Starting phenix.real_space_refine on Thu Feb 5 04:31:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9upf_64394/02_2026/9upf_64394.cif Found real_map, /net/cci-nas-00/data/ceres_data/9upf_64394/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9upf_64394/02_2026/9upf_64394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9upf_64394/02_2026/9upf_64394.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9upf_64394/02_2026/9upf_64394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9upf_64394/02_2026/9upf_64394.map" } 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-2.0-5952/lib/python3.9/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, 24 Unusual residues: {' CA': 2} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 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: 3.21, per 1000 atoms: 0.22 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: 1.08 Conformation dependent library (CDL) restraints added in 388.7 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: 0.43 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: 2.32 Time building geometry restraints manager: 1.49 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: 8.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.530 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 covalent geometry : bond 0.00456 (14950) covalent geometry : angle 0.85456 (20290) hydrogen bonds : bond 0.24642 ( 875) hydrogen bonds : angle 6.67608 ( 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 : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.7746 (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: 0.7075 (tmm) REVERT: D 384 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7428 (mt-10) REVERT: D 386 TYR cc_start: 0.7746 (m-10) cc_final: 0.7068 (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: 0.7253 (p90) REVERT: C 557 MET cc_start: 0.7959 (mmp) cc_final: 0.7431 (mtm) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.1020 time to fit residues: 37.9741 Evaluate side-chains 215 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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: 0.7980 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: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 805 ASN B 864 ASN ** 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 = 0.3766 r_free = 0.3766 target = 0.122623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.094508 restraints weight = 31171.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.096153 restraints weight = 13744.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.097013 restraints weight = 9442.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.097440 restraints weight = 8946.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097542 restraints weight = 7806.419| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14950 Z= 0.143 Angle : 0.610 14.620 20290 Z= 0.311 Chirality : 0.038 0.143 2261 Planarity : 0.004 0.052 2504 Dihedral : 11.413 150.240 2025 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.16 % Allowed : 16.08 % Favored : 81.75 % 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: 1.21 (0.19), residues: 1760 helix: 1.35 (0.15), residues: 1124 sheet: 0.75 (0.63), residues: 68 loop : -0.18 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 140 TYR 0.023 0.001 TYR C 319 PHE 0.023 0.001 PHE C 519 TRP 0.018 0.001 TRP C 412 HIS 0.005 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00301 (14950) covalent geometry : angle 0.61016 (20290) hydrogen bonds : bond 0.05166 ( 875) hydrogen bonds : angle 4.41345 ( 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 254 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 893 TYR cc_start: 0.8814 (t80) cc_final: 0.8579 (t80) REVERT: B 896 CYS cc_start: 0.8042 (m) cc_final: 0.7768 (t) REVERT: B 915 ASN cc_start: 0.8929 (t0) cc_final: 0.8530 (t0) REVERT: B 994 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7692 (mt-10) REVERT: B 998 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7541 (mp0) REVERT: A 405 MET cc_start: 0.8460 (tpp) cc_final: 0.8161 (mtt) REVERT: A 489 LYS cc_start: 0.8405 (mmtm) cc_final: 0.7591 (tptt) REVERT: A 555 ASP cc_start: 0.9036 (m-30) cc_final: 0.8754 (m-30) REVERT: D 113 TRP cc_start: 0.7823 (t60) cc_final: 0.7328 (t-100) REVERT: D 262 MET cc_start: 0.8396 (mmm) cc_final: 0.7038 (tmm) REVERT: C 168 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8402 (tm-30) REVERT: C 480 TYR cc_start: 0.7629 (p90) cc_final: 0.7415 (p90) REVERT: C 494 ILE cc_start: 0.9378 (mt) cc_final: 0.9139 (mp) REVERT: C 557 MET cc_start: 0.7929 (mmp) cc_final: 0.7495 (mtm) outliers start: 34 outliers final: 18 residues processed: 238 average time/residue: 0.0903 time to fit residues: 33.3982 Evaluate side-chains 215 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 132 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 94 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 121 optimal weight: 0.0040 chunk 117 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 283 HIS C 386 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.125760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.097878 restraints weight = 31333.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.098582 restraints weight = 14471.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099016 restraints weight = 12124.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.099304 restraints weight = 10456.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.099579 restraints weight = 9678.782| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 14950 Z= 0.115 Angle : 0.556 14.914 20290 Z= 0.276 Chirality : 0.037 0.168 2261 Planarity : 0.004 0.048 2504 Dihedral : 11.319 149.225 2025 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.72 % Allowed : 16.97 % Favored : 81.31 % 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: 1.74 (0.15), residues: 1129 sheet: 0.62 (0.63), residues: 67 loop : -0.10 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 426 TYR 0.017 0.001 TYR C 319 PHE 0.022 0.001 PHE C 519 TRP 0.020 0.001 TRP C 412 HIS 0.002 0.000 HIS D 283 Details of bonding type rmsd covalent geometry : bond 0.00234 (14950) covalent geometry : angle 0.55572 (20290) hydrogen bonds : bond 0.04397 ( 875) hydrogen bonds : angle 4.09690 ( 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 242 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 665 MET cc_start: 0.8100 (tpp) cc_final: 0.7889 (tpp) REVERT: B 740 MET cc_start: 0.8317 (mmp) cc_final: 0.7996 (tpp) REVERT: B 790 ARG cc_start: 0.8346 (mtt90) cc_final: 0.7942 (mtt90) REVERT: B 893 TYR cc_start: 0.8770 (t80) cc_final: 0.8567 (t80) REVERT: B 896 CYS cc_start: 0.8159 (m) cc_final: 0.7829 (t) REVERT: B 915 ASN cc_start: 0.8910 (t0) cc_final: 0.8534 (t0) REVERT: B 994 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7717 (mt-10) REVERT: B 998 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7613 (mp0) REVERT: A 215 TYR cc_start: 0.8515 (t80) cc_final: 0.8289 (t80) REVERT: A 386 GLN cc_start: 0.8343 (mm110) cc_final: 0.8042 (tp40) REVERT: A 555 ASP cc_start: 0.8961 (m-30) cc_final: 0.8677 (m-30) REVERT: D 262 MET cc_start: 0.8325 (mmm) cc_final: 0.7138 (tmm) REVERT: C 473 GLN cc_start: 0.6697 (mt0) cc_final: 0.6480 (mt0) outliers start: 27 outliers final: 17 residues processed: 231 average time/residue: 0.0953 time to fit residues: 34.2840 Evaluate side-chains 211 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 312 ILE Chi-restraints excluded: chain A residue 396 MET 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 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 554 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 137 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 683 GLN A 419 ASN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.117888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.087904 restraints weight = 32158.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.090648 restraints weight = 15576.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.092411 restraints weight = 10170.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.093489 restraints weight = 7890.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.094042 restraints weight = 6784.589| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14950 Z= 0.258 Angle : 0.671 14.485 20290 Z= 0.343 Chirality : 0.042 0.180 2261 Planarity : 0.005 0.082 2504 Dihedral : 11.239 148.776 2025 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.43 % Allowed : 17.86 % Favored : 78.70 % 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: 1.37 (0.20), residues: 1760 helix: 1.60 (0.15), residues: 1121 sheet: 0.59 (0.66), residues: 62 loop : -0.35 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 483 TYR 0.027 0.002 TYR C 329 PHE 0.016 0.002 PHE C 398 TRP 0.019 0.002 TRP C 412 HIS 0.005 0.001 HIS D 135 Details of bonding type rmsd covalent geometry : bond 0.00596 (14950) covalent geometry : angle 0.67112 (20290) hydrogen bonds : bond 0.05066 ( 875) hydrogen bonds : angle 4.27684 ( 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 251 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 710 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8366 (mm-40) REVERT: B 896 CYS cc_start: 0.8278 (m) cc_final: 0.7904 (t) REVERT: B 915 ASN cc_start: 0.9055 (t0) cc_final: 0.8619 (t0) REVERT: B 994 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 998 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7560 (mp0) REVERT: B 1068 HIS cc_start: 0.7633 (m90) cc_final: 0.7379 (m90) REVERT: A 462 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7530 (mt) REVERT: A 489 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7620 (tptt) REVERT: A 555 ASP cc_start: 0.9026 (m-30) cc_final: 0.8750 (m-30) REVERT: D 262 MET cc_start: 0.8444 (mmm) cc_final: 0.7197 (tmm) REVERT: D 283 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7702 (m-70) REVERT: C 133 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8931 (mp) outliers start: 54 outliers final: 28 residues processed: 229 average time/residue: 0.0882 time to fit residues: 30.8292 Evaluate side-chains 218 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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 194 LEU 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 396 MET Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 489 LYS 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 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 269 TYR 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: 4.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 39 optimal weight: 0.6980 chunk 172 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN D 183 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.121453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.091529 restraints weight = 31598.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.094417 restraints weight = 15094.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.096255 restraints weight = 9733.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.097394 restraints weight = 7495.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.097976 restraints weight = 6391.458| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14950 Z= 0.122 Angle : 0.576 15.739 20290 Z= 0.282 Chirality : 0.038 0.141 2261 Planarity : 0.004 0.064 2504 Dihedral : 11.293 146.696 2025 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.42 % Allowed : 18.63 % Favored : 78.96 % 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: 1.83 (0.15), residues: 1131 sheet: 0.51 (0.59), residues: 76 loop : -0.34 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 140 TYR 0.018 0.001 TYR B 892 PHE 0.015 0.001 PHE D 177 TRP 0.027 0.001 TRP C 412 HIS 0.012 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00264 (14950) covalent geometry : angle 0.57619 (20290) hydrogen bonds : bond 0.04020 ( 875) hydrogen bonds : angle 3.91448 ( 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 247 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 209 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 665 MET cc_start: 0.8180 (tpp) cc_final: 0.7976 (tpp) REVERT: B 915 ASN cc_start: 0.8990 (t0) cc_final: 0.8598 (t0) REVERT: B 937 MET cc_start: 0.8603 (mmm) cc_final: 0.7872 (mmp) REVERT: B 945 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.8962 (ttm110) REVERT: B 994 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7464 (mt-10) REVERT: B 998 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7698 (mp0) REVERT: B 1083 MET cc_start: 0.7976 (tmm) cc_final: 0.7675 (tmm) REVERT: A 264 GLU cc_start: 0.8557 (tt0) cc_final: 0.8089 (tm-30) REVERT: A 489 LYS cc_start: 0.8419 (mmtm) cc_final: 0.7557 (tptt) REVERT: A 555 ASP cc_start: 0.8988 (m-30) cc_final: 0.8742 (m-30) REVERT: D 123 MET cc_start: 0.8070 (tmm) cc_final: 0.7728 (tmm) REVERT: D 262 MET cc_start: 0.8343 (mmm) cc_final: 0.7133 (tmm) REVERT: D 283 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.7781 (m-70) REVERT: C 473 GLN cc_start: 0.6677 (mt0) cc_final: 0.6407 (mt0) outliers start: 38 outliers final: 26 residues processed: 234 average time/residue: 0.0918 time to fit residues: 32.9791 Evaluate side-chains 217 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 930 MET Chi-restraints excluded: chain B residue 945 ARG Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain A residue 176 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 359 ILE Chi-restraints excluded: chain A residue 396 MET 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 570 LEU Chi-restraints excluded: chain A residue 579 MET 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 366 THR Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 507 VAL 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: 0.2980 chunk 111 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN ** 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 = 0.3759 r_free = 0.3759 target = 0.122077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.094357 restraints weight = 31723.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095839 restraints weight = 13498.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096416 restraints weight = 9843.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096730 restraints weight = 9130.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.096903 restraints weight = 8515.693| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14950 Z= 0.121 Angle : 0.577 15.589 20290 Z= 0.282 Chirality : 0.038 0.140 2261 Planarity : 0.004 0.055 2504 Dihedral : 11.260 146.778 2025 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.35 % Allowed : 18.82 % Favored : 78.83 % 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: 1.72 (0.20), residues: 1760 helix: 1.91 (0.15), residues: 1132 sheet: 0.46 (0.64), residues: 66 loop : -0.32 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 471 TYR 0.021 0.001 TYR D 439 PHE 0.020 0.001 PHE C 398 TRP 0.018 0.001 TRP C 412 HIS 0.018 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00261 (14950) covalent geometry : angle 0.57654 (20290) hydrogen bonds : bond 0.03832 ( 875) hydrogen bonds : angle 3.82531 ( 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 246 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 710 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8250 (mm-40) REVERT: B 790 ARG cc_start: 0.8359 (mtt90) cc_final: 0.7796 (mtt90) REVERT: B 896 CYS cc_start: 0.8460 (t) cc_final: 0.8221 (t) REVERT: B 915 ASN cc_start: 0.8986 (t0) cc_final: 0.8587 (t0) REVERT: B 937 MET cc_start: 0.8622 (mmm) cc_final: 0.8347 (mmt) REVERT: B 994 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7460 (mt-10) REVERT: B 998 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7717 (mp0) REVERT: A 264 GLU cc_start: 0.8491 (tt0) cc_final: 0.8144 (tm-30) REVERT: A 489 LYS cc_start: 0.8476 (mmtm) cc_final: 0.7719 (tptt) REVERT: A 555 ASP cc_start: 0.8978 (m-30) cc_final: 0.8728 (m-30) REVERT: D 262 MET cc_start: 0.8282 (mmm) cc_final: 0.7155 (tmm) REVERT: D 283 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.8123 (m-70) REVERT: C 168 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8290 (tm-30) REVERT: C 473 GLN cc_start: 0.6732 (mt0) cc_final: 0.6484 (mt0) outliers start: 37 outliers final: 24 residues processed: 232 average time/residue: 0.0938 time to fit residues: 34.0374 Evaluate side-chains 218 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 990 CYS Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain A residue 144 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 396 MET Chi-restraints excluded: chain A residue 423 VAL 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 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 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 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: 3.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 83 optimal weight: 0.0170 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1049 HIS A 431 ASN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.118138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.090059 restraints weight = 31718.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.091624 restraints weight = 15083.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.091829 restraints weight = 10223.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.092742 restraints weight = 10138.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092818 restraints weight = 8928.297| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14950 Z= 0.199 Angle : 0.649 15.049 20290 Z= 0.317 Chirality : 0.040 0.138 2261 Planarity : 0.004 0.053 2504 Dihedral : 11.227 146.032 2025 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.35 % Allowed : 19.39 % Favored : 78.26 % 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: 1.84 (0.15), residues: 1121 sheet: 0.49 (0.61), residues: 71 loop : -0.43 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 471 TYR 0.019 0.002 TYR C 329 PHE 0.023 0.002 PHE C 519 TRP 0.016 0.001 TRP C 412 HIS 0.005 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00456 (14950) covalent geometry : angle 0.64884 (20290) hydrogen bonds : bond 0.04293 ( 875) hydrogen bonds : angle 3.98552 ( 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 233 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 665 MET cc_start: 0.8239 (tpp) cc_final: 0.8026 (tpp) REVERT: B 710 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8435 (mm-40) REVERT: B 915 ASN cc_start: 0.9016 (t0) cc_final: 0.8605 (t0) REVERT: B 937 MET cc_start: 0.8639 (mmm) cc_final: 0.8018 (mmm) REVERT: B 998 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7660 (mp0) REVERT: A 264 GLU cc_start: 0.8479 (tt0) cc_final: 0.8152 (tm-30) REVERT: A 489 LYS cc_start: 0.8528 (mmtm) cc_final: 0.7666 (tptt) REVERT: A 555 ASP cc_start: 0.9041 (m-30) cc_final: 0.8806 (m-30) REVERT: D 123 MET cc_start: 0.8239 (tmm) cc_final: 0.7840 (tmm) REVERT: D 262 MET cc_start: 0.8382 (mmm) cc_final: 0.7168 (tmm) REVERT: D 283 HIS cc_start: 0.8455 (m-70) cc_final: 0.8182 (m-70) REVERT: C 168 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8360 (tm-30) REVERT: C 473 GLN cc_start: 0.6838 (mt0) cc_final: 0.6535 (mt0) REVERT: C 557 MET cc_start: 0.8178 (mmp) cc_final: 0.7250 (mtm) outliers start: 37 outliers final: 30 residues processed: 219 average time/residue: 0.0981 time to fit residues: 33.4301 Evaluate side-chains 217 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 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 1049 HIS Chi-restraints excluded: chain B residue 1062 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 423 VAL 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 570 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 260 THR 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 296 ILE Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 367 ILE 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: 0.9990 chunk 97 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 134 optimal weight: 0.2980 chunk 68 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.121134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.091531 restraints weight = 31521.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.094440 restraints weight = 15094.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096276 restraints weight = 9746.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.097396 restraints weight = 7508.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.097948 restraints weight = 6432.745| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14950 Z= 0.117 Angle : 0.599 14.893 20290 Z= 0.289 Chirality : 0.038 0.140 2261 Planarity : 0.004 0.049 2504 Dihedral : 11.289 146.957 2025 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.84 % Allowed : 20.47 % Favored : 77.69 % 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: 1.77 (0.20), residues: 1760 helix: 1.96 (0.15), residues: 1123 sheet: 0.91 (0.73), residues: 47 loop : -0.30 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 471 TYR 0.037 0.001 TYR D 439 PHE 0.012 0.001 PHE C 398 TRP 0.015 0.001 TRP C 412 HIS 0.010 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00249 (14950) covalent geometry : angle 0.59896 (20290) hydrogen bonds : bond 0.03773 ( 875) hydrogen bonds : angle 3.79472 ( 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: 29 poor density : 196 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 665 MET cc_start: 0.8168 (tpp) cc_final: 0.7951 (tpp) REVERT: B 790 ARG cc_start: 0.8394 (mtt90) cc_final: 0.7735 (mtt180) REVERT: B 915 ASN cc_start: 0.8992 (t0) cc_final: 0.8597 (t0) REVERT: B 937 MET cc_start: 0.8525 (mmm) cc_final: 0.7769 (mmm) REVERT: B 994 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7484 (mt-10) REVERT: B 998 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7680 (mp0) REVERT: A 264 GLU cc_start: 0.8453 (tt0) cc_final: 0.8142 (tm-30) REVERT: A 489 LYS cc_start: 0.8479 (mmtm) cc_final: 0.7688 (tptt) REVERT: D 123 MET cc_start: 0.8143 (tmm) cc_final: 0.7736 (tmm) REVERT: D 262 MET cc_start: 0.8251 (mmm) cc_final: 0.7163 (tmm) REVERT: C 168 GLN cc_start: 0.8846 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 473 GLN cc_start: 0.6702 (mt0) cc_final: 0.6440 (mt0) REVERT: C 555 ASP cc_start: 0.8250 (m-30) cc_final: 0.8015 (m-30) REVERT: C 557 MET cc_start: 0.8096 (mmp) cc_final: 0.7893 (mmt) outliers start: 29 outliers final: 25 residues processed: 215 average time/residue: 0.0931 time to fit residues: 31.1219 Evaluate side-chains 214 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 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 396 MET Chi-restraints excluded: chain A residue 423 VAL 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 570 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ILE 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 493 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 18 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.121066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.093201 restraints weight = 31665.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.094789 restraints weight = 14601.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095086 restraints weight = 9970.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.095590 restraints weight = 9787.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095754 restraints weight = 8700.013| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14950 Z= 0.123 Angle : 0.599 14.876 20290 Z= 0.289 Chirality : 0.038 0.148 2261 Planarity : 0.004 0.047 2504 Dihedral : 11.292 146.729 2025 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.59 % Allowed : 20.53 % Favored : 77.88 % 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: 1.99 (0.15), residues: 1122 sheet: 1.02 (0.73), residues: 47 loop : -0.28 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 471 TYR 0.027 0.001 TYR D 439 PHE 0.013 0.001 PHE C 398 TRP 0.011 0.001 TRP C 412 HIS 0.004 0.001 HIS B1049 Details of bonding type rmsd covalent geometry : bond 0.00273 (14950) covalent geometry : angle 0.59943 (20290) hydrogen bonds : bond 0.03715 ( 875) hydrogen bonds : angle 3.75756 ( 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 220 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 665 MET cc_start: 0.8200 (tpp) cc_final: 0.7987 (tpp) REVERT: B 710 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8323 (mm-40) REVERT: B 790 ARG cc_start: 0.8415 (mtt90) cc_final: 0.7754 (mtt90) REVERT: B 915 ASN cc_start: 0.8989 (t0) cc_final: 0.8592 (t0) REVERT: B 926 HIS cc_start: 0.8891 (m90) cc_final: 0.8606 (m90) REVERT: B 935 GLU cc_start: 0.8888 (pp20) cc_final: 0.8674 (pp20) REVERT: B 937 MET cc_start: 0.8489 (mmm) cc_final: 0.7401 (mmt) REVERT: B 945 ARG cc_start: 0.9248 (ttm110) cc_final: 0.8858 (ttm110) REVERT: B 994 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7548 (mt-10) REVERT: B 998 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7708 (mp0) REVERT: A 264 GLU cc_start: 0.8488 (tt0) cc_final: 0.8137 (tm-30) REVERT: A 489 LYS cc_start: 0.8497 (mmtm) cc_final: 0.7638 (tptt) REVERT: D 123 MET cc_start: 0.8093 (tmm) cc_final: 0.7677 (tmm) REVERT: D 262 MET cc_start: 0.8225 (mmm) cc_final: 0.7132 (tmm) REVERT: D 283 HIS cc_start: 0.8437 (m-70) cc_final: 0.7939 (m170) REVERT: D 412 TYR cc_start: 0.7223 (p90) cc_final: 0.6991 (p90) REVERT: C 168 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8351 (tm-30) REVERT: C 473 GLN cc_start: 0.6790 (mt0) cc_final: 0.6538 (mt0) REVERT: C 555 ASP cc_start: 0.8292 (m-30) cc_final: 0.8031 (m-30) REVERT: C 557 MET cc_start: 0.8083 (mmp) cc_final: 0.7871 (mmt) outliers start: 25 outliers final: 23 residues processed: 211 average time/residue: 0.0913 time to fit residues: 29.4788 Evaluate side-chains 210 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 245 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 423 VAL 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 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 368 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 367 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 153 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3753 r_free = 0.3753 target = 0.120895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.092178 restraints weight = 30665.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.094997 restraints weight = 14458.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.096818 restraints weight = 9207.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097940 restraints weight = 7012.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.098534 restraints weight = 5952.383| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3118 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= 0.120 Angle : 0.601 14.426 20290 Z= 0.289 Chirality : 0.038 0.148 2261 Planarity : 0.004 0.049 2504 Dihedral : 11.283 146.871 2025 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.65 % Allowed : 20.85 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.20), residues: 1760 helix: 2.03 (0.15), residues: 1120 sheet: 0.83 (0.70), residues: 53 loop : -0.32 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 471 TYR 0.025 0.001 TYR B 893 PHE 0.033 0.001 PHE C 519 TRP 0.014 0.001 TRP C 412 HIS 0.003 0.000 HIS C 287 Details of bonding type rmsd covalent geometry : bond 0.00265 (14950) covalent geometry : angle 0.60118 (20290) hydrogen bonds : bond 0.03600 ( 875) hydrogen bonds : angle 3.72476 ( 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 221 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 665 MET cc_start: 0.8164 (tpp) cc_final: 0.7944 (tpp) REVERT: B 790 ARG cc_start: 0.8369 (mtt90) cc_final: 0.7834 (mtt90) REVERT: B 915 ASN cc_start: 0.8989 (t0) cc_final: 0.8591 (t0) REVERT: B 926 HIS cc_start: 0.8839 (m90) cc_final: 0.8536 (m90) REVERT: B 937 MET cc_start: 0.8425 (mmm) cc_final: 0.7231 (mmt) REVERT: B 945 ARG cc_start: 0.9191 (ttm110) cc_final: 0.8805 (ttm110) REVERT: B 994 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7527 (mt-10) REVERT: B 998 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7682 (mp0) REVERT: A 264 GLU cc_start: 0.8450 (tt0) cc_final: 0.8043 (tm-30) REVERT: A 489 LYS cc_start: 0.8424 (mmtm) cc_final: 0.7470 (tptt) REVERT: D 123 MET cc_start: 0.8003 (tmm) cc_final: 0.7620 (tmm) REVERT: D 262 MET cc_start: 0.8191 (mmm) cc_final: 0.7146 (tmm) REVERT: D 412 TYR cc_start: 0.7187 (p90) cc_final: 0.6947 (p90) REVERT: C 168 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8368 (tm-30) REVERT: C 473 GLN cc_start: 0.6771 (mt0) cc_final: 0.6532 (mt0) REVERT: C 518 CYS cc_start: 0.7955 (p) cc_final: 0.7514 (p) REVERT: C 555 ASP cc_start: 0.8265 (m-30) cc_final: 0.7959 (m-30) REVERT: C 557 MET cc_start: 0.8106 (mmp) cc_final: 0.7197 (mtm) outliers start: 26 outliers final: 24 residues processed: 213 average time/residue: 0.0960 time to fit residues: 31.6038 Evaluate side-chains 214 residues out of total 1573 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain A residue 194 LEU 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 396 MET Chi-restraints excluded: chain A residue 423 VAL 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 570 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 368 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain C residue 296 ILE Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 367 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 0.3980 chunk 136 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.121878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.094638 restraints weight = 31473.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.096080 restraints weight = 13524.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.096743 restraints weight = 9969.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097063 restraints weight = 9065.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097194 restraints weight = 8468.355| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3173 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= 0.117 Angle : 0.610 14.382 20290 Z= 0.292 Chirality : 0.038 0.156 2261 Planarity : 0.004 0.049 2504 Dihedral : 11.295 147.089 2025 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.59 % Allowed : 20.85 % 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: 1.86 (0.20), residues: 1760 helix: 2.04 (0.15), residues: 1121 sheet: 0.89 (0.70), residues: 53 loop : -0.30 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 471 TYR 0.029 0.001 TYR B 893 PHE 0.034 0.001 PHE C 519 TRP 0.014 0.001 TRP C 412 HIS 0.018 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00255 (14950) covalent geometry : angle 0.61004 (20290) hydrogen bonds : bond 0.03519 ( 875) hydrogen bonds : angle 3.70720 ( 2535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2101.85 seconds wall clock time: 37 minutes 12.38 seconds (2232.38 seconds total)