restraints excluded: chain A residue 571 LEU 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 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 297 ARG 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 571 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 133 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 191 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 138 optimal weight: 0.0470 chunk 83 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.4079 r_free = 0.4079 target = 0.137271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.102892 restraints weight = 27827.611| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.79 r_work: 0.3473 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 15975 Z= 0.128 Angle : 0.600 10.168 21552 Z= 0.310 Chirality : 0.042 0.190 2275 Planarity : 0.004 0.055 2780 Dihedral : 4.742 54.220 2267 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.10 % Favored : 94.85 % Rotamer: Outliers : 3.01 % Allowed : 22.58 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.20), residues: 2039 helix: 1.94 (0.15), residues: 1309 sheet: -0.66 (0.68), residues: 61 loop : -1.22 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP D 783 HIS 0.005 0.001 HIS A 310 PHE 0.019 0.001 PHE A 421 TYR 0.020 0.001 TYR D 810 ARG 0.005 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 1018) hydrogen bonds : angle 3.76409 ( 2967) covalent geometry : bond 0.00295 (15975) covalent geometry : angle 0.59957 (21552) ********************** 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 216 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 828 GLN cc_start: 0.6112 (OUTLIER) cc_final: 0.5757 (pt0) REVERT: D 1087 ASP cc_start: 0.7660 (t0) cc_final: 0.7450 (t0) REVERT: D 1117 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6218 (tm-30) REVERT: B 222 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7121 (pp) REVERT: B 258 TYR cc_start: 0.5787 (OUTLIER) cc_final: 0.4941 (t80) REVERT: B 412 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7571 (tt) REVERT: B 450 GLU cc_start: 0.8193 (tp30) cc_final: 0.7862 (tp30) REVERT: B 532 GLN cc_start: 0.6258 (mm-40) cc_final: 0.5968 (mm-40) REVERT: C 297 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7759 (ptm160) REVERT: C 303 MET cc_start: 0.8332 (ttm) cc_final: 0.8104 (ttt) outliers start: 47 outliers final: 32 residues processed: 201 average time/residue: 0.9741 time to fit residues: 223.2406 Evaluate side-chains 202 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 980 PHE 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 154 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 254 THR 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 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 412 ILE Chi-restraints excluded: chain B residue 530 ILE 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 297 ARG 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 571 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 174 optimal weight: 0.7980 chunk 93 optimal weight: 20.0000 chunk 80 optimal weight: 0.8980 chunk 157 optimal weight: 0.2980 chunk 132 optimal weight: 0.0970 chunk 141 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 198 optimal weight: 40.0000 chunk 158 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.138413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.104338 restraints weight = 27496.985| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.78 r_work: 0.3489 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 0.069 15975 Z= 0.121 Angle : 0.588 10.439 21552 Z= 0.303 Chirality : 0.041 0.204 2275 Planarity : 0.003 0.055 2780 Dihedral : 4.586 52.994 2267 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 2.82 % Allowed : 22.78 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.20), residues: 2039 helix: 1.98 (0.15), residues: 1312 sheet: -0.76 (0.70), residues: 58 loop : -1.19 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP D 783 HIS 0.005 0.001 HIS A 310 PHE 0.034 0.001 PHE A 374 TYR 0.020 0.001 TYR D 810 ARG 0.005 0.000 ARG A 269 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 1018) hydrogen bonds : angle 3.69443 ( 2967) covalent geometry : bond 0.00277 (15975) covalent geometry : angle 0.58817 (21552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11362.00 seconds wall clock time: 198 minutes 22.37 seconds (11902.37 seconds total)