Starting phenix.real_space_refine on Fri Jul 3 17:01:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9upf_64394/07_2026/9upf_64394.cif Found real_map, /net/cci-nas-00/data/ceres_data/9upf_64394/07_2026/9upf_64394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9upf_64394/07_2026/9upf_64394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9upf_64394/07_2026/9upf_64394.map" model { file = "/net/cci-nas-00/data/ceres_data/9upf_64394/07_2026/9upf_64394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9upf_64394/07_2026/9upf_64394.cif" } resolution = 3.59 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= 0.003 sd= 0.042 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 84 5.16 5 C 9512 2.51 5 N 2415 2.21 5 O 2564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14581 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3542 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 1 Chain: "A" Number of atoms: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3638 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 14, 'TRANS': 431} Chain breaks: 1 Chain: "D" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3673 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 19, 'TRANS': 430} Chain: "C" Number of atoms: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3638 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 14, 'TRANS': 431} Chain breaks: 1 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Ad-hoc single atom residues: {' CA': 2} Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain breaks: 2 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 3.63, per 1000 atoms: 0.25 Number of scatterers: 14581 At special positions: 0 Unit cell: (124.722, 116.604, 118.818, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 84 16.00 P 4 15.00 O 2564 8.00 N 2415 7.00 C 9512 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: 1.03 Conformation dependent library (CDL) restraints added in 533.4 milliseconds 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3350 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 12 sheets defined 69.4% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 653 through 680 Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 687 through 708 removed outlier: 3.663A pdb=" N ILE B 706 " --> pdb=" O TYR B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 734 Processing helix chain 'B' and resid 735 through 746 removed outlier: 3.691A pdb=" N LYS B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 removed outlier: 3.798A pdb=" N ARG B 762 " --> pdb=" O PRO B 759 " (cutoff:3.500A) Proline residue: B 764 - end of helix removed outlier: 3.955A pdb=" N LYS B 768 " --> pdb=" O ARG B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 783 Processing helix chain 'B' and resid 786 through 816 Processing helix chain 'B' and resid 830 through 844 removed outlier: 3.661A pdb=" N ARG B 834 " --> pdb=" O ASN B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 907 removed outlier: 5.102A pdb=" N GLY B 889 " --> pdb=" O ALA B 885 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N GLN B 890 " --> pdb=" O ALA B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 929 Processing helix chain 'B' and resid 933 through 940 Processing helix chain 'B' and resid 941 through 959 removed outlier: 5.679A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 978 Processing helix chain 'B' and resid 1029 through 1034 removed outlier: 3.900A pdb=" N LEU B1033 " --> pdb=" O GLY B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1069 removed outlier: 3.874A pdb=" N HIS B1068 " --> pdb=" O GLU B1064 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR B1069 " --> pdb=" O ILE B1065 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1084 removed outlier: 3.774A pdb=" N LEU B1084 " --> pdb=" O ALA B1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 164 removed outlier: 3.555A pdb=" N MET A 149 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Proline residue: A 150 - end of helix removed outlier: 3.525A pdb=" N LEU A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N VAL A 159 " --> pdb=" O TRP A 155 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 removed outlier: 4.346A pdb=" N GLN A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LYS A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 196 Processing helix chain 'A' and resid 207 through 218 removed outlier: 3.918A pdb=" N HIS A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 4.138A pdb=" N LYS A 222 " --> pdb=" O THR A 218 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 252 removed outlier: 3.640A pdb=" N PHE A 247 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN A 248 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.524A pdb=" N PHE A 257 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 301 Processing helix chain 'A' and resid 319 through 336 Processing helix chain 'A' and resid 346 through 363 Processing helix chain 'A' and resid 363 through 400 removed outlier: 3.740A pdb=" N ASN A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG A 382 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 419 removed outlier: 3.736A pdb=" N LYS A 408 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 409 " --> pdb=" O MET A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 445 through 452 removed outlier: 3.750A pdb=" N LYS A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 3.723A pdb=" N VAL A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 467 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.689A pdb=" N ILE A 524 " --> pdb=" O GLY A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 563 through 580 removed outlier: 3.915A pdb=" N LYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 580 " --> pdb=" O GLU A 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 58 removed outlier: 3.627A pdb=" N TYR D 35 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) Proline residue: D 44 - end of helix removed outlier: 4.047A pdb=" N LEU D 52 " --> pdb=" O ASN D 48 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 removed outlier: 3.806A pdb=" N GLN D 62 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N HIS D 63 " --> pdb=" O PRO D 59 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 89 removed outlier: 3.573A pdb=" N LEU D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL D 71 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 72 " --> pdb=" O ALA D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 3.560A pdb=" N ARG D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 122 removed outlier: 4.030A pdb=" N PHE D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 133 removed outlier: 3.993A pdb=" N VAL D 130 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ARG D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 145 removed outlier: 3.755A pdb=" N LEU D 141 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN D 142 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 161 removed outlier: 3.843A pdb=" N LEU D 150 " --> pdb=" O ARG D 146 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG D 160 " --> pdb=" O ARG D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 195 removed outlier: 3.625A pdb=" N PHE D 167 " --> pdb=" O TYR D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 212 removed outlier: 3.669A pdb=" N GLU D 212 " --> pdb=" O PRO D 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 209 through 212' Processing helix chain 'D' and resid 213 through 230 removed outlier: 3.590A pdb=" N ILE D 228 " --> pdb=" O PHE D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 279 removed outlier: 3.718A pdb=" N MET D 256 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 294 removed outlier: 3.541A pdb=" N TYR D 289 " --> pdb=" O LEU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 313 removed outlier: 3.573A pdb=" N LEU D 310 " --> pdb=" O TRP D 306 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN D 311 " --> pdb=" O TYR D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 326 removed outlier: 3.809A pdb=" N HIS D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU D 326 " --> pdb=" O ILE D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 339 removed outlier: 3.577A pdb=" N GLU D 333 " --> pdb=" O ARG D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 346 Processing helix chain 'D' and resid 355 through 364 removed outlier: 4.074A pdb=" N GLU D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU D 362 " --> pdb=" O GLU D 358 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS D 363 " --> pdb=" O GLU D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 419 removed outlier: 4.296A pdb=" N ILE D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 457 Processing helix chain 'D' and resid 457 through 474 removed outlier: 3.735A pdb=" N GLN D 461 " --> pdb=" O TYR D 457 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 472 " --> pdb=" O GLY D 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 164 removed outlier: 3.548A pdb=" N TYR C 141 " --> pdb=" O GLY C 137 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET C 149 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Proline residue: C 150 - end of helix removed outlier: 4.458A pdb=" N VAL C 159 " --> pdb=" O TRP C 155 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 171 removed outlier: 3.740A pdb=" N GLN C 168 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 195 removed outlier: 3.646A pdb=" N VAL C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 190 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 191 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 218 through 228 removed outlier: 4.130A pdb=" N LYS C 222 " --> pdb=" O THR C 218 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 252 removed outlier: 3.588A pdb=" N LEU C 251 " --> pdb=" O ASN C 248 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HIS C 252 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.579A pdb=" N PHE C 260 " --> pdb=" O MET C 256 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR C 265 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 301 removed outlier: 3.535A pdb=" N PHE C 273 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE C 285 " --> pdb=" O TYR C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 319 through 336 Processing helix chain 'C' and resid 346 through 379 removed outlier: 3.522A pdb=" N PHE C 352 " --> pdb=" O GLU C 348 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 362 " --> pdb=" O LEU C 358 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 371 " --> pdb=" O ILE C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 400 removed outlier: 3.587A pdb=" N PHE C 385 " --> pdb=" O THR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 420 Processing helix chain 'C' and resid 424 through 429 Processing helix chain 'C' and resid 433 through 445 removed outlier: 3.743A pdb=" N ASN C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 452 Processing helix chain 'C' and resid 452 through 459 removed outlier: 3.579A pdb=" N CYS C 458 " --> pdb=" O ILE C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 removed outlier: 4.388A pdb=" N LEU C 468 " --> pdb=" O VAL C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 removed outlier: 3.705A pdb=" N ILE C 524 " --> pdb=" O GLY C 520 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C 525 " --> pdb=" O GLU C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 525' Processing helix chain 'C' and resid 553 through 563 removed outlier: 3.602A pdb=" N GLU C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 580 removed outlier: 3.561A pdb=" N VAL C 569 " --> pdb=" O ASP C 565 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE C 577 " --> pdb=" O ARG C 573 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 578 " --> pdb=" O GLY C 574 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET C 579 " --> pdb=" O ARG C 575 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS C 580 " --> pdb=" O GLU C 576 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 715 through 717 removed outlier: 3.948A pdb=" N PHE B 715 " --> pdb=" O ILE B 722 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 979 through 983 removed outlier: 3.592A pdb=" N VAL B 981 " --> pdb=" O LEU B1054 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B1054 " --> pdb=" O VAL B 981 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN B1053 " --> pdb=" O GLN B1003 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 988 through 990 removed outlier: 7.085A pdb=" N TYR B 988 " --> pdb=" O ALA B1048 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA B1048 " --> pdb=" O TYR B 988 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 990 " --> pdb=" O VAL B1046 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN B1045 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA5, first strand: chain 'A' and resid 471 through 475 removed outlier: 6.355A pdb=" N ARG A 541 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL A 502 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 543 " --> pdb=" O ALA A 500 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 500 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR A 545 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS A 498 " --> pdb=" O TYR A 545 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 496 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 549 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE A 494 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU A 551 " --> pdb=" O TYR A 492 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR A 492 " --> pdb=" O LEU A 551 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 499 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA A 511 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 480 through 482 removed outlier: 6.590A pdb=" N ILE A 540 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG A 541 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL A 502 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 543 " --> pdb=" O ALA A 500 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 500 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR A 545 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS A 498 " --> pdb=" O TYR A 545 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU A 496 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 549 " --> pdb=" O ILE A 494 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE A 494 " --> pdb=" O PHE A 549 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU A 551 " --> pdb=" O TYR A 492 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR A 492 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'D' and resid 365 through 369 removed outlier: 7.027A pdb=" N ASP D 441 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG D 389 " --> pdb=" O ASP D 441 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 374 through 376 removed outlier: 6.849A pdb=" N TYR D 374 " --> pdb=" O SER D 436 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N SER D 436 " --> pdb=" O TYR D 374 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N CYS D 376 " --> pdb=" O ILE D 434 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN D 433 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 405 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 199 through 200 Processing sheet with id=AB2, first strand: chain 'C' and resid 471 through 475 removed outlier: 6.914A pdb=" N ASP C 547 " --> pdb=" O LYS C 495 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 480 through 482 removed outlier: 6.415A pdb=" N TYR C 480 " --> pdb=" O SER C 542 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER C 542 " --> pdb=" O TYR C 480 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2535 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: 2.46 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4473 1.34 - 1.46: 3290 1.46 - 1.58: 7043 1.58 - 1.70: 8 1.70 - 1.82: 136 Bond restraints: 14950 Sorted by residual: bond pdb=" N VAL B1047 " pdb=" CA VAL B1047 " ideal model delta sigma weight residual 1.456 1.493 -0.038 1.15e-02 7.56e+03 1.08e+01 bond pdb=" N VAL B1007 " pdb=" CA VAL B1007 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.15e-02 7.56e+03 1.05e+01 bond pdb=" N VAL B 982 " pdb=" CA VAL B 982 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.56e+00 bond pdb=" N VAL B 981 " pdb=" CA VAL B 981 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.42e+00 bond pdb=" N ILE C 540 " pdb=" CA ILE C 540 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.17e-02 7.31e+03 9.12e+00 ... (remaining 14945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 19741 2.35 - 4.70: 458 4.70 - 7.05: 50 7.05 - 9.40: 27 9.40 - 11.75: 14 Bond angle restraints: 20290 Sorted by residual: angle pdb=" N ILE B 844 " pdb=" CA ILE B 844 " pdb=" C ILE B 844 " ideal model delta sigma weight residual 112.98 106.82 6.16 1.25e+00 6.40e-01 2.43e+01 angle pdb=" CA SER D 370 " pdb=" C SER D 370 " pdb=" O SER D 370 " ideal model delta sigma weight residual 120.60 117.06 3.54 9.00e-01 1.23e+00 1.55e+01 angle pdb=" CB MET D 123 " pdb=" CG MET D 123 " pdb=" SD MET D 123 " ideal model delta sigma weight residual 112.70 124.45 -11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" CA GLY B1011 " pdb=" C GLY B1011 " pdb=" O GLY B1011 " ideal model delta sigma weight residual 121.19 117.68 3.51 9.10e-01 1.21e+00 1.49e+01 angle pdb=" N HIS B1049 " pdb=" CA HIS B1049 " pdb=" C HIS B1049 " ideal model delta sigma weight residual 111.71 107.28 4.43 1.15e+00 7.56e-01 1.48e+01 ... (remaining 20285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.88: 8478 29.88 - 59.76: 322 59.76 - 89.65: 11 89.65 - 119.53: 0 119.53 - 149.41: 12 Dihedral angle restraints: 8823 sinusoidal: 3596 harmonic: 5227 Sorted by residual: dihedral pdb=" C5' CMP D 601 " pdb=" O5' CMP D 601 " pdb=" P CMP D 601 " pdb=" O1P CMP D 601 " ideal model delta sinusoidal sigma weight residual 60.00 -150.59 -149.41 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" C5' CMP A 701 " pdb=" O5' CMP A 701 " pdb=" P CMP A 701 " pdb=" O1P CMP A 701 " ideal model delta sinusoidal sigma weight residual 60.00 -153.29 -146.71 1 2.00e+01 2.50e-03 4.41e+01 dihedral pdb=" C3' CMP D 601 " pdb=" O3' CMP D 601 " pdb=" P CMP D 601 " pdb=" O1P CMP D 601 " ideal model delta sinusoidal sigma weight residual 300.00 156.45 143.55 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 8820 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1787 0.054 - 0.108: 364 0.108 - 0.161: 79 0.161 - 0.215: 26 0.215 - 0.269: 5 Chirality restraints: 2261 Sorted by residual: chirality pdb=" CA ILE C 540 " pdb=" N ILE C 540 " pdb=" C ILE C 540 " pdb=" CB ILE C 540 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CB ILE A 229 " pdb=" CA ILE A 229 " pdb=" CG1 ILE A 229 " pdb=" CG2 ILE A 229 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB VAL B1047 " pdb=" CA VAL B1047 " pdb=" CG1 VAL B1047 " pdb=" CG2 VAL B1047 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2258 not shown) Planarity restraints: 2504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 309 " 0.018 2.00e-02 2.50e+03 2.18e-02 7.15e+00 pdb=" CG HIS D 309 " -0.047 2.00e-02 2.50e+03 pdb=" ND1 HIS D 309 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS D 309 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 HIS D 309 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS D 309 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 439 " -0.016 2.00e-02 2.50e+03 1.88e-02 7.10e+00 pdb=" CG TYR D 439 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR D 439 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR D 439 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR D 439 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR D 439 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 439 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR D 439 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 412 " -0.016 2.00e-02 2.50e+03 1.41e-02 4.94e+00 pdb=" CG TRP C 412 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP C 412 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 412 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 412 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 412 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 412 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 412 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 412 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 412 " -0.002 2.00e-02 2.50e+03 ... (remaining 2501 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2551 2.77 - 3.30: 14237 3.30 - 3.84: 24021 3.84 - 4.37: 27569 4.37 - 4.90: 46753 Nonbonded interactions: 115131 Sorted by model distance: nonbonded pdb=" OG1 THR A 231 " pdb=" O VAL A 245 " model vdw 2.238 3.040 nonbonded pdb=" OG SER D 355 " pdb=" OH TYR D 457 " model vdw 2.264 3.040 nonbonded pdb=" O THR C 332 " pdb=" OG1 THR C 336 " model vdw 2.271 3.040 nonbonded pdb=" OD1 ASP B 932 " pdb=" OG SER B 934 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR B 903 " pdb=" OE1 GLU A 425 " model vdw 2.311 3.040 ... (remaining 115126 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 130 through 233 or resid 240 through 701)) selection = (chain 'C' and (resid 130 through 233 or resid 240 through 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.110 Find NCS groups from input model: 0.150 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: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.005 0.057 14950 Z= 0.297 Angle : 0.855 11.750 20290 Z= 0.487 Chirality : 0.050 0.269 2261 Planarity : 0.005 0.054 2504 Dihedral : 15.506 149.410 5473 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.06 % Allowed : 17.23 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.18), residues: 1760 helix: 0.04 (0.13), residues: 1077 sheet: 0.79 (0.52), residues: 79 loop : -0.14 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 790 TYR 0.044 0.001 TYR D 439 PHE 0.034 0.001 PHE A 398 TRP 0.038 0.001 TRP C 412 HIS 0.026 0.001 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.30 (14950) covalent geometry : angle 0.85456 / 0.49 (20290) hydrogen bonds : bond 0.24642 / 16.37 ( 875) hydrogen bonds : angle 6.67608 / 4.88 ( 2535) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 0.484 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: B 896 CYS cc_start: 0.7977 (m) cc_final: 0.7701 (t) REVERT: B 915 ASN cc_start: 0.8939 (t0) cc_final: 0.8539 (t0) REVERT: B 994 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7745 (mt-10) REVERT: B 1071 GLU cc_start: 0.7775 (pm20) cc_final: 0.7210 (tm-30) REVERT: A 215 TYR cc_start: 0.8567 (t80) cc_final: 0.8154 (t80) REVERT: A 405 MET cc_start: 0.8540 (tpp) cc_final: 0.8115 (mtt) REVERT: A 489 LYS cc_start: 0.8429 (mmtm) cc_final: 0.7308 (tptt) REVERT: D 262 MET cc_start: 0.8568 (mmm) cc_final: 0.7076 (tmm) REVERT: D 384 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7422 (mt-10) REVERT: D 386 TYR cc_start: 0.7746 (m-10) cc_final: 0.7070 (m-10) REVERT: C 201 GLN cc_start: 0.6671 (mm-40) cc_final: 0.6290 (mm-40) REVERT: C 480 TYR cc_start: 0.7642 (p90) cc_final: 0.7254 (p90) REVERT: C 557 MET cc_start: 0.7959 (mmp) cc_final: 0.7430 (mtm) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.1007 time to fit residues: 37.9110 Evaluate side-chains 216 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 805 ASN B 864 ASN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.122317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.092742 restraints weight = 30576.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.095683 restraints weight = 14192.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.097545 restraints weight = 9024.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.098685 restraints weight = 6904.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099296 restraints weight = 5887.246| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14950 Z= 0.147 Angle : 0.618 13.925 20290 Z= 0.316 Chirality : 0.039 0.143 2261 Planarity : 0.004 0.053 2504 Dihedral : 11.386 149.900 2025 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.16 % Allowed : 15.89 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.19), residues: 1760 helix: 1.36 (0.15), residues: 1121 sheet: 0.70 (0.67), residues: 62 loop : -0.16 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 880 TYR 0.020 0.001 TYR C 319 PHE 0.021 0.001 PHE C 519 TRP 0.021 0.001 TRP C 412 HIS 0.004 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (14950) covalent geometry : angle 0.61762 / 0.32 (20290) hydrogen bonds : bond 0.05621 / 3.72 ( 875) hydrogen bonds : angle 4.48263 / 3.26 ( 2535) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 896 CYS cc_start: 0.8063 (m) cc_final: 0.7786 (t) REVERT: B 915 ASN cc_start: 0.8935 (t0) cc_final: 0.8533 (t0) REVERT: B 994 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7680 (mt-10) REVERT: B 998 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7483 (mp0) REVERT: A 405 MET cc_start: 0.8424 (tpp) cc_final: 0.8116 (mtt) REVERT: A 489 LYS cc_start: 0.8389 (mmtm) cc_final: 0.7580 (tptt) REVERT: A 555 ASP cc_start: 0.9042 (m-30) cc_final: 0.8766 (m-30) REVERT: D 113 TRP cc_start: 0.7792 (t60) cc_final: 0.7355 (t-100) REVERT: D 262 MET cc_start: 0.8453 (mmm) cc_final: 0.7074 (tmm) REVERT: D 415 GLU cc_start: 0.8059 (pm20) cc_final: 0.7850 (pm20) REVERT: D 418 ILE cc_start: 0.8883 (mp) cc_final: 0.8681 (mm) REVERT: C 168 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8366 (tm-30) REVERT: C 480 TYR cc_start: 0.7625 (p90) cc_final: 0.7404 (p90) REVERT: C 494 ILE cc_start: 0.9389 (mt) cc_final: 0.9133 (mp) REVERT: C 557 MET cc_start: 0.7931 (mmp) cc_final: 0.7496 (mtm) outliers start: 34 outliers final: 19 residues processed: 243 average time/residue: 0.0920 time to fit residues: 34.9482 Evaluate side-chains 218 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 822 HIS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 518 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 0.1980 chunk 121 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1008 GLN D 283 HIS C 386 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.092629 restraints weight = 30715.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095545 restraints weight = 14326.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.097394 restraints weight = 9086.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.098511 restraints weight = 6911.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.099149 restraints weight = 5907.675| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14950 Z= 0.127 Angle : 0.562 14.564 20290 Z= 0.282 Chirality : 0.038 0.160 2261 Planarity : 0.004 0.050 2504 Dihedral : 11.330 149.680 2025 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.84 % Allowed : 17.10 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.20), residues: 1760 helix: 1.71 (0.15), residues: 1126 sheet: 0.61 (0.62), residues: 67 loop : -0.14 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 880 TYR 0.018 0.001 TYR C 319 PHE 0.021 0.001 PHE C 519 TRP 0.019 0.001 TRP C 412 HIS 0.004 0.001 HIS D 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (14950) covalent geometry : angle 0.56191 / 0.28 (20290) hydrogen bonds : bond 0.04532 / 3.01 ( 875) hydrogen bonds : angle 4.14424 / 3.02 ( 2535) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 211 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.8334 (mmp) cc_final: 0.7998 (tpp) REVERT: B 790 ARG cc_start: 0.8326 (mtt90) cc_final: 0.7912 (mtt90) REVERT: B 896 CYS cc_start: 0.8164 (m) cc_final: 0.7847 (t) REVERT: B 915 ASN cc_start: 0.8953 (t0) cc_final: 0.8566 (t0) REVERT: B 994 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7729 (mt-10) REVERT: B 998 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7525 (mp0) REVERT: A 215 TYR cc_start: 0.8473 (t80) cc_final: 0.7972 (t80) REVERT: A 386 GLN cc_start: 0.8448 (mm110) cc_final: 0.8132 (tp40) REVERT: A 555 ASP cc_start: 0.8986 (m-30) cc_final: 0.8695 (m-30) REVERT: D 262 MET cc_start: 0.8387 (mmm) cc_final: 0.7168 (tmm) REVERT: D 415 GLU cc_start: 0.8063 (pm20) cc_final: 0.7804 (pm20) REVERT: C 473 GLN cc_start: 0.6636 (mt0) cc_final: 0.6412 (mt0) REVERT: C 494 ILE cc_start: 0.9349 (mt) cc_final: 0.9129 (mp) outliers start: 29 outliers final: 20 residues processed: 227 average time/residue: 0.0945 time to fit residues: 32.9016 Evaluate side-chains 217 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 518 CYS Chi-restraints excluded: chain C residue 554 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 141 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 83 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 683 GLN A 419 ASN D 183 ASN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.120055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.089881 restraints weight = 31849.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.092732 restraints weight = 15372.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.094552 restraints weight = 9978.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.095662 restraints weight = 7701.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.096342 restraints weight = 6585.669| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14950 Z= 0.200 Angle : 0.616 14.543 20290 Z= 0.311 Chirality : 0.040 0.143 2261 Planarity : 0.004 0.050 2504 Dihedral : 11.256 147.267 2025 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.86 % Allowed : 17.74 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.20), residues: 1760 helix: 1.72 (0.15), residues: 1121 sheet: 0.51 (0.69), residues: 57 loop : -0.33 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 246 TYR 0.021 0.002 TYR C 172 PHE 0.019 0.001 PHE C 519 TRP 0.020 0.001 TRP C 412 HIS 0.003 0.001 HIS D 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (14950) covalent geometry : angle 0.61592 / 0.31 (20290) hydrogen bonds : bond 0.04634 / 3.08 ( 875) hydrogen bonds : angle 4.14179 / 3.00 ( 2535) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.8339 (mmp) cc_final: 0.8066 (tpp) REVERT: B 790 ARG cc_start: 0.8405 (mtt90) cc_final: 0.7961 (mtt90) REVERT: B 896 CYS cc_start: 0.8262 (m) cc_final: 0.7863 (t) REVERT: B 915 ASN cc_start: 0.9012 (t0) cc_final: 0.8601 (t0) REVERT: B 994 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7548 (mt-10) REVERT: B 998 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7578 (mp0) REVERT: B 1068 HIS cc_start: 0.7602 (m90) cc_final: 0.7380 (m90) REVERT: B 1083 MET cc_start: 0.8153 (tmm) cc_final: 0.7705 (tmm) REVERT: A 489 LYS cc_start: 0.8418 (mmtm) cc_final: 0.7734 (tptt) REVERT: A 555 ASP cc_start: 0.9023 (m-30) cc_final: 0.8742 (m-30) REVERT: D 262 MET cc_start: 0.8471 (mmm) cc_final: 0.7213 (tmm) REVERT: D 283 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.7579 (m-70) REVERT: D 415 GLU cc_start: 0.8221 (pm20) cc_final: 0.8020 (pm20) REVERT: C 133 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8894 (mp) REVERT: C 473 GLN cc_start: 0.6769 (mt0) cc_final: 0.6460 (mt0) outliers start: 45 outliers final: 24 residues processed: 226 average time/residue: 0.0997 time to fit residues: 34.6946 Evaluate side-chains 216 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 779 LEU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 990 CYS Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 518 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 73 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 ASN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.121115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.091125 restraints weight = 31702.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.093986 restraints weight = 15232.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.095818 restraints weight = 9880.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.096845 restraints weight = 7598.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.097623 restraints weight = 6533.301| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14950 Z= 0.144 Angle : 0.587 15.105 20290 Z= 0.290 Chirality : 0.038 0.144 2261 Planarity : 0.004 0.049 2504 Dihedral : 11.279 147.037 2025 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.67 % Allowed : 18.31 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.20), residues: 1760 helix: 1.76 (0.15), residues: 1134 sheet: 0.56 (0.65), residues: 65 loop : -0.35 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 945 TYR 0.017 0.001 TYR C 319 PHE 0.015 0.001 PHE D 177 TRP 0.025 0.001 TRP C 412 HIS 0.013 0.001 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (14950) covalent geometry : angle 0.58731 / 0.29 (20290) hydrogen bonds : bond 0.04199 / 2.79 ( 875) hydrogen bonds : angle 3.96662 / 2.88 ( 2535) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.8325 (mmp) cc_final: 0.8038 (tpp) REVERT: B 790 ARG cc_start: 0.8422 (mtt90) cc_final: 0.8046 (mtt90) REVERT: B 896 CYS cc_start: 0.8148 (m) cc_final: 0.7945 (t) REVERT: B 915 ASN cc_start: 0.8992 (t0) cc_final: 0.8596 (t0) REVERT: B 994 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7693 (mt-10) REVERT: B 998 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7616 (mp0) REVERT: B 1083 MET cc_start: 0.8035 (tmm) cc_final: 0.7688 (tmm) REVERT: A 489 LYS cc_start: 0.8420 (mmtm) cc_final: 0.7724 (tptt) REVERT: A 555 ASP cc_start: 0.9014 (m-30) cc_final: 0.8741 (m-30) REVERT: D 123 MET cc_start: 0.8060 (tmm) cc_final: 0.7756 (tmm) REVERT: D 262 MET cc_start: 0.8339 (mmm) cc_final: 0.7145 (tmm) REVERT: D 283 HIS cc_start: 0.7888 (OUTLIER) cc_final: 0.7569 (m-70) REVERT: D 415 GLU cc_start: 0.8055 (pm20) cc_final: 0.7817 (pm20) REVERT: C 201 GLN cc_start: 0.6805 (mm-40) cc_final: 0.6548 (mm-40) outliers start: 42 outliers final: 27 residues processed: 226 average time/residue: 0.1049 time to fit residues: 37.0677 Evaluate side-chains 215 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 990 CYS Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 518 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 24 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 131 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 419 ASN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.118651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.090288 restraints weight = 31872.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.092003 restraints weight = 15284.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092810 restraints weight = 10188.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.093149 restraints weight = 9957.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.093320 restraints weight = 8611.416| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14950 Z= 0.185 Angle : 0.615 15.285 20290 Z= 0.306 Chirality : 0.040 0.138 2261 Planarity : 0.004 0.048 2504 Dihedral : 11.242 146.164 2025 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.80 % Allowed : 18.69 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.20), residues: 1760 helix: 1.75 (0.15), residues: 1123 sheet: 0.35 (0.64), residues: 66 loop : -0.42 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 140 TYR 0.019 0.001 TYR C 329 PHE 0.022 0.001 PHE C 398 TRP 0.026 0.001 TRP C 412 HIS 0.011 0.001 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 (14950) covalent geometry : angle 0.61465 / 0.31 (20290) hydrogen bonds : bond 0.04359 / 2.90 ( 875) hydrogen bonds : angle 4.01725 / 2.92 ( 2535) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 204 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 710 GLN cc_start: 0.8750 (mm-40) cc_final: 0.8373 (mm-40) REVERT: B 740 MET cc_start: 0.8323 (mmp) cc_final: 0.8106 (tpp) REVERT: B 790 ARG cc_start: 0.8467 (mtt90) cc_final: 0.8210 (mtt90) REVERT: B 915 ASN cc_start: 0.9008 (t0) cc_final: 0.8609 (t0) REVERT: B 998 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7672 (mp0) REVERT: B 1083 MET cc_start: 0.7967 (tmm) cc_final: 0.7729 (tmm) REVERT: A 264 GLU cc_start: 0.8577 (tt0) cc_final: 0.8068 (tm-30) REVERT: A 489 LYS cc_start: 0.8517 (mmtm) cc_final: 0.7541 (tptt) REVERT: A 555 ASP cc_start: 0.9048 (m-30) cc_final: 0.8783 (m-30) REVERT: D 262 MET cc_start: 0.8415 (mmm) cc_final: 0.7122 (tmm) REVERT: D 283 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7754 (m-70) REVERT: D 418 ILE cc_start: 0.8932 (mm) cc_final: 0.8671 (mp) REVERT: C 133 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8953 (mp) REVERT: C 168 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 201 GLN cc_start: 0.6848 (mm-40) cc_final: 0.6519 (mm-40) REVERT: C 473 GLN cc_start: 0.6733 (mt0) cc_final: 0.6523 (mt0) outliers start: 44 outliers final: 32 residues processed: 235 average time/residue: 0.1090 time to fit residues: 39.7903 Evaluate side-chains 218 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 990 CYS Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 168 GLN Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 507 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 431 ASN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.120782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.090968 restraints weight = 31632.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093837 restraints weight = 15229.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095662 restraints weight = 9915.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.096770 restraints weight = 7648.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.097462 restraints weight = 6546.700| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14950 Z= 0.124 Angle : 0.593 15.469 20290 Z= 0.290 Chirality : 0.038 0.140 2261 Planarity : 0.004 0.049 2504 Dihedral : 11.278 146.252 2025 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.97 % Allowed : 19.71 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.20), residues: 1760 helix: 1.86 (0.15), residues: 1126 sheet: 0.40 (0.64), residues: 66 loop : -0.37 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 945 TYR 0.017 0.001 TYR B 893 PHE 0.014 0.001 PHE C 398 TRP 0.029 0.001 TRP C 412 HIS 0.007 0.001 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (14950) covalent geometry : angle 0.59339 / 0.29 (20290) hydrogen bonds : bond 0.03925 / 2.62 ( 875) hydrogen bonds : angle 3.85669 / 2.81 ( 2535) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 710 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8335 (mm-40) REVERT: B 740 MET cc_start: 0.8327 (mmp) cc_final: 0.8068 (tpp) REVERT: B 915 ASN cc_start: 0.8991 (t0) cc_final: 0.8599 (t0) REVERT: B 945 ARG cc_start: 0.9255 (ttp-110) cc_final: 0.9009 (ttm110) REVERT: B 994 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7540 (mt-10) REVERT: B 998 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7680 (mp0) REVERT: A 264 GLU cc_start: 0.8508 (tt0) cc_final: 0.8188 (tm-30) REVERT: A 489 LYS cc_start: 0.8530 (mmtm) cc_final: 0.7744 (tptt) REVERT: A 555 ASP cc_start: 0.8995 (m-30) cc_final: 0.8748 (m-30) REVERT: D 123 MET cc_start: 0.8191 (tmm) cc_final: 0.7846 (tmm) REVERT: D 262 MET cc_start: 0.8298 (mmm) cc_final: 0.7166 (tmm) REVERT: D 283 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.7667 (m-70) REVERT: C 168 GLN cc_start: 0.8820 (tm-30) cc_final: 0.8321 (tm-30) REVERT: C 201 GLN cc_start: 0.6870 (mm-40) cc_final: 0.6520 (mm-40) outliers start: 31 outliers final: 25 residues processed: 224 average time/residue: 0.1060 time to fit residues: 36.3824 Evaluate side-chains 215 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 990 CYS Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 493 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 149 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1008 GLN B1049 HIS ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.121412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093706 restraints weight = 31700.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.094595 restraints weight = 15055.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095014 restraints weight = 11485.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095246 restraints weight = 10565.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.095490 restraints weight = 10178.782| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14950 Z= 0.123 Angle : 0.610 15.005 20290 Z= 0.292 Chirality : 0.038 0.142 2261 Planarity : 0.004 0.048 2504 Dihedral : 11.290 147.338 2025 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.91 % Allowed : 20.28 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.20), residues: 1760 helix: 1.93 (0.15), residues: 1124 sheet: 0.44 (0.64), residues: 66 loop : -0.36 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 790 TYR 0.028 0.001 TYR D 439 PHE 0.025 0.001 PHE C 519 TRP 0.031 0.001 TRP C 412 HIS 0.007 0.001 HIS D 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (14950) covalent geometry : angle 0.61016 / 0.29 (20290) hydrogen bonds : bond 0.03795 / 2.52 ( 875) hydrogen bonds : angle 3.80552 / 2.77 ( 2535) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 710 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8206 (mm-40) REVERT: B 740 MET cc_start: 0.8350 (mmp) cc_final: 0.8083 (tpp) REVERT: B 790 ARG cc_start: 0.8356 (mtt90) cc_final: 0.7762 (mtt180) REVERT: B 894 ARG cc_start: 0.8681 (ttt-90) cc_final: 0.8471 (tpp-160) REVERT: B 915 ASN cc_start: 0.8992 (t0) cc_final: 0.8600 (t0) REVERT: B 926 HIS cc_start: 0.8893 (m90) cc_final: 0.8587 (m90) REVERT: B 945 ARG cc_start: 0.9272 (ttp-110) cc_final: 0.8993 (ttm110) REVERT: B 994 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7528 (mt-10) REVERT: B 998 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7706 (mp0) REVERT: A 264 GLU cc_start: 0.8550 (tt0) cc_final: 0.7942 (tm-30) REVERT: A 489 LYS cc_start: 0.8578 (mmtm) cc_final: 0.7746 (tptt) REVERT: A 555 ASP cc_start: 0.9018 (m-30) cc_final: 0.8772 (m-30) REVERT: D 262 MET cc_start: 0.8254 (mmm) cc_final: 0.7122 (tmm) REVERT: D 283 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.7929 (m-70) REVERT: C 168 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8336 (tm-30) REVERT: C 201 GLN cc_start: 0.6935 (mm-40) cc_final: 0.6559 (mm-40) REVERT: C 473 GLN cc_start: 0.6634 (mt0) cc_final: 0.6404 (mt0) outliers start: 30 outliers final: 26 residues processed: 215 average time/residue: 0.1075 time to fit residues: 35.3971 Evaluate side-chains 221 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 990 CYS Chi-restraints excluded: chain B residue 1049 HIS Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 493 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 18 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1008 GLN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.093714 restraints weight = 31895.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095407 restraints weight = 14986.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.096340 restraints weight = 10110.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.096700 restraints weight = 9732.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096876 restraints weight = 8390.054| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14950 Z= 0.119 Angle : 0.608 15.339 20290 Z= 0.292 Chirality : 0.038 0.139 2261 Planarity : 0.004 0.049 2504 Dihedral : 11.297 147.652 2025 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.84 % Allowed : 20.60 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.20), residues: 1760 helix: 1.96 (0.15), residues: 1125 sheet: 0.45 (0.65), residues: 66 loop : -0.35 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 790 TYR 0.022 0.001 TYR B 893 PHE 0.014 0.001 PHE B 703 TRP 0.033 0.001 TRP C 412 HIS 0.009 0.001 HIS B1049 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (14950) covalent geometry : angle 0.60796 / 0.29 (20290) hydrogen bonds : bond 0.03684 / 2.46 ( 875) hydrogen bonds : angle 3.76686 / 2.74 ( 2535) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 202 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 710 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8278 (mm-40) REVERT: B 740 MET cc_start: 0.8355 (mmp) cc_final: 0.8076 (tpp) REVERT: B 790 ARG cc_start: 0.8300 (mtt90) cc_final: 0.7724 (mtt180) REVERT: B 894 ARG cc_start: 0.8673 (ttt-90) cc_final: 0.8472 (tpp-160) REVERT: B 915 ASN cc_start: 0.8986 (t0) cc_final: 0.8594 (t0) REVERT: B 926 HIS cc_start: 0.8884 (m90) cc_final: 0.8549 (m90) REVERT: B 945 ARG cc_start: 0.9259 (ttp-110) cc_final: 0.8980 (ttm110) REVERT: B 994 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 998 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7694 (mp0) REVERT: A 264 GLU cc_start: 0.8545 (tt0) cc_final: 0.7946 (tm-30) REVERT: A 489 LYS cc_start: 0.8555 (mmtm) cc_final: 0.7731 (tptt) REVERT: A 555 ASP cc_start: 0.9007 (m-30) cc_final: 0.8762 (m-30) REVERT: D 123 MET cc_start: 0.8185 (tmm) cc_final: 0.7833 (tmm) REVERT: D 262 MET cc_start: 0.8212 (mmm) cc_final: 0.7156 (tmm) REVERT: D 283 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7898 (m-70) REVERT: C 168 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8346 (tm-30) REVERT: C 201 GLN cc_start: 0.6878 (mm-40) cc_final: 0.6498 (mm-40) outliers start: 29 outliers final: 26 residues processed: 221 average time/residue: 0.0956 time to fit residues: 32.3425 Evaluate side-chains 218 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 990 CYS Chi-restraints excluded: chain B residue 1049 HIS Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 493 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 152 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 0.0980 chunk 136 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.122547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.095845 restraints weight = 30642.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.097410 restraints weight = 13999.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098117 restraints weight = 9706.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.098277 restraints weight = 8485.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.098598 restraints weight = 8059.767| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 14950 Z= 0.110 Angle : 0.615 15.115 20290 Z= 0.291 Chirality : 0.038 0.143 2261 Planarity : 0.004 0.048 2504 Dihedral : 11.312 148.723 2025 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.53 % Allowed : 21.17 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.20), residues: 1760 helix: 2.04 (0.15), residues: 1122 sheet: 0.67 (0.67), residues: 57 loop : -0.26 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 790 TYR 0.023 0.001 TYR B 893 PHE 0.013 0.001 PHE A 413 TRP 0.036 0.001 TRP C 412 HIS 0.003 0.001 HIS D 339 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (14950) covalent geometry : angle 0.61512 / 0.29 (20290) hydrogen bonds : bond 0.03447 / 2.30 ( 875) hydrogen bonds : angle 3.69189 / 2.69 ( 2535) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3520 Ramachandran restraints generated. 1760 Oldfield, 0 Emsley, 1760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 699 ASP cc_start: 0.8792 (m-30) cc_final: 0.8463 (m-30) REVERT: B 710 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8209 (mm-40) REVERT: B 740 MET cc_start: 0.8361 (mmp) cc_final: 0.8049 (tpp) REVERT: B 915 ASN cc_start: 0.8936 (t0) cc_final: 0.8576 (t0) REVERT: B 926 HIS cc_start: 0.8830 (m90) cc_final: 0.8517 (m90) REVERT: B 945 ARG cc_start: 0.9225 (ttp-110) cc_final: 0.8988 (ttm110) REVERT: B 994 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7535 (mt-10) REVERT: B 998 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7700 (mp0) REVERT: A 264 GLU cc_start: 0.8537 (tt0) cc_final: 0.8009 (tm-30) REVERT: A 489 LYS cc_start: 0.8528 (mmtm) cc_final: 0.7737 (tptt) REVERT: A 555 ASP cc_start: 0.8979 (m-30) cc_final: 0.8727 (m-30) REVERT: D 123 MET cc_start: 0.8150 (tmm) cc_final: 0.7801 (tmm) REVERT: D 262 MET cc_start: 0.8152 (mmm) cc_final: 0.7176 (tmm) REVERT: D 283 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7893 (m-70) REVERT: C 168 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8336 (tm-30) REVERT: C 201 GLN cc_start: 0.6895 (mm-40) cc_final: 0.6514 (mm-40) REVERT: C 557 MET cc_start: 0.8061 (mmp) cc_final: 0.7177 (mtm) outliers start: 24 outliers final: 22 residues processed: 227 average time/residue: 0.1098 time to fit residues: 38.2469 Evaluate side-chains 223 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 876 ILE Chi-restraints excluded: chain B residue 944 MET Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain A residue 241 HIS Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 550 CYS Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 283 HIS Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 241 HIS Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 431 ASN Chi-restraints excluded: chain C residue 466 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.0980 chunk 136 optimal weight: 0.5980 chunk 78 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.120830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.092392 restraints weight = 31685.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.094202 restraints weight = 15055.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.095028 restraints weight = 10004.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095460 restraints weight = 9729.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.095588 restraints weight = 8421.337| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14950 Z= 0.145 Angle : 0.639 14.552 20290 Z= 0.306 Chirality : 0.039 0.167 2261 Planarity : 0.004 0.049 2504 Dihedral : 11.276 147.124 2025 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.78 % Allowed : 20.66 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.20), residues: 1760 helix: 2.02 (0.15), residues: 1121 sheet: 0.42 (0.60), residues: 71 loop : -0.31 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 246 TYR 0.025 0.001 TYR B 893 PHE 0.034 0.001 PHE C 519 TRP 0.034 0.001 TRP C 412 HIS 0.003 0.001 HIS C 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (14950) covalent geometry : angle 0.63868 / 0.31 (20290) hydrogen bonds : bond 0.03718 / 2.48 ( 875) hydrogen bonds : angle 3.77716 / 2.75 ( 2535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2388.67 seconds wall clock time: 42 minutes 12.03 seconds (2532.03 seconds total)