Starting phenix.real_space_refine on Sat Aug 23 22:25:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r7l_18979/08_2025/8r7l_18979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r7l_18979/08_2025/8r7l_18979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r7l_18979/08_2025/8r7l_18979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r7l_18979/08_2025/8r7l_18979.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r7l_18979/08_2025/8r7l_18979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r7l_18979/08_2025/8r7l_18979.map" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.020 sd= 0.087 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 94 5.16 5 C 9575 2.51 5 N 2555 2.21 5 O 2737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14961 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 2974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2974 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 14, 'TRANS': 352} Chain breaks: 2 Chain: "A" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2730 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 321} Chain breaks: 10 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 48 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 6666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 850, 6666 Classifications: {'peptide': 850} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 30, 'TRANS': 819} Chain breaks: 18 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 310 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 6, 'PHE:plan': 1, 'GLU:plan': 9, 'HIS:plan': 3, 'TYR:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 146 Chain: "C" Number of atoms: 2433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2433 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 295} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 158 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Time building chain proxies: 3.33, per 1000 atoms: 0.22 Number of scatterers: 14961 At special positions: 0 Unit cell: (145.08, 146.32, 156.24, 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 94 16.00 O 2737 8.00 N 2555 7.00 C 9575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 677.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3608 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 9 sheets defined 60.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'H' and resid 53 through 64 removed outlier: 3.517A pdb=" N VAL H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP H 62 " --> pdb=" O ARG H 58 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY H 64 " --> pdb=" O ILE H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 80 Proline residue: H 77 - end of helix Processing helix chain 'H' and resid 95 through 107 removed outlier: 4.212A pdb=" N PHE H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 137 removed outlier: 3.633A pdb=" N SER H 137 " --> pdb=" O TYR H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 163 removed outlier: 3.892A pdb=" N ASP H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU H 159 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 181 Processing helix chain 'H' and resid 197 through 204 removed outlier: 3.519A pdb=" N GLU H 203 " --> pdb=" O ASP H 199 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN H 204 " --> pdb=" O LYS H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 218 removed outlier: 3.666A pdb=" N ASP H 210 " --> pdb=" O ASP H 206 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL H 211 " --> pdb=" O MET H 207 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET H 217 " --> pdb=" O GLU H 213 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR H 218 " --> pdb=" O ILE H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 240 removed outlier: 3.597A pdb=" N CYS H 239 " --> pdb=" O ILE H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 243 No H-bonds generated for 'chain 'H' and resid 241 through 243' Processing helix chain 'H' and resid 273 through 285 Processing helix chain 'H' and resid 296 through 310 Processing helix chain 'H' and resid 322 through 335 Processing helix chain 'H' and resid 367 through 376 Processing helix chain 'H' and resid 393 through 408 removed outlier: 3.752A pdb=" N ALA H 397 " --> pdb=" O ASP H 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 65 Processing helix chain 'A' and resid 72 through 84 Processing helix chain 'A' and resid 92 through 104 Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.783A pdb=" N VAL A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 147 Processing helix chain 'A' and resid 152 through 167 removed outlier: 3.901A pdb=" N PHE A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 247 removed outlier: 3.555A pdb=" N ASN A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 251 removed outlier: 3.679A pdb=" N CYS A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 254 through 275 removed outlier: 4.453A pdb=" N LYS A 275 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.565A pdb=" N ASP A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 334 removed outlier: 3.762A pdb=" N ARG A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 366 Processing helix chain 'A' and resid 370 through 389 removed outlier: 3.927A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 443 removed outlier: 3.954A pdb=" N ARG A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 503 removed outlier: 4.205A pdb=" N ARG A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ARG A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.661A pdb=" N LYS A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 156 Processing helix chain 'B' and resid 168 through 180 removed outlier: 3.714A pdb=" N TYR B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 206 through 221 Processing helix chain 'B' and resid 225 through 237 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.946A pdb=" N TYR B 267 " --> pdb=" O PRO B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 287 removed outlier: 4.208A pdb=" N LEU B 284 " --> pdb=" O ASP B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 308 removed outlier: 4.007A pdb=" N MET B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.626A pdb=" N ALA B 351 " --> pdb=" O GLY B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 376 through 399 Proline residue: B 393 - end of helix Processing helix chain 'B' and resid 425 through 437 removed outlier: 3.649A pdb=" N CYS B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR B 437 " --> pdb=" O ASN B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 444 removed outlier: 3.770A pdb=" N HIS B 444 " --> pdb=" O HIS B 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 444' Processing helix chain 'B' and resid 445 through 464 removed outlier: 3.954A pdb=" N PHE B 449 " --> pdb=" O ASP B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 490 Processing helix chain 'B' and resid 490 through 496 removed outlier: 3.756A pdb=" N SER B 496 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 removed outlier: 4.636A pdb=" N TRP B 509 " --> pdb=" O SER B 505 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B 511 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 513 " --> pdb=" O TRP B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 530 Processing helix chain 'B' and resid 535 through 554 removed outlier: 3.896A pdb=" N LYS B 554 " --> pdb=" O LYS B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 575 Processing helix chain 'B' and resid 575 through 591 removed outlier: 3.574A pdb=" N LEU B 579 " --> pdb=" O ASN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 593 through 601 Processing helix chain 'B' and resid 605 through 622 Processing helix chain 'B' and resid 636 through 653 removed outlier: 3.571A pdb=" N TYR B 653 " --> pdb=" O VAL B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 671 removed outlier: 4.040A pdb=" N GLN B 662 " --> pdb=" O ALA B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 686 removed outlier: 3.587A pdb=" N LEU B 679 " --> pdb=" O ASP B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 702 Processing helix chain 'B' and resid 708 through 713 Processing helix chain 'B' and resid 722 through 737 removed outlier: 3.705A pdb=" N SER B 726 " --> pdb=" O THR B 722 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 728 " --> pdb=" O LYS B 724 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N HIS B 736 " --> pdb=" O ALA B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 756 removed outlier: 3.544A pdb=" N GLN B 748 " --> pdb=" O LEU B 744 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN B 751 " --> pdb=" O ALA B 747 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 754 " --> pdb=" O ARG B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 788 removed outlier: 3.809A pdb=" N LYS B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 797 removed outlier: 3.614A pdb=" N LYS B 795 " --> pdb=" O GLU B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 807 removed outlier: 3.504A pdb=" N CYS B 804 " --> pdb=" O ILE B 800 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN B 805 " --> pdb=" O ASP B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 823 Proline residue: B 820 - end of helix Processing helix chain 'B' and resid 861 through 869 Processing helix chain 'B' and resid 878 through 887 removed outlier: 3.863A pdb=" N LEU B 887 " --> pdb=" O THR B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 908 Processing helix chain 'B' and resid 929 through 961 removed outlier: 3.798A pdb=" N ARG B 955 " --> pdb=" O ARG B 951 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS B 957 " --> pdb=" O LEU B 953 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU B 959 " --> pdb=" O ARG B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 989 removed outlier: 3.684A pdb=" N LYS B 976 " --> pdb=" O GLU B 972 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE B 977 " --> pdb=" O THR B 973 " (cutoff:3.500A) Proline residue: B 984 - end of helix removed outlier: 4.013A pdb=" N SER B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1006 removed outlier: 3.729A pdb=" N VAL B1000 " --> pdb=" O CYS B 996 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B1006 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1023 removed outlier: 3.507A pdb=" N ASP B1023 " --> pdb=" O ARG B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1030 removed outlier: 4.020A pdb=" N THR B1027 " --> pdb=" O ASP B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1034 through 1055 removed outlier: 3.577A pdb=" N PHE B1042 " --> pdb=" O ARG B1038 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP B1053 " --> pdb=" O THR B1049 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER B1055 " --> pdb=" O THR B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1113 Processing helix chain 'B' and resid 1117 through 1130 Processing helix chain 'B' and resid 1138 through 1154 removed outlier: 3.727A pdb=" N GLU B1154 " --> pdb=" O LYS B1150 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1176 Processing helix chain 'C' and resid 32 through 45 removed outlier: 3.683A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 8 through 21 removed outlier: 3.555A pdb=" N ARG D 20 " --> pdb=" O ASN D 16 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY D 21 " --> pdb=" O ARG D 17 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 145 through 148 removed outlier: 6.475A pdb=" N VAL H 116 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLY H 171 " --> pdb=" O VAL H 116 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL H 118 " --> pdb=" O GLY H 171 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU H 117 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ASP H 196 " --> pdb=" O LEU H 117 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N MET H 119 " --> pdb=" O ASP H 196 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE H 193 " --> pdb=" O MET H 225 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N PHE H 227 " --> pdb=" O PHE H 193 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU H 195 " --> pdb=" O PHE H 227 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER H 228 " --> pdb=" O CYS H 87 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU H 86 " --> pdb=" O ILE H 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 314 through 317 removed outlier: 6.999A pdb=" N VAL H 290 " --> pdb=" O LEU H 341 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ALA H 343 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ILE H 292 " --> pdb=" O ALA H 343 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLN H 289 " --> pdb=" O ASN H 357 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA H 359 " --> pdb=" O GLN H 289 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 291 " --> pdb=" O ALA H 359 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASN H 361 " --> pdb=" O VAL H 291 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N PHE H 293 " --> pdb=" O ASN H 361 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLN H 263 " --> pdb=" O ALA H 387 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR H 389 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR H 265 " --> pdb=" O THR H 389 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL H 391 " --> pdb=" O TYR H 265 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL H 267 " --> pdb=" O VAL H 391 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N SER H 412 " --> pdb=" O LEU H 262 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLN H 264 " --> pdb=" O SER H 412 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 54 removed outlier: 3.875A pdb=" N ALA C 53 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLY C 340 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA C 323 " --> pdb=" O ALA C 314 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 314 " --> pdb=" O ALA C 323 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 4.394A pdb=" N THR C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ALA C 79 " --> pdb=" O ASN C 94 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASN C 94 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL C 81 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 107 removed outlier: 3.588A pdb=" N GLN C 104 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA C 136 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASP C 128 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N CYS C 134 " --> pdb=" O ASP C 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 144 through 149 removed outlier: 6.827A pdb=" N GLY C 159 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE C 147 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ALA C 157 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N TRP C 149 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR C 155 " --> pdb=" O TRP C 149 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL C 164 " --> pdb=" O ASN C 160 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASP C 169 " --> pdb=" O SER C 175 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N SER C 175 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 185 through 190 removed outlier: 4.245A pdb=" N GLU C 187 " --> pdb=" O THR C 200 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS C 205 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N SER C 210 " --> pdb=" O PRO C 216 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 227 through 232 removed outlier: 3.895A pdb=" N CYS C 229 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG C 260 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASP C 252 " --> pdb=" O CYS C 258 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N CYS C 258 " --> pdb=" O ASP C 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 269 through 274 removed outlier: 6.955A pdb=" N ALA C 284 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU C 272 " --> pdb=" O ALA C 282 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA C 282 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N PHE C 274 " --> pdb=" O MET C 280 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N MET C 280 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER C 285 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N PHE C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) 800 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3607 1.33 - 1.46: 3606 1.46 - 1.58: 7892 1.58 - 1.71: 3 1.71 - 1.83: 139 Bond restraints: 15247 Sorted by residual: bond pdb=" C LEU B 289 " pdb=" N PRO B 290 " ideal model delta sigma weight residual 1.336 1.429 -0.093 1.08e-02 8.57e+03 7.40e+01 bond pdb=" C LEU C 347 " pdb=" N PRO C 348 " ideal model delta sigma weight residual 1.335 1.417 -0.082 1.38e-02 5.25e+03 3.54e+01 bond pdb=" C TYR C 211 " pdb=" N PRO C 212 " ideal model delta sigma weight residual 1.335 1.383 -0.048 1.19e-02 7.06e+03 1.65e+01 bond pdb=" C GLY H 171 " pdb=" N THR H 172 " ideal model delta sigma weight residual 1.333 1.430 -0.097 2.74e-02 1.33e+03 1.26e+01 bond pdb=" C SER A 504 " pdb=" N PRO A 505 " ideal model delta sigma weight residual 1.336 1.369 -0.034 1.08e-02 8.57e+03 9.74e+00 ... (remaining 15242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.20: 20203 5.20 - 10.40: 327 10.40 - 15.61: 43 15.61 - 20.81: 5 20.81 - 26.01: 3 Bond angle restraints: 20581 Sorted by residual: angle pdb=" C GLY H 171 " pdb=" N THR H 172 " pdb=" CA THR H 172 " ideal model delta sigma weight residual 122.15 148.16 -26.01 3.47e+00 8.31e-02 5.62e+01 angle pdb=" CA LEU B 556 " pdb=" CB LEU B 556 " pdb=" CG LEU B 556 " ideal model delta sigma weight residual 116.30 138.71 -22.41 3.50e+00 8.16e-02 4.10e+01 angle pdb=" CA LEU H 195 " pdb=" CB LEU H 195 " pdb=" CG LEU H 195 " ideal model delta sigma weight residual 116.30 138.29 -21.99 3.50e+00 8.16e-02 3.95e+01 angle pdb=" C LEU B 556 " pdb=" N THR B 557 " pdb=" CA THR B 557 " ideal model delta sigma weight residual 121.54 133.52 -11.98 1.91e+00 2.74e-01 3.93e+01 angle pdb=" CB GLN B 160 " pdb=" CG GLN B 160 " pdb=" CD GLN B 160 " ideal model delta sigma weight residual 112.60 123.25 -10.65 1.70e+00 3.46e-01 3.92e+01 ... (remaining 20576 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.35: 8482 18.35 - 36.69: 618 36.69 - 55.04: 91 55.04 - 73.38: 15 73.38 - 91.73: 10 Dihedral angle restraints: 9216 sinusoidal: 3706 harmonic: 5510 Sorted by residual: dihedral pdb=" CA LYS B 562 " pdb=" C LYS B 562 " pdb=" N PRO B 563 " pdb=" CA PRO B 563 " ideal model delta harmonic sigma weight residual 180.00 130.80 49.20 0 5.00e+00 4.00e-02 9.68e+01 dihedral pdb=" CA GLU B1116 " pdb=" C GLU B1116 " pdb=" N TYR B1117 " pdb=" CA TYR B1117 " ideal model delta harmonic sigma weight residual -180.00 -138.80 -41.20 0 5.00e+00 4.00e-02 6.79e+01 dihedral pdb=" CA LEU B 164 " pdb=" C LEU B 164 " pdb=" N LEU B 165 " pdb=" CA LEU B 165 " ideal model delta harmonic sigma weight residual 180.00 138.88 41.12 0 5.00e+00 4.00e-02 6.76e+01 ... (remaining 9213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 2233 0.173 - 0.346: 80 0.346 - 0.519: 5 0.519 - 0.691: 2 0.691 - 0.864: 2 Chirality restraints: 2322 Sorted by residual: chirality pdb=" CB ILE H 292 " pdb=" CA ILE H 292 " pdb=" CG1 ILE H 292 " pdb=" CG2 ILE H 292 " both_signs ideal model delta sigma weight residual False 2.64 1.78 0.86 2.00e-01 2.50e+01 1.87e+01 chirality pdb=" CB THR B 557 " pdb=" CA THR B 557 " pdb=" OG1 THR B 557 " pdb=" CG2 THR B 557 " both_signs ideal model delta sigma weight residual False 2.55 1.78 0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" CG LEU C 301 " pdb=" CB LEU C 301 " pdb=" CD1 LEU C 301 " pdb=" CD2 LEU C 301 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.67e+00 ... (remaining 2319 not shown) Planarity restraints: 2619 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 149 " 0.037 2.00e-02 2.50e+03 3.22e-02 2.59e+01 pdb=" CG TRP C 149 " -0.087 2.00e-02 2.50e+03 pdb=" CD1 TRP C 149 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP C 149 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 149 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 149 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP C 149 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 149 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 149 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 149 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 509 " -0.036 2.00e-02 2.50e+03 2.87e-02 2.06e+01 pdb=" CG TRP B 509 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP B 509 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 509 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 509 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 509 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 509 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 509 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 509 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 509 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 107 " -0.014 2.00e-02 2.50e+03 2.78e-02 1.94e+01 pdb=" CG TRP C 107 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TRP C 107 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP C 107 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 107 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 107 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 107 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 107 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 107 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C 107 " -0.005 2.00e-02 2.50e+03 ... (remaining 2616 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2979 2.79 - 3.32: 13804 3.32 - 3.85: 24454 3.85 - 4.37: 28012 4.37 - 4.90: 47376 Nonbonded interactions: 116625 Sorted by model distance: nonbonded pdb=" OG SER B 496 " pdb=" OD1 ASN B 575 " model vdw 2.263 3.040 nonbonded pdb=" OG SER C 243 " pdb=" OD1 ASP C 245 " model vdw 2.281 3.040 nonbonded pdb=" O ASP B 499 " pdb=" OG SER B 574 " model vdw 2.290 3.040 nonbonded pdb=" O GLN B 772 " pdb=" OG1 THR B 776 " model vdw 2.295 3.040 nonbonded pdb=" OG SER C 285 " pdb=" OD1 ASP C 287 " model vdw 2.300 3.040 ... (remaining 116620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.340 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 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 : 0.008 0.110 15247 Z= 0.392 Angle : 1.622 26.011 20581 Z= 0.814 Chirality : 0.083 0.864 2322 Planarity : 0.012 0.160 2619 Dihedral : 13.102 91.729 5608 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.97 % Favored : 92.92 % Rotamer: Outliers : 0.06 % Allowed : 1.11 % Favored : 98.83 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.87 (0.17), residues: 1807 helix: -1.58 (0.13), residues: 1024 sheet: -0.01 (0.41), residues: 157 loop : -2.76 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG C 88 TYR 0.064 0.004 TYR B 395 PHE 0.045 0.005 PHE A 245 TRP 0.087 0.007 TRP C 149 HIS 0.047 0.004 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00800 (15247) covalent geometry : angle 1.62233 (20581) hydrogen bonds : bond 0.17482 ( 800) hydrogen bonds : angle 7.31147 ( 2382) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 457 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 PHE cc_start: 0.8531 (m-80) cc_final: 0.8237 (m-80) REVERT: H 96 THR cc_start: 0.7387 (m) cc_final: 0.6936 (t) REVERT: H 124 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8152 (tp30) REVERT: H 132 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7544 (tp30) REVERT: H 176 ILE cc_start: 0.9056 (mm) cc_final: 0.8753 (mm) REVERT: H 207 MET cc_start: 0.4714 (mtm) cc_final: 0.4481 (mtp) REVERT: H 214 ILE cc_start: 0.8378 (mm) cc_final: 0.8165 (mm) REVERT: H 351 MET cc_start: 0.6011 (ptm) cc_final: 0.5590 (tpp) REVERT: H 361 ASN cc_start: 0.6854 (t0) cc_final: 0.6380 (t0) REVERT: H 406 ARG cc_start: 0.8317 (mmm160) cc_final: 0.8107 (tpp80) REVERT: A 97 LEU cc_start: 0.8522 (tp) cc_final: 0.8300 (pp) REVERT: A 113 PHE cc_start: 0.8991 (t80) cc_final: 0.8725 (t80) REVERT: A 136 LEU cc_start: 0.9107 (tt) cc_final: 0.8865 (tp) REVERT: A 163 LEU cc_start: 0.9044 (mt) cc_final: 0.8801 (mt) REVERT: A 260 PHE cc_start: 0.9149 (t80) cc_final: 0.8365 (t80) REVERT: A 377 MET cc_start: 0.9125 (mtm) cc_final: 0.8876 (mtt) REVERT: A 525 MET cc_start: 0.7506 (mtt) cc_final: 0.6896 (mtt) REVERT: B 267 TYR cc_start: 0.6583 (m-80) cc_final: 0.5910 (m-80) REVERT: B 348 LEU cc_start: 0.9207 (tt) cc_final: 0.8660 (tt) REVERT: B 372 TYR cc_start: 0.7932 (t80) cc_final: 0.7615 (t80) REVERT: B 388 HIS cc_start: 0.7588 (p-80) cc_final: 0.7037 (p-80) REVERT: B 395 TYR cc_start: 0.6760 (t80) cc_final: 0.6242 (t80) REVERT: B 487 THR cc_start: 0.9139 (m) cc_final: 0.8853 (m) REVERT: B 495 LEU cc_start: 0.9469 (tp) cc_final: 0.9052 (tp) REVERT: B 498 MET cc_start: 0.8386 (mpp) cc_final: 0.8037 (mpp) REVERT: B 604 LEU cc_start: 0.9001 (mp) cc_final: 0.8790 (mt) REVERT: B 686 MET cc_start: 0.8934 (ppp) cc_final: 0.8458 (ppp) REVERT: B 703 MET cc_start: 0.7710 (tpp) cc_final: 0.7404 (tpp) REVERT: B 746 MET cc_start: 0.8840 (mtt) cc_final: 0.8292 (mtp) REVERT: B 776 THR cc_start: 0.9396 (m) cc_final: 0.9151 (p) REVERT: B 793 TYR cc_start: 0.8185 (t80) cc_final: 0.7585 (t80) REVERT: C 146 ASN cc_start: 0.5984 (p0) cc_final: 0.5752 (p0) REVERT: C 248 VAL cc_start: 0.9317 (t) cc_final: 0.9016 (m) REVERT: C 255 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6623 (tp30) REVERT: C 297 THR cc_start: 0.6872 (m) cc_final: 0.6629 (m) outliers start: 1 outliers final: 0 residues processed: 458 average time/residue: 0.1147 time to fit residues: 77.3719 Evaluate side-chains 307 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 HIS H 88 GLN A 71 ASN A 242 GLN ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN B 242 GLN B 362 GLN B 441 HIS B 630 HIS B 699 GLN C 186 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.126263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.104856 restraints weight = 59388.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.104822 restraints weight = 37294.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.105649 restraints weight = 27730.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.105811 restraints weight = 25672.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.106069 restraints weight = 22181.813| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3900 r_free = 0.3900 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15247 Z= 0.151 Angle : 0.768 10.716 20581 Z= 0.386 Chirality : 0.045 0.311 2322 Planarity : 0.006 0.108 2619 Dihedral : 6.000 49.456 1989 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.87 % Favored : 93.97 % Rotamer: Outliers : 0.12 % Allowed : 3.83 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.19), residues: 1807 helix: -0.11 (0.15), residues: 1056 sheet: -0.11 (0.39), residues: 183 loop : -2.63 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 123 TYR 0.020 0.001 TYR B1039 PHE 0.022 0.002 PHE B 435 TRP 0.044 0.003 TRP C 107 HIS 0.010 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00330 (15247) covalent geometry : angle 0.76776 (20581) hydrogen bonds : bond 0.04307 ( 800) hydrogen bonds : angle 4.85814 ( 2382) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 96 THR cc_start: 0.6472 (m) cc_final: 0.6131 (t) REVERT: H 124 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8203 (tp30) REVERT: H 132 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8122 (tp30) REVERT: H 207 MET cc_start: 0.4638 (mtm) cc_final: 0.4328 (mtp) REVERT: H 218 THR cc_start: 0.7621 (p) cc_final: 0.7349 (p) REVERT: H 282 LEU cc_start: 0.8885 (mm) cc_final: 0.8681 (mm) REVERT: H 351 MET cc_start: 0.6090 (ptt) cc_final: 0.5102 (tpp) REVERT: H 361 ASN cc_start: 0.7612 (t0) cc_final: 0.6843 (t0) REVERT: A 97 LEU cc_start: 0.8891 (tp) cc_final: 0.8629 (pp) REVERT: A 139 MET cc_start: 0.6817 (mmt) cc_final: 0.6396 (mmt) REVERT: A 260 PHE cc_start: 0.8809 (t80) cc_final: 0.8576 (t80) REVERT: A 377 MET cc_start: 0.9225 (mtm) cc_final: 0.8703 (mtt) REVERT: B 245 CYS cc_start: 0.8096 (m) cc_final: 0.7593 (m) REVERT: B 283 ASP cc_start: 0.7356 (t70) cc_final: 0.6740 (t70) REVERT: B 395 TYR cc_start: 0.7192 (t80) cc_final: 0.6696 (t80) REVERT: B 487 THR cc_start: 0.9324 (m) cc_final: 0.9100 (m) REVERT: B 495 LEU cc_start: 0.9379 (tp) cc_final: 0.8995 (tp) REVERT: B 498 MET cc_start: 0.8042 (mpp) cc_final: 0.7567 (mpp) REVERT: B 686 MET cc_start: 0.8938 (ppp) cc_final: 0.8400 (ppp) REVERT: B 703 MET cc_start: 0.7855 (tpp) cc_final: 0.7593 (tpp) REVERT: B 746 MET cc_start: 0.8791 (mtt) cc_final: 0.8346 (mtp) REVERT: B 770 TYR cc_start: 0.8343 (t80) cc_final: 0.8035 (t80) REVERT: B 772 GLN cc_start: 0.8799 (pt0) cc_final: 0.8305 (pt0) REVERT: B 793 TYR cc_start: 0.8309 (t80) cc_final: 0.7616 (t80) REVERT: C 255 GLU cc_start: 0.6987 (mm-30) cc_final: 0.6597 (tp30) outliers start: 2 outliers final: 0 residues processed: 368 average time/residue: 0.0974 time to fit residues: 54.8185 Evaluate side-chains 254 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 79 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN A 160 GLN ** A 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN B 575 ASN B 699 GLN B 779 GLN B1101 HIS C 98 HIS C 144 ASN ** C 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 305 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.122856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.101689 restraints weight = 59454.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.101330 restraints weight = 35258.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.102080 restraints weight = 28649.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.102241 restraints weight = 26092.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.102432 restraints weight = 23064.740| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15247 Z= 0.150 Angle : 0.715 10.559 20581 Z= 0.358 Chirality : 0.045 0.220 2322 Planarity : 0.005 0.109 2619 Dihedral : 5.568 46.494 1989 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.53 % Favored : 93.41 % Rotamer: Outliers : 0.12 % Allowed : 3.83 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.20), residues: 1807 helix: 0.57 (0.16), residues: 1068 sheet: 0.46 (0.41), residues: 174 loop : -2.39 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 123 TYR 0.017 0.002 TYR B 437 PHE 0.020 0.002 PHE A 271 TRP 0.017 0.002 TRP C 302 HIS 0.013 0.001 HIS A 320 Details of bonding type rmsd covalent geometry : bond 0.00325 (15247) covalent geometry : angle 0.71502 (20581) hydrogen bonds : bond 0.03766 ( 800) hydrogen bonds : angle 4.57824 ( 2382) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 330 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 96 THR cc_start: 0.6479 (m) cc_final: 0.6041 (t) REVERT: H 124 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8182 (tp30) REVERT: H 132 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7963 (tm-30) REVERT: H 207 MET cc_start: 0.4904 (mtm) cc_final: 0.4546 (mtp) REVERT: H 226 MET cc_start: 0.4819 (mpp) cc_final: 0.4071 (mtm) REVERT: H 282 LEU cc_start: 0.8953 (mm) cc_final: 0.8698 (mm) REVERT: H 351 MET cc_start: 0.6545 (ptt) cc_final: 0.5345 (tpp) REVERT: H 361 ASN cc_start: 0.7659 (t0) cc_final: 0.6945 (t0) REVERT: A 97 LEU cc_start: 0.8947 (tp) cc_final: 0.8494 (pp) REVERT: A 162 PHE cc_start: 0.9058 (t80) cc_final: 0.8782 (t80) REVERT: A 166 LEU cc_start: 0.8333 (mt) cc_final: 0.7995 (mt) REVERT: A 251 CYS cc_start: 0.4334 (p) cc_final: 0.3934 (p) REVERT: A 260 PHE cc_start: 0.8823 (t80) cc_final: 0.8542 (t80) REVERT: A 276 LEU cc_start: 0.7552 (pp) cc_final: 0.7302 (pp) REVERT: A 377 MET cc_start: 0.9124 (mtm) cc_final: 0.8639 (mtt) REVERT: B 167 GLU cc_start: -0.0670 (mm-30) cc_final: -0.1216 (mm-30) REVERT: B 200 ILE cc_start: 0.8116 (pt) cc_final: 0.7544 (tt) REVERT: B 245 CYS cc_start: 0.7833 (m) cc_final: 0.7349 (m) REVERT: B 283 ASP cc_start: 0.7383 (t70) cc_final: 0.6831 (t70) REVERT: B 495 LEU cc_start: 0.9387 (tp) cc_final: 0.9063 (tp) REVERT: B 498 MET cc_start: 0.8032 (mpp) cc_final: 0.7714 (mpp) REVERT: B 703 MET cc_start: 0.7921 (tpp) cc_final: 0.7658 (tpp) REVERT: B 746 MET cc_start: 0.8656 (mtt) cc_final: 0.8347 (mtp) REVERT: C 166 THR cc_start: 0.7702 (m) cc_final: 0.7425 (t) REVERT: C 190 TRP cc_start: 0.6852 (m100) cc_final: 0.6342 (m100) REVERT: C 266 ASP cc_start: 0.7092 (p0) cc_final: 0.6849 (p0) REVERT: C 345 PHE cc_start: 0.7669 (t80) cc_final: 0.7324 (t80) outliers start: 2 outliers final: 0 residues processed: 331 average time/residue: 0.0954 time to fit residues: 48.4147 Evaluate side-chains 236 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 21 optimal weight: 0.4980 chunk 124 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 288 ASN H 323 GLN A 160 GLN B 204 ASN B 575 ASN B 699 GLN B1054 HIS C 144 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.120906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.099562 restraints weight = 59517.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.099403 restraints weight = 35910.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.100606 restraints weight = 29192.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.100608 restraints weight = 24435.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.100876 restraints weight = 22156.077| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15247 Z= 0.143 Angle : 0.688 10.408 20581 Z= 0.345 Chirality : 0.045 0.379 2322 Planarity : 0.005 0.106 2619 Dihedral : 5.364 45.310 1989 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.09 % Favored : 93.80 % Rotamer: Outliers : 0.12 % Allowed : 2.97 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.20), residues: 1807 helix: 0.95 (0.16), residues: 1061 sheet: 0.24 (0.40), residues: 172 loop : -2.30 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 166 TYR 0.018 0.001 TYR B 372 PHE 0.018 0.002 PHE B 650 TRP 0.016 0.002 TRP B 963 HIS 0.011 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00304 (15247) covalent geometry : angle 0.68848 (20581) hydrogen bonds : bond 0.03574 ( 800) hydrogen bonds : angle 4.40608 ( 2382) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 319 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 MET cc_start: 0.3324 (pmm) cc_final: 0.3059 (pmm) REVERT: H 96 THR cc_start: 0.6597 (m) cc_final: 0.6225 (t) REVERT: H 124 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8076 (tp30) REVERT: H 132 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7986 (tm-30) REVERT: H 207 MET cc_start: 0.5061 (mtm) cc_final: 0.4677 (mtp) REVERT: H 282 LEU cc_start: 0.9066 (mm) cc_final: 0.8691 (mm) REVERT: H 351 MET cc_start: 0.6080 (ptt) cc_final: 0.5095 (tpp) REVERT: H 361 ASN cc_start: 0.7691 (t0) cc_final: 0.6909 (t0) REVERT: A 97 LEU cc_start: 0.8977 (tp) cc_final: 0.8482 (pp) REVERT: A 166 LEU cc_start: 0.8411 (mt) cc_final: 0.7951 (mt) REVERT: A 251 CYS cc_start: 0.4119 (p) cc_final: 0.3915 (p) REVERT: A 260 PHE cc_start: 0.8857 (t80) cc_final: 0.8484 (t80) REVERT: A 276 LEU cc_start: 0.7575 (pp) cc_final: 0.7362 (pp) REVERT: A 312 LEU cc_start: 0.8291 (tt) cc_final: 0.7763 (tt) REVERT: A 377 MET cc_start: 0.9101 (mtm) cc_final: 0.8634 (mtt) REVERT: A 521 TYR cc_start: 0.8280 (t80) cc_final: 0.7750 (t80) REVERT: B 200 ILE cc_start: 0.8025 (pt) cc_final: 0.7376 (tt) REVERT: B 283 ASP cc_start: 0.7465 (t70) cc_final: 0.7012 (t70) REVERT: B 433 ASN cc_start: 0.8438 (m-40) cc_final: 0.8117 (m110) REVERT: B 434 MET cc_start: 0.8470 (ptp) cc_final: 0.8233 (ptp) REVERT: B 611 VAL cc_start: 0.9515 (m) cc_final: 0.9310 (m) REVERT: B 681 GLU cc_start: 0.8866 (tp30) cc_final: 0.8461 (tp30) REVERT: B 684 GLN cc_start: 0.8388 (tt0) cc_final: 0.8110 (tm-30) REVERT: B 703 MET cc_start: 0.7973 (tpp) cc_final: 0.7690 (tpp) REVERT: B 1032 THR cc_start: 0.8162 (p) cc_final: 0.7464 (t) REVERT: C 243 SER cc_start: 0.8552 (t) cc_final: 0.7678 (p) REVERT: C 255 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7124 (mm-30) REVERT: C 266 ASP cc_start: 0.7241 (p0) cc_final: 0.7016 (p0) REVERT: C 345 PHE cc_start: 0.7668 (t80) cc_final: 0.7114 (t80) outliers start: 2 outliers final: 0 residues processed: 319 average time/residue: 0.1006 time to fit residues: 49.1161 Evaluate side-chains 230 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 143 optimal weight: 0.0870 chunk 87 optimal weight: 0.5980 chunk 150 optimal weight: 0.6980 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN A 160 GLN B 575 ASN B 699 GLN C 45 HIS C 59 HIS ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.119965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.098252 restraints weight = 58974.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.098029 restraints weight = 35671.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.098965 restraints weight = 28975.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.099165 restraints weight = 24602.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.099301 restraints weight = 22486.157| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15247 Z= 0.133 Angle : 0.684 11.248 20581 Z= 0.343 Chirality : 0.045 0.421 2322 Planarity : 0.005 0.105 2619 Dihedral : 5.220 43.945 1989 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.14 % Favored : 93.80 % Rotamer: Outliers : 0.06 % Allowed : 2.41 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.20), residues: 1807 helix: 1.11 (0.16), residues: 1067 sheet: 0.16 (0.40), residues: 171 loop : -2.20 (0.24), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 166 TYR 0.020 0.001 TYR B 372 PHE 0.025 0.002 PHE B 884 TRP 0.025 0.002 TRP A 442 HIS 0.007 0.001 HIS C 223 Details of bonding type rmsd covalent geometry : bond 0.00286 (15247) covalent geometry : angle 0.68386 (20581) hydrogen bonds : bond 0.03513 ( 800) hydrogen bonds : angle 4.31695 ( 2382) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 96 THR cc_start: 0.6212 (m) cc_final: 0.5777 (t) REVERT: H 124 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8163 (tp30) REVERT: H 132 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7701 (tm-30) REVERT: H 207 MET cc_start: 0.4971 (mtm) cc_final: 0.4635 (mtp) REVERT: H 351 MET cc_start: 0.6310 (ptt) cc_final: 0.5181 (tpp) REVERT: H 361 ASN cc_start: 0.7697 (t0) cc_final: 0.6925 (t0) REVERT: H 414 LEU cc_start: 0.8092 (tp) cc_final: 0.7839 (tp) REVERT: A 97 LEU cc_start: 0.9004 (tp) cc_final: 0.8545 (pp) REVERT: A 113 PHE cc_start: 0.9084 (t80) cc_final: 0.8843 (t80) REVERT: A 162 PHE cc_start: 0.9158 (t80) cc_final: 0.8957 (t80) REVERT: A 166 LEU cc_start: 0.8399 (mt) cc_final: 0.7929 (mt) REVERT: A 260 PHE cc_start: 0.8850 (t80) cc_final: 0.8487 (t80) REVERT: A 276 LEU cc_start: 0.7393 (pp) cc_final: 0.7111 (pp) REVERT: A 377 MET cc_start: 0.9098 (mtm) cc_final: 0.8647 (mtt) REVERT: A 388 TRP cc_start: 0.8687 (m100) cc_final: 0.8452 (m100) REVERT: A 525 MET cc_start: 0.6876 (mtt) cc_final: 0.6470 (mtt) REVERT: B 228 PHE cc_start: 0.8572 (m-80) cc_final: 0.8152 (m-80) REVERT: B 283 ASP cc_start: 0.7488 (t70) cc_final: 0.7008 (t70) REVERT: B 433 ASN cc_start: 0.8404 (m-40) cc_final: 0.8113 (m110) REVERT: B 681 GLU cc_start: 0.8827 (tp30) cc_final: 0.8445 (tp30) REVERT: B 684 GLN cc_start: 0.8406 (tt0) cc_final: 0.8046 (tm-30) REVERT: B 703 MET cc_start: 0.8075 (tpp) cc_final: 0.7783 (tpp) REVERT: B 890 TYR cc_start: 0.7878 (t80) cc_final: 0.7582 (t80) REVERT: B 949 VAL cc_start: 0.8536 (t) cc_final: 0.8254 (p) REVERT: B 998 ARG cc_start: 0.8541 (ttp80) cc_final: 0.8301 (ttp80) REVERT: B 1032 THR cc_start: 0.8188 (p) cc_final: 0.7469 (t) REVERT: C 243 SER cc_start: 0.8467 (t) cc_final: 0.7627 (p) REVERT: C 255 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6697 (tp30) REVERT: C 345 PHE cc_start: 0.7843 (t80) cc_final: 0.7305 (t80) REVERT: C 347 LEU cc_start: 0.7282 (pt) cc_final: 0.6988 (pt) outliers start: 1 outliers final: 0 residues processed: 306 average time/residue: 0.0937 time to fit residues: 44.5646 Evaluate side-chains 224 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 2 optimal weight: 0.0270 chunk 16 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 167 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 263 GLN H 323 GLN A 160 GLN B 699 GLN C 45 HIS ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.119852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.098513 restraints weight = 59286.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.097708 restraints weight = 41182.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.098873 restraints weight = 34946.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.099022 restraints weight = 27307.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.099276 restraints weight = 25048.800| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15247 Z= 0.123 Angle : 0.683 11.655 20581 Z= 0.340 Chirality : 0.045 0.456 2322 Planarity : 0.005 0.101 2619 Dihedral : 5.160 42.850 1989 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.20), residues: 1807 helix: 1.15 (0.16), residues: 1076 sheet: -0.07 (0.39), residues: 182 loop : -2.06 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 166 TYR 0.017 0.001 TYR B 372 PHE 0.022 0.001 PHE B 983 TRP 0.012 0.001 TRP A 239 HIS 0.010 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00259 (15247) covalent geometry : angle 0.68327 (20581) hydrogen bonds : bond 0.03436 ( 800) hydrogen bonds : angle 4.27733 ( 2382) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 MET cc_start: 0.6341 (mpp) cc_final: 0.5763 (ptp) REVERT: H 93 MET cc_start: 0.2903 (pmm) cc_final: 0.2687 (pmm) REVERT: H 96 THR cc_start: 0.6463 (m) cc_final: 0.6014 (t) REVERT: H 105 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8804 (pp30) REVERT: H 124 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7970 (tp30) REVERT: H 132 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7737 (tm-30) REVERT: H 207 MET cc_start: 0.5099 (mtm) cc_final: 0.4749 (mtp) REVERT: H 243 MET cc_start: 0.5357 (tpp) cc_final: 0.4883 (tmm) REVERT: H 317 ILE cc_start: 0.7778 (mt) cc_final: 0.7489 (mt) REVERT: H 351 MET cc_start: 0.6113 (ptt) cc_final: 0.5135 (tpp) REVERT: H 361 ASN cc_start: 0.7538 (t0) cc_final: 0.6867 (t0) REVERT: H 414 LEU cc_start: 0.7890 (tp) cc_final: 0.7628 (tp) REVERT: A 97 LEU cc_start: 0.9003 (tp) cc_final: 0.8496 (pp) REVERT: A 113 PHE cc_start: 0.8928 (t80) cc_final: 0.8674 (t80) REVERT: A 260 PHE cc_start: 0.8873 (t80) cc_final: 0.8446 (t80) REVERT: A 276 LEU cc_start: 0.7213 (pp) cc_final: 0.6974 (pp) REVERT: A 377 MET cc_start: 0.9060 (mtm) cc_final: 0.8636 (mtt) REVERT: A 388 TRP cc_start: 0.8664 (m100) cc_final: 0.8445 (m100) REVERT: B 228 PHE cc_start: 0.8541 (m-80) cc_final: 0.8228 (m-80) REVERT: B 283 ASP cc_start: 0.7511 (t70) cc_final: 0.7035 (t70) REVERT: B 395 TYR cc_start: 0.7928 (t80) cc_final: 0.7254 (t80) REVERT: B 433 ASN cc_start: 0.8373 (m-40) cc_final: 0.8097 (m110) REVERT: B 617 ILE cc_start: 0.9529 (mt) cc_final: 0.9308 (mt) REVERT: B 681 GLU cc_start: 0.8828 (tp30) cc_final: 0.8480 (tp30) REVERT: B 684 GLN cc_start: 0.8396 (tt0) cc_final: 0.8024 (tm-30) REVERT: B 703 MET cc_start: 0.8070 (tpp) cc_final: 0.7775 (tpp) REVERT: B 949 VAL cc_start: 0.8515 (t) cc_final: 0.8251 (p) REVERT: B 998 ARG cc_start: 0.8518 (ttp80) cc_final: 0.8285 (ttp80) REVERT: B 1032 THR cc_start: 0.8282 (p) cc_final: 0.7689 (t) REVERT: C 82 PHE cc_start: 0.7226 (m-80) cc_final: 0.6882 (m-80) REVERT: C 184 GLU cc_start: 0.7394 (mp0) cc_final: 0.7010 (tp30) REVERT: C 243 SER cc_start: 0.8536 (t) cc_final: 0.7737 (p) REVERT: C 255 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6589 (tp30) REVERT: C 315 TRP cc_start: 0.7482 (m100) cc_final: 0.7170 (m100) REVERT: C 345 PHE cc_start: 0.7949 (t80) cc_final: 0.7567 (t80) REVERT: C 347 LEU cc_start: 0.7397 (pt) cc_final: 0.7010 (pt) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.0876 time to fit residues: 41.5313 Evaluate side-chains 236 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 160 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 323 GLN ** H 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN A 324 GLN B 699 GLN C 45 HIS ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.114568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.092742 restraints weight = 55248.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.092863 restraints weight = 34853.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.093170 restraints weight = 27841.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.093587 restraints weight = 23702.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.093809 restraints weight = 21817.586| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15247 Z= 0.132 Angle : 0.683 11.927 20581 Z= 0.343 Chirality : 0.046 0.401 2322 Planarity : 0.004 0.098 2619 Dihedral : 5.120 42.315 1989 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.20 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.20), residues: 1807 helix: 1.17 (0.16), residues: 1072 sheet: 0.02 (0.39), residues: 185 loop : -1.96 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 166 TYR 0.023 0.001 TYR A 521 PHE 0.016 0.001 PHE A 329 TRP 0.019 0.002 TRP A 442 HIS 0.007 0.001 HIS H 318 Details of bonding type rmsd covalent geometry : bond 0.00285 (15247) covalent geometry : angle 0.68294 (20581) hydrogen bonds : bond 0.03467 ( 800) hydrogen bonds : angle 4.30865 ( 2382) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 MET cc_start: 0.3046 (pmm) cc_final: 0.2606 (pmm) REVERT: H 96 THR cc_start: 0.6606 (m) cc_final: 0.6084 (t) REVERT: H 105 GLN cc_start: 0.9222 (tm-30) cc_final: 0.8829 (pp30) REVERT: H 124 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7956 (tp30) REVERT: H 132 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7763 (tm-30) REVERT: H 207 MET cc_start: 0.5229 (mtm) cc_final: 0.4934 (mtp) REVERT: H 351 MET cc_start: 0.5960 (ptt) cc_final: 0.4991 (tpp) REVERT: H 361 ASN cc_start: 0.7607 (t0) cc_final: 0.6877 (t0) REVERT: H 414 LEU cc_start: 0.7901 (tp) cc_final: 0.7638 (tp) REVERT: A 113 PHE cc_start: 0.8900 (t80) cc_final: 0.8688 (t80) REVERT: A 162 PHE cc_start: 0.9159 (t80) cc_final: 0.8813 (t80) REVERT: A 260 PHE cc_start: 0.8839 (t80) cc_final: 0.8405 (t80) REVERT: A 377 MET cc_start: 0.9062 (mtm) cc_final: 0.8653 (mtt) REVERT: A 385 GLU cc_start: 0.7549 (tp30) cc_final: 0.7267 (tm-30) REVERT: B 228 PHE cc_start: 0.8620 (m-80) cc_final: 0.8266 (m-80) REVERT: B 433 ASN cc_start: 0.8467 (m-40) cc_final: 0.8160 (m110) REVERT: B 498 MET cc_start: 0.8152 (mpp) cc_final: 0.7914 (mpp) REVERT: B 524 TYR cc_start: 0.9020 (m-80) cc_final: 0.8794 (m-80) REVERT: B 681 GLU cc_start: 0.9050 (tp30) cc_final: 0.8692 (tp30) REVERT: B 684 GLN cc_start: 0.8556 (tt0) cc_final: 0.8096 (tm-30) REVERT: B 703 MET cc_start: 0.8146 (tpp) cc_final: 0.7829 (tpp) REVERT: B 949 VAL cc_start: 0.8657 (t) cc_final: 0.8427 (p) REVERT: B 1032 THR cc_start: 0.8330 (p) cc_final: 0.7769 (t) REVERT: C 105 LEU cc_start: 0.8628 (mt) cc_final: 0.8374 (mt) REVERT: C 184 GLU cc_start: 0.7649 (mp0) cc_final: 0.7055 (tp30) REVERT: C 243 SER cc_start: 0.8614 (t) cc_final: 0.7761 (p) REVERT: C 255 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6725 (tp30) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1171 time to fit residues: 53.5221 Evaluate side-chains 228 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 101 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 135 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN ** H 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN B 699 GLN B 948 HIS C 45 HIS ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.114265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.092721 restraints weight = 55681.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.092952 restraints weight = 35570.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.093437 restraints weight = 27177.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.093745 restraints weight = 22727.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.093963 restraints weight = 21308.430| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.5659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15247 Z= 0.129 Angle : 0.706 12.076 20581 Z= 0.351 Chirality : 0.045 0.342 2322 Planarity : 0.004 0.095 2619 Dihedral : 5.141 41.115 1989 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.20), residues: 1807 helix: 1.17 (0.16), residues: 1079 sheet: 0.21 (0.42), residues: 167 loop : -2.00 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 998 TYR 0.031 0.002 TYR A 521 PHE 0.031 0.002 PHE A 55 TRP 0.033 0.002 TRP A 442 HIS 0.010 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00275 (15247) covalent geometry : angle 0.70595 (20581) hydrogen bonds : bond 0.03475 ( 800) hydrogen bonds : angle 4.30075 ( 2382) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 MET cc_start: 0.5827 (ptp) cc_final: 0.4623 (mmt) REVERT: H 93 MET cc_start: 0.2830 (pmm) cc_final: 0.2359 (pmm) REVERT: H 96 THR cc_start: 0.6602 (m) cc_final: 0.6085 (t) REVERT: H 105 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8823 (pp30) REVERT: H 124 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7935 (tp30) REVERT: H 132 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7953 (tm-30) REVERT: H 207 MET cc_start: 0.5486 (mtm) cc_final: 0.5146 (ttt) REVERT: H 351 MET cc_start: 0.5814 (ptt) cc_final: 0.5031 (tpp) REVERT: H 361 ASN cc_start: 0.7649 (t0) cc_final: 0.7074 (t0) REVERT: H 414 LEU cc_start: 0.7937 (tp) cc_final: 0.7678 (tp) REVERT: A 113 PHE cc_start: 0.8877 (t80) cc_final: 0.8622 (t80) REVERT: A 162 PHE cc_start: 0.9204 (t80) cc_final: 0.8996 (t80) REVERT: A 260 PHE cc_start: 0.8844 (t80) cc_final: 0.8401 (t80) REVERT: A 312 LEU cc_start: 0.8203 (tt) cc_final: 0.7548 (tt) REVERT: A 357 THR cc_start: 0.7068 (p) cc_final: 0.6855 (p) REVERT: A 377 MET cc_start: 0.9022 (mtm) cc_final: 0.8620 (mtt) REVERT: A 525 MET cc_start: 0.6749 (mtt) cc_final: 0.5876 (mmp) REVERT: B 200 ILE cc_start: 0.7946 (pt) cc_final: 0.7305 (tt) REVERT: B 433 ASN cc_start: 0.8509 (m-40) cc_final: 0.8196 (m110) REVERT: B 498 MET cc_start: 0.8219 (mpp) cc_final: 0.7983 (mpp) REVERT: B 681 GLU cc_start: 0.9076 (tp30) cc_final: 0.8714 (tp30) REVERT: B 684 GLN cc_start: 0.8579 (tt0) cc_final: 0.8074 (tm-30) REVERT: B 703 MET cc_start: 0.8150 (tpp) cc_final: 0.7829 (tpp) REVERT: B 890 TYR cc_start: 0.7604 (t80) cc_final: 0.7186 (t80) REVERT: B 949 VAL cc_start: 0.8823 (t) cc_final: 0.8614 (p) REVERT: B 1032 THR cc_start: 0.8411 (p) cc_final: 0.7955 (t) REVERT: C 184 GLU cc_start: 0.7593 (mp0) cc_final: 0.7040 (tp30) REVERT: C 243 SER cc_start: 0.8725 (t) cc_final: 0.7768 (p) REVERT: C 255 GLU cc_start: 0.7398 (mm-30) cc_final: 0.6981 (tp30) REVERT: C 276 HIS cc_start: 0.7752 (p90) cc_final: 0.7379 (p90) REVERT: C 321 LEU cc_start: 0.8098 (tt) cc_final: 0.7837 (mp) REVERT: C 345 PHE cc_start: 0.6884 (t80) cc_final: 0.5969 (t80) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.1201 time to fit residues: 54.4941 Evaluate side-chains 229 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 144 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 128 optimal weight: 0.0670 chunk 3 optimal weight: 30.0000 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN B 699 GLN ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.114167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.093030 restraints weight = 56441.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.091088 restraints weight = 39771.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.092117 restraints weight = 32517.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.092518 restraints weight = 25627.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.092766 restraints weight = 22989.537| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15247 Z= 0.130 Angle : 0.718 11.954 20581 Z= 0.358 Chirality : 0.045 0.324 2322 Planarity : 0.005 0.094 2619 Dihedral : 5.079 40.221 1989 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.70 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.20), residues: 1807 helix: 1.23 (0.16), residues: 1072 sheet: -0.01 (0.39), residues: 186 loop : -1.88 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 209 TYR 0.028 0.001 TYR B 524 PHE 0.022 0.001 PHE B 983 TRP 0.039 0.002 TRP A 442 HIS 0.008 0.001 HIS H 318 Details of bonding type rmsd covalent geometry : bond 0.00278 (15247) covalent geometry : angle 0.71816 (20581) hydrogen bonds : bond 0.03478 ( 800) hydrogen bonds : angle 4.34884 ( 2382) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 83 MET cc_start: 0.6272 (ptp) cc_final: 0.4944 (mmt) REVERT: H 93 MET cc_start: 0.3069 (pmm) cc_final: 0.2620 (pmm) REVERT: H 96 THR cc_start: 0.6246 (m) cc_final: 0.5813 (t) REVERT: H 124 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8013 (tp30) REVERT: H 132 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7935 (tm-30) REVERT: H 207 MET cc_start: 0.5250 (mtm) cc_final: 0.5016 (mtp) REVERT: H 226 MET cc_start: 0.6074 (mpp) cc_final: 0.5210 (mtt) REVERT: H 351 MET cc_start: 0.6183 (ptt) cc_final: 0.5146 (tpp) REVERT: H 361 ASN cc_start: 0.7737 (t0) cc_final: 0.7053 (t0) REVERT: H 414 LEU cc_start: 0.8082 (tp) cc_final: 0.7847 (tp) REVERT: A 113 PHE cc_start: 0.9018 (t80) cc_final: 0.8702 (t80) REVERT: A 260 PHE cc_start: 0.8911 (t80) cc_final: 0.8474 (t80) REVERT: A 377 MET cc_start: 0.9107 (mtm) cc_final: 0.8634 (mtt) REVERT: A 525 MET cc_start: 0.7037 (mtt) cc_final: 0.6092 (mmp) REVERT: B 200 ILE cc_start: 0.7848 (pt) cc_final: 0.7192 (tt) REVERT: B 433 ASN cc_start: 0.8529 (m-40) cc_final: 0.8220 (m110) REVERT: B 524 TYR cc_start: 0.8933 (m-80) cc_final: 0.8432 (m-80) REVERT: B 681 GLU cc_start: 0.9061 (tp30) cc_final: 0.8692 (tp30) REVERT: B 684 GLN cc_start: 0.8567 (tt0) cc_final: 0.8151 (tm-30) REVERT: B 703 MET cc_start: 0.8205 (tpp) cc_final: 0.7855 (tpp) REVERT: B 890 TYR cc_start: 0.7538 (t80) cc_final: 0.7189 (t80) REVERT: B 1032 THR cc_start: 0.8402 (p) cc_final: 0.8067 (t) REVERT: C 36 LEU cc_start: 0.9341 (mm) cc_final: 0.9125 (pp) REVERT: C 125 ARG cc_start: 0.5791 (mpt180) cc_final: 0.5238 (mpt180) REVERT: C 184 GLU cc_start: 0.7627 (mp0) cc_final: 0.7072 (tp30) REVERT: C 243 SER cc_start: 0.8676 (t) cc_final: 0.7779 (p) REVERT: C 255 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6954 (tp30) REVERT: C 276 HIS cc_start: 0.7799 (p90) cc_final: 0.7249 (p90) REVERT: C 345 PHE cc_start: 0.6907 (t80) cc_final: 0.6008 (t80) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.1208 time to fit residues: 53.5335 Evaluate side-chains 227 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 84 optimal weight: 10.0000 chunk 180 optimal weight: 0.9990 chunk 175 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN ** B 388 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 ASN B 699 GLN ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 HIS ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.112709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.090797 restraints weight = 57128.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.090819 restraints weight = 35988.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.091664 restraints weight = 28882.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.091880 restraints weight = 23338.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.092024 restraints weight = 21804.223| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15247 Z= 0.137 Angle : 0.727 11.643 20581 Z= 0.362 Chirality : 0.046 0.453 2322 Planarity : 0.005 0.092 2619 Dihedral : 5.121 39.767 1989 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.36 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.21), residues: 1807 helix: 1.38 (0.16), residues: 1063 sheet: 0.03 (0.40), residues: 187 loop : -1.93 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 998 TYR 0.027 0.002 TYR A 521 PHE 0.022 0.002 PHE A 55 TRP 0.020 0.002 TRP B 527 HIS 0.010 0.001 HIS H 318 Details of bonding type rmsd covalent geometry : bond 0.00300 (15247) covalent geometry : angle 0.72652 (20581) hydrogen bonds : bond 0.03566 ( 800) hydrogen bonds : angle 4.33727 ( 2382) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3614 Ramachandran restraints generated. 1807 Oldfield, 0 Emsley, 1807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 PHE cc_start: 0.7980 (m-80) cc_final: 0.7511 (m-80) REVERT: H 83 MET cc_start: 0.5930 (ptp) cc_final: 0.4761 (mmt) REVERT: H 93 MET cc_start: 0.2875 (pmm) cc_final: 0.2499 (pmm) REVERT: H 105 GLN cc_start: 0.9284 (tm-30) cc_final: 0.8867 (pp30) REVERT: H 124 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7970 (tp30) REVERT: H 207 MET cc_start: 0.5385 (mtm) cc_final: 0.5111 (mtp) REVERT: H 226 MET cc_start: 0.6045 (mpp) cc_final: 0.5027 (mtt) REVERT: H 351 MET cc_start: 0.5642 (ptt) cc_final: 0.4662 (tpp) REVERT: H 414 LEU cc_start: 0.7927 (tp) cc_final: 0.7700 (tp) REVERT: A 94 PHE cc_start: 0.6275 (m-10) cc_final: 0.5736 (m-10) REVERT: A 97 LEU cc_start: 0.9131 (tp) cc_final: 0.8646 (pp) REVERT: A 260 PHE cc_start: 0.8882 (t80) cc_final: 0.8420 (t80) REVERT: A 377 MET cc_start: 0.9083 (mtm) cc_final: 0.8646 (mtt) REVERT: A 525 MET cc_start: 0.7113 (mtt) cc_final: 0.6281 (mmp) REVERT: B 200 ILE cc_start: 0.7888 (pt) cc_final: 0.7195 (tt) REVERT: B 388 HIS cc_start: 0.6867 (p-80) cc_final: 0.6567 (p-80) REVERT: B 433 ASN cc_start: 0.8435 (m-40) cc_final: 0.8168 (m110) REVERT: B 495 LEU cc_start: 0.9261 (tp) cc_final: 0.9044 (tp) REVERT: B 524 TYR cc_start: 0.8974 (m-80) cc_final: 0.8608 (m-80) REVERT: B 681 GLU cc_start: 0.9041 (tp30) cc_final: 0.8691 (tp30) REVERT: B 684 GLN cc_start: 0.8599 (tt0) cc_final: 0.8092 (tm-30) REVERT: B 703 MET cc_start: 0.8197 (tpp) cc_final: 0.7839 (tpp) REVERT: B 768 LYS cc_start: 0.8759 (ptpp) cc_final: 0.8452 (pttm) REVERT: B 1032 THR cc_start: 0.8439 (p) cc_final: 0.8153 (t) REVERT: C 36 LEU cc_start: 0.9323 (mm) cc_final: 0.9080 (pp) REVERT: C 125 ARG cc_start: 0.6081 (mpt180) cc_final: 0.5403 (mpt180) REVERT: C 238 TYR cc_start: 0.8803 (m-80) cc_final: 0.8602 (m-10) REVERT: C 255 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7242 (tp30) REVERT: C 276 HIS cc_start: 0.7967 (p90) cc_final: 0.7451 (p90) REVERT: C 345 PHE cc_start: 0.7128 (t80) cc_final: 0.6268 (t80) REVERT: C 347 LEU cc_start: 0.7792 (pt) cc_final: 0.7438 (pp) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1170 time to fit residues: 51.7875 Evaluate side-chains 224 residues out of total 1698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 141 optimal weight: 0.0170 chunk 137 optimal weight: 0.9980 chunk 35 optimal weight: 0.0030 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 overall best weight: 0.6030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 GLN B 575 ASN B 699 GLN ** B 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 HIS C 45 HIS ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.113380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.091442 restraints weight = 56366.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.091428 restraints weight = 35632.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.092242 restraints weight = 30566.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.092375 restraints weight = 24656.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.092572 restraints weight = 21735.802| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.6563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15247 Z= 0.130 Angle : 0.736 11.922 20581 Z= 0.365 Chirality : 0.046 0.465 2322 Planarity : 0.004 0.092 2619 Dihedral : 5.085 38.783 1989 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.21), residues: 1807 helix: 1.41 (0.16), residues: 1067 sheet: -0.01 (0.39), residues: 192 loop : -1.92 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 138 TYR 0.027 0.002 TYR B 524 PHE 0.027 0.002 PHE B 435 TRP 0.046 0.002 TRP A 442 HIS 0.010 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00278 (15247) covalent geometry : angle 0.73573 (20581) hydrogen bonds : bond 0.03486 ( 800) hydrogen bonds : angle 4.31210 ( 2382) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2450.93 seconds wall clock time: 43 minutes 22.19 seconds (2602.19 seconds total)