Starting phenix.real_space_refine on Wed Jan 14 20:04:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m2x_23636/01_2026/7m2x_23636.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m2x_23636/01_2026/7m2x_23636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m2x_23636/01_2026/7m2x_23636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m2x_23636/01_2026/7m2x_23636.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m2x_23636/01_2026/7m2x_23636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m2x_23636/01_2026/7m2x_23636.map" } resolution = 3.6 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= 0.005 sd= 0.773 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 80 5.16 5 C 11906 2.51 5 N 3140 2.21 5 O 3574 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18704 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3474 Classifications: {'peptide': 444} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 423} Chain breaks: 1 Chain: "B" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3486 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 1 Chain: "C" Number of atoms: 5853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5853 Classifications: {'peptide': 701} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 675} Chain breaks: 5 Chain: "D" Number of atoms: 5560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5560 Classifications: {'peptide': 673} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 653} Chain breaks: 1 Chain: "U" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 275 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 2, 'TRANS': 30} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.22, per 1000 atoms: 0.23 Number of scatterers: 18704 At special positions: 0 Unit cell: (141.83, 138.993, 164.523, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 4 15.00 O 3574 8.00 N 3140 7.00 C 11906 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: 1.85 Conformation dependent library (CDL) restraints added in 887.2 milliseconds 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4402 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 11 sheets defined 63.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 11 through 29 Processing helix chain 'A' and resid 72 through 81 removed outlier: 4.322A pdb=" N ILE A 76 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 144 through 162 removed outlier: 3.807A pdb=" N ASP A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 198 removed outlier: 5.383A pdb=" N TYR A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 removed outlier: 4.330A pdb=" N LYS A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 239 through 244 Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.572A pdb=" N LEU A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 327 through 339 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 387 through 398 Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.090A pdb=" N ASN A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 415 removed outlier: 3.733A pdb=" N LEU A 412 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N SER A 415 " --> pdb=" O LEU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 440 removed outlier: 3.688A pdb=" N GLU A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 451 removed outlier: 4.648A pdb=" N VAL A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL A 451 " --> pdb=" O ASP A 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 29 removed outlier: 3.739A pdb=" N LYS B 19 " --> pdb=" O ASN B 15 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 20 " --> pdb=" O HIS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 83 removed outlier: 4.311A pdb=" N ILE B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 144 through 162 removed outlier: 3.505A pdb=" N ASP B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 198 removed outlier: 4.967A pdb=" N TYR B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 223 through 239 removed outlier: 5.480A pdb=" N GLN B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 231 " --> pdb=" O THR B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.874A pdb=" N LEU B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 Processing helix chain 'B' and resid 327 through 342 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 383 through 401 removed outlier: 3.679A pdb=" N ASN B 389 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA B 390 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALA B 399 " --> pdb=" O ASP B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 440 Processing helix chain 'B' and resid 446 through 451 Processing helix chain 'C' and resid 42 through 47 Processing helix chain 'C' and resid 51 through 68 Processing helix chain 'C' and resid 99 through 126 removed outlier: 4.859A pdb=" N TYR C 112 " --> pdb=" O ARG C 108 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 131 removed outlier: 5.907A pdb=" N SER C 130 " --> pdb=" O SER C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 149 Processing helix chain 'C' and resid 149 through 165 removed outlier: 4.473A pdb=" N ARG C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 180 Processing helix chain 'C' and resid 181 through 206 Processing helix chain 'C' and resid 244 through 256 removed outlier: 4.012A pdb=" N ILE C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 274 Processing helix chain 'C' and resid 276 through 290 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 337 through 362 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'C' and resid 388 through 412 Processing helix chain 'C' and resid 414 through 427 Processing helix chain 'C' and resid 431 through 442 Processing helix chain 'C' and resid 443 through 446 removed outlier: 3.831A pdb=" N LEU C 446 " --> pdb=" O MET C 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 443 through 446' Processing helix chain 'C' and resid 458 through 470 Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'C' and resid 490 through 499 Processing helix chain 'C' and resid 569 through 573 Processing helix chain 'C' and resid 575 through 609 Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 625 through 651 Processing helix chain 'C' and resid 651 through 664 Processing helix chain 'C' and resid 668 through 685 Processing helix chain 'C' and resid 686 through 691 Processing helix chain 'C' and resid 692 through 710 Processing helix chain 'C' and resid 711 through 717 Processing helix chain 'C' and resid 718 through 720 No H-bonds generated for 'chain 'C' and resid 718 through 720' Processing helix chain 'C' and resid 721 through 726 Processing helix chain 'C' and resid 754 through 788 removed outlier: 3.707A pdb=" N LEU C 758 " --> pdb=" O GLU C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 812 removed outlier: 4.122A pdb=" N VAL C 807 " --> pdb=" O GLY C 803 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 172 Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.623A pdb=" N TYR D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER D 189 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR D 190 " --> pdb=" O LYS D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 243 removed outlier: 4.366A pdb=" N LEU D 220 " --> pdb=" O PHE D 216 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ALA D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY D 228 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET D 243 " --> pdb=" O GLU D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 275 removed outlier: 3.705A pdb=" N GLY D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 301 removed outlier: 4.698A pdb=" N GLU D 289 " --> pdb=" O ARG D 285 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ASN D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 304 No H-bonds generated for 'chain 'D' and resid 302 through 304' Processing helix chain 'D' and resid 308 through 320 Processing helix chain 'D' and resid 324 through 353 removed outlier: 4.037A pdb=" N LEU D 341 " --> pdb=" O SER D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 395 through 415 Processing helix chain 'D' and resid 418 through 436 Processing helix chain 'D' and resid 437 through 440 Processing helix chain 'D' and resid 443 through 465 Processing helix chain 'D' and resid 469 through 481 Processing helix chain 'D' and resid 485 through 496 Processing helix chain 'D' and resid 496 through 502 Processing helix chain 'D' and resid 503 through 507 removed outlier: 3.530A pdb=" N LEU D 507 " --> pdb=" O SER D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 509 No H-bonds generated for 'chain 'D' and resid 508 through 509' Processing helix chain 'D' and resid 510 through 522 removed outlier: 3.654A pdb=" N ARG D 514 " --> pdb=" O TYR D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 530 Processing helix chain 'D' and resid 534 through 539 Processing helix chain 'D' and resid 553 through 558 Processing helix chain 'D' and resid 581 through 612 removed outlier: 3.608A pdb=" N PHE D 593 " --> pdb=" O PHE D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 623 removed outlier: 4.975A pdb=" N ASN D 621 " --> pdb=" O ARG D 618 " (cutoff:3.500A) Proline residue: D 622 - end of helix Processing helix chain 'D' and resid 624 through 656 removed outlier: 3.765A pdb=" N PHE D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 669 Processing helix chain 'D' and resid 670 through 673 Processing helix chain 'D' and resid 720 through 736 Processing helix chain 'D' and resid 737 through 742 removed outlier: 5.716A pdb=" N LEU D 740 " --> pdb=" O SER D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 793 removed outlier: 3.556A pdb=" N SER D 761 " --> pdb=" O PRO D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 832 removed outlier: 3.519A pdb=" N LEU D 802 " --> pdb=" O SER D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 845 Processing helix chain 'U' and resid 118 through 142 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.012A pdb=" N TRP A 93 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N MET A 68 " --> pdb=" O TRP A 93 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ILE A 67 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR A 7 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N MET A 69 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLN A 9 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU A 4 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLN A 137 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A 6 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU A 139 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 8 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N SER A 141 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ALA A 10 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLU A 134 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR A 168 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N PHE A 136 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N TYR A 170 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 138 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL A 172 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N HIS A 140 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR A 201 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL A 203 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N PHE A 272 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 13.134A pdb=" N ASP A 205 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N PHE A 267 " --> pdb=" O MET A 380 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N MET A 380 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN A 379 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN A 317 " --> pdb=" O ASN A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 56 Processing sheet with id=AA3, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.397A pdb=" N TRP B 93 " --> pdb=" O ALA B 66 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET B 68 " --> pdb=" O TRP B 93 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N ILE B 67 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR B 7 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N MET B 69 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN B 9 " --> pdb=" O MET B 69 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU B 4 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N GLN B 137 " --> pdb=" O GLU B 4 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE B 6 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU B 139 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 8 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR B 201 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N VAL B 203 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 10.816A pdb=" N PHE B 272 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 14.029A pdb=" N ASP B 205 " --> pdb=" O PHE B 272 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 374 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET B 375 " --> pdb=" O THR B 321 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR B 321 " --> pdb=" O MET B 375 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 318 " --> pdb=" O HIS B 353 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ASN B 355 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ASN B 320 " --> pdb=" O ASN B 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 54 through 56 Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 10 Processing sheet with id=AA6, first strand: chain 'C' and resid 75 through 77 Processing sheet with id=AA7, first strand: chain 'C' and resid 232 through 235 Processing sheet with id=AA8, first strand: chain 'C' and resid 482 through 486 Processing sheet with id=AA9, first strand: chain 'D' and resid 364 through 366 Processing sheet with id=AB1, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AB2, first strand: chain 'D' and resid 681 through 683 1061 hydrogen bonds defined for protein. 3081 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: 3.28 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 3186 1.30 - 1.43: 5337 1.43 - 1.56: 10327 1.56 - 1.70: 99 1.70 - 1.83: 141 Bond restraints: 19090 Sorted by residual: bond pdb=" CB HIS A 226 " pdb=" CG HIS A 226 " ideal model delta sigma weight residual 1.497 1.398 0.099 1.40e-02 5.10e+03 5.00e+01 bond pdb=" CB HIS C 559 " pdb=" CG HIS C 559 " ideal model delta sigma weight residual 1.497 1.401 0.096 1.40e-02 5.10e+03 4.66e+01 bond pdb=" CA SER A 246 " pdb=" C SER A 246 " ideal model delta sigma weight residual 1.533 1.495 0.038 5.60e-03 3.19e+04 4.58e+01 bond pdb=" CB HIS A 29 " pdb=" CG HIS A 29 " ideal model delta sigma weight residual 1.497 1.404 0.093 1.40e-02 5.10e+03 4.39e+01 bond pdb=" CB TYR D 583 " pdb=" CG TYR D 583 " ideal model delta sigma weight residual 1.512 1.376 0.136 2.20e-02 2.07e+03 3.82e+01 ... (remaining 19085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 24082 3.28 - 6.57: 1632 6.57 - 9.85: 114 9.85 - 13.14: 10 13.14 - 16.42: 3 Bond angle restraints: 25841 Sorted by residual: angle pdb=" N SER C 611 " pdb=" CA SER C 611 " pdb=" C SER C 611 " ideal model delta sigma weight residual 113.50 98.90 14.60 1.23e+00 6.61e-01 1.41e+02 angle pdb=" CA PHE A 86 " pdb=" CB PHE A 86 " pdb=" CG PHE A 86 " ideal model delta sigma weight residual 113.80 124.95 -11.15 1.00e+00 1.00e+00 1.24e+02 angle pdb=" N VAL B 383 " pdb=" CA VAL B 383 " pdb=" C VAL B 383 " ideal model delta sigma weight residual 113.71 103.27 10.44 9.50e-01 1.11e+00 1.21e+02 angle pdb=" N LEU C 427 " pdb=" CA LEU C 427 " pdb=" C LEU C 427 " ideal model delta sigma weight residual 113.97 100.62 13.35 1.28e+00 6.10e-01 1.09e+02 angle pdb=" N VAL C 165 " pdb=" CA VAL C 165 " pdb=" C VAL C 165 " ideal model delta sigma weight residual 107.73 118.84 -11.11 1.14e+00 7.69e-01 9.49e+01 ... (remaining 25836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.38: 11252 23.38 - 46.75: 229 46.75 - 70.13: 52 70.13 - 93.51: 10 93.51 - 116.89: 3 Dihedral angle restraints: 11546 sinusoidal: 4753 harmonic: 6793 Sorted by residual: dihedral pdb=" C4' GDP B 501 " pdb=" O5' GDP B 501 " pdb=" C5' GDP B 501 " pdb=" PA GDP B 501 " ideal model delta sinusoidal sigma weight residual 180.02 63.13 116.89 1 2.00e+01 2.50e-03 3.49e+01 dihedral pdb=" C5' GDP A1400 " pdb=" O5' GDP A1400 " pdb=" PA GDP A1400 " pdb=" O3A GDP A1400 " ideal model delta sinusoidal sigma weight residual 179.98 -76.56 -103.46 1 2.00e+01 2.50e-03 2.96e+01 dihedral pdb=" C4' GDP A1400 " pdb=" O5' GDP A1400 " pdb=" C5' GDP A1400 " pdb=" PA GDP A1400 " ideal model delta sinusoidal sigma weight residual 180.02 80.17 99.85 1 2.00e+01 2.50e-03 2.81e+01 ... (remaining 11543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1907 0.098 - 0.197: 799 0.197 - 0.295: 145 0.295 - 0.394: 23 0.394 - 0.492: 2 Chirality restraints: 2876 Sorted by residual: chirality pdb=" CA TYR B 315 " pdb=" N TYR B 315 " pdb=" C TYR B 315 " pdb=" CB TYR B 315 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CA TYR A 247 " pdb=" N TYR A 247 " pdb=" C TYR A 247 " pdb=" CB TYR A 247 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CB VAL A 419 " pdb=" CA VAL A 419 " pdb=" CG1 VAL A 419 " pdb=" CG2 VAL A 419 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 2873 not shown) Planarity restraints: 3326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GDP A1400 " 0.367 2.00e-02 2.50e+03 1.51e-01 6.87e+02 pdb=" N9 GDP A1400 " -0.107 2.00e-02 2.50e+03 pdb=" C8 GDP A1400 " -0.215 2.00e-02 2.50e+03 pdb=" N7 GDP A1400 " -0.117 2.00e-02 2.50e+03 pdb=" C5 GDP A1400 " -0.001 2.00e-02 2.50e+03 pdb=" C6 GDP A1400 " 0.091 2.00e-02 2.50e+03 pdb=" O6 GDP A1400 " 0.153 2.00e-02 2.50e+03 pdb=" N1 GDP A1400 " 0.101 2.00e-02 2.50e+03 pdb=" C2 GDP A1400 " -0.019 2.00e-02 2.50e+03 pdb=" N2 GDP A1400 " -0.142 2.00e-02 2.50e+03 pdb=" N3 GDP A1400 " -0.061 2.00e-02 2.50e+03 pdb=" C4 GDP A1400 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GDP B 501 " 0.177 2.00e-02 2.50e+03 7.57e-02 1.72e+02 pdb=" N9 GDP B 501 " -0.066 2.00e-02 2.50e+03 pdb=" C8 GDP B 501 " -0.072 2.00e-02 2.50e+03 pdb=" N7 GDP B 501 " -0.052 2.00e-02 2.50e+03 pdb=" C5 GDP B 501 " -0.025 2.00e-02 2.50e+03 pdb=" C6 GDP B 501 " 0.024 2.00e-02 2.50e+03 pdb=" O6 GDP B 501 " 0.140 2.00e-02 2.50e+03 pdb=" N1 GDP B 501 " -0.045 2.00e-02 2.50e+03 pdb=" C2 GDP B 501 " -0.022 2.00e-02 2.50e+03 pdb=" N2 GDP B 501 " -0.008 2.00e-02 2.50e+03 pdb=" N3 GDP B 501 " -0.014 2.00e-02 2.50e+03 pdb=" C4 GDP B 501 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 297 " 0.060 2.00e-02 2.50e+03 3.54e-02 2.51e+01 pdb=" CG TYR D 297 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR D 297 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR D 297 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR D 297 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR D 297 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR D 297 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 297 " 0.058 2.00e-02 2.50e+03 ... (remaining 3323 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 340 2.62 - 3.19: 18861 3.19 - 3.76: 32083 3.76 - 4.33: 44945 4.33 - 4.90: 69289 Nonbonded interactions: 165518 Sorted by model distance: nonbonded pdb=" CB PHE B 316 " pdb=" O ASN B 379 " model vdw 2.044 3.440 nonbonded pdb=" N SER C 611 " pdb=" N TRP C 612 " model vdw 2.274 2.560 nonbonded pdb=" NZ LYS C 581 " pdb=" OG1 THR C 681 " model vdw 2.296 3.120 nonbonded pdb=" N LEU C 427 " pdb=" N GLY C 428 " model vdw 2.320 2.560 nonbonded pdb=" OG SER A 104 " pdb=" OH TYR A 185 " model vdw 2.331 3.040 ... (remaining 165513 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' selection = (chain 'B' and resid 3 through 501) } 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: 7.000 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.990 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 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 : 0.023 0.142 19090 Z= 1.247 Angle : 1.758 16.420 25841 Z= 1.217 Chirality : 0.105 0.492 2876 Planarity : 0.010 0.151 3326 Dihedral : 10.709 116.887 7144 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.35 % Allowed : 2.03 % Favored : 97.62 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.33 (0.17), residues: 2271 helix: 0.23 (0.13), residues: 1301 sheet: -0.01 (0.40), residues: 166 loop : 0.58 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 714 TYR 0.060 0.010 TYR D 297 PHE 0.052 0.008 PHE B 136 TRP 0.056 0.012 TRP C 320 HIS 0.014 0.003 HIS D 728 Details of bonding type rmsd covalent geometry : bond 0.02251 (19090) covalent geometry : angle 1.75813 (25841) hydrogen bonds : bond 0.15768 ( 1061) hydrogen bonds : angle 7.09123 ( 3081) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 859 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ILE cc_start: 0.8528 (mt) cc_final: 0.8185 (mm) REVERT: A 22 TRP cc_start: 0.8621 (m100) cc_final: 0.8109 (m100) REVERT: A 28 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8410 (mt-10) REVERT: A 121 ASN cc_start: 0.8921 (m-40) cc_final: 0.8713 (m-40) REVERT: A 136 PHE cc_start: 0.8062 (m-80) cc_final: 0.7722 (m-80) REVERT: A 248 MET cc_start: 0.7941 (tpt) cc_final: 0.7602 (tpp) REVERT: A 260 ILE cc_start: 0.8463 (mm) cc_final: 0.8149 (mm) REVERT: A 293 ASP cc_start: 0.8888 (m-30) cc_final: 0.8681 (t70) REVERT: A 297 ASP cc_start: 0.8584 (m-30) cc_final: 0.8029 (m-30) REVERT: A 314 THR cc_start: 0.8342 (m) cc_final: 0.8095 (p) REVERT: A 318 VAL cc_start: 0.8824 (t) cc_final: 0.7075 (t) REVERT: A 319 TYR cc_start: 0.8221 (t80) cc_final: 0.7713 (t80) REVERT: A 320 ASN cc_start: 0.8456 (p0) cc_final: 0.7883 (p0) REVERT: A 322 ILE cc_start: 0.9510 (mm) cc_final: 0.8872 (mm) REVERT: A 335 MET cc_start: 0.8835 (mtm) cc_final: 0.8634 (mmp) REVERT: A 354 VAL cc_start: 0.9510 (t) cc_final: 0.9051 (m) REVERT: A 377 LEU cc_start: 0.9323 (mt) cc_final: 0.8916 (mt) REVERT: A 448 ASP cc_start: 0.8331 (m-30) cc_final: 0.8050 (p0) REVERT: B 22 TRP cc_start: 0.7889 (m100) cc_final: 0.6744 (m100) REVERT: B 132 ASN cc_start: 0.8346 (t0) cc_final: 0.7907 (t0) REVERT: B 165 LYS cc_start: 0.8350 (mmtm) cc_final: 0.7887 (mmtt) REVERT: B 325 ASN cc_start: 0.8540 (t0) cc_final: 0.8269 (t0) REVERT: B 335 MET cc_start: 0.9018 (tpp) cc_final: 0.8425 (tpp) REVERT: B 343 LYS cc_start: 0.7418 (mtmt) cc_final: 0.7085 (pttm) REVERT: B 394 PHE cc_start: 0.5395 (OUTLIER) cc_final: 0.5194 (p90) REVERT: C 55 GLN cc_start: 0.8654 (tt0) cc_final: 0.8429 (tt0) REVERT: C 65 ASN cc_start: 0.8597 (m-40) cc_final: 0.8234 (m-40) REVERT: C 133 MET cc_start: 0.8677 (ptt) cc_final: 0.7429 (ptp) REVERT: C 178 ASN cc_start: 0.8697 (m-40) cc_final: 0.8354 (m110) REVERT: C 193 TYR cc_start: 0.9114 (t80) cc_final: 0.8848 (t80) REVERT: C 195 GLU cc_start: 0.8412 (tp30) cc_final: 0.8134 (tp30) REVERT: C 343 LEU cc_start: 0.9458 (tp) cc_final: 0.9221 (tt) REVERT: C 379 ASN cc_start: 0.8404 (p0) cc_final: 0.7924 (p0) REVERT: C 446 LEU cc_start: 0.8802 (mp) cc_final: 0.8354 (mm) REVERT: C 458 TYR cc_start: 0.7509 (p90) cc_final: 0.6966 (p90) REVERT: C 565 ASN cc_start: 0.7321 (t0) cc_final: 0.7119 (t0) REVERT: C 585 ILE cc_start: 0.9358 (mt) cc_final: 0.8976 (mt) REVERT: C 592 LEU cc_start: 0.9543 (mt) cc_final: 0.9335 (mt) REVERT: C 704 TYR cc_start: 0.8952 (t80) cc_final: 0.8614 (t80) REVERT: C 708 LYS cc_start: 0.8776 (pttt) cc_final: 0.8381 (tptt) REVERT: D 217 GLU cc_start: 0.7238 (mp0) cc_final: 0.6834 (mp0) REVERT: D 337 SER cc_start: 0.8606 (m) cc_final: 0.8200 (t) REVERT: D 338 MET cc_start: 0.7597 (mtp) cc_final: 0.7154 (mtp) REVERT: D 400 TYR cc_start: 0.8504 (t80) cc_final: 0.8242 (t80) REVERT: D 404 MET cc_start: 0.8415 (mmm) cc_final: 0.7479 (mmm) REVERT: D 416 CYS cc_start: 0.8584 (m) cc_final: 0.8194 (m) REVERT: D 488 PHE cc_start: 0.9086 (t80) cc_final: 0.8843 (t80) REVERT: D 492 LEU cc_start: 0.9221 (mt) cc_final: 0.8780 (mt) REVERT: D 526 ARG cc_start: 0.8712 (ptt-90) cc_final: 0.8479 (ptp90) REVERT: D 558 PHE cc_start: 0.8561 (t80) cc_final: 0.7948 (t80) REVERT: D 584 LEU cc_start: 0.9165 (mt) cc_final: 0.8868 (mp) REVERT: D 587 PHE cc_start: 0.9133 (t80) cc_final: 0.8919 (t80) REVERT: D 593 PHE cc_start: 0.8807 (m-80) cc_final: 0.8392 (m-10) REVERT: D 648 MET cc_start: 0.9246 (mmm) cc_final: 0.8882 (mmm) REVERT: D 689 ILE cc_start: 0.8636 (mm) cc_final: 0.8090 (tp) REVERT: D 808 ASN cc_start: 0.8966 (m-40) cc_final: 0.8612 (m-40) REVERT: D 819 PHE cc_start: 0.8592 (t80) cc_final: 0.8203 (t80) outliers start: 3 outliers final: 1 residues processed: 861 average time/residue: 0.1479 time to fit residues: 190.1344 Evaluate side-chains 503 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 501 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain C residue 617 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.6980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS A 38 GLN A 137 GLN A 221 ASN A 226 HIS A 379 ASN A 406 ASN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS B 229 GLN B 385 ASN C 191 ASN C 430 GLN ** C 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 ASN C 696 GLN D 177 ASN D 290 ASN D 430 HIS D 458 ASN D 573 ASN D 596 ASN D 642 GLN D 660 ASN D 729 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.096802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072237 restraints weight = 67964.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.074940 restraints weight = 32801.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.076672 restraints weight = 19728.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.077826 restraints weight = 13645.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078603 restraints weight = 10414.511| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 19090 Z= 0.192 Angle : 0.810 11.775 25841 Z= 0.430 Chirality : 0.049 0.213 2876 Planarity : 0.005 0.068 3326 Dihedral : 6.495 116.255 2530 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.99 % Favored : 96.87 % Rotamer: Outliers : 2.47 % Allowed : 12.38 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.67 (0.17), residues: 2271 helix: 0.85 (0.14), residues: 1273 sheet: -0.64 (0.42), residues: 156 loop : 0.24 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 243 TYR 0.026 0.002 TYR C 725 PHE 0.048 0.003 PHE D 445 TRP 0.018 0.002 TRP D 421 HIS 0.013 0.002 HIS U 127 Details of bonding type rmsd covalent geometry : bond 0.00411 (19090) covalent geometry : angle 0.80993 (25841) hydrogen bonds : bond 0.06299 ( 1061) hydrogen bonds : angle 5.52226 ( 3081) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 604 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8425 (t80) cc_final: 0.8127 (t80) REVERT: A 121 ASN cc_start: 0.8982 (m-40) cc_final: 0.8749 (m-40) REVERT: A 126 GLU cc_start: 0.7806 (tp30) cc_final: 0.7492 (tp30) REVERT: A 239 THR cc_start: 0.9393 (m) cc_final: 0.9124 (t) REVERT: A 293 ASP cc_start: 0.8955 (m-30) cc_final: 0.8486 (t70) REVERT: A 314 THR cc_start: 0.9023 (m) cc_final: 0.8639 (p) REVERT: A 320 ASN cc_start: 0.9283 (p0) cc_final: 0.8326 (p0) REVERT: A 322 ILE cc_start: 0.9452 (mm) cc_final: 0.8870 (mm) REVERT: A 333 ARG cc_start: 0.9014 (mtm-85) cc_final: 0.8710 (mtm-85) REVERT: A 338 LEU cc_start: 0.9689 (mt) cc_final: 0.9319 (mt) REVERT: A 375 MET cc_start: 0.8622 (ttp) cc_final: 0.8151 (ttp) REVERT: A 406 ASN cc_start: 0.7511 (m110) cc_final: 0.7169 (m110) REVERT: B 27 LYS cc_start: 0.9224 (ptmt) cc_final: 0.9013 (ptmt) REVERT: B 28 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8876 (pt0) REVERT: B 132 ASN cc_start: 0.8497 (t0) cc_final: 0.7686 (t0) REVERT: B 137 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7836 (mm-40) REVERT: B 160 ASP cc_start: 0.8282 (t0) cc_final: 0.8016 (p0) REVERT: B 162 TYR cc_start: 0.7697 (m-80) cc_final: 0.7273 (m-80) REVERT: B 185 TYR cc_start: 0.6715 (t80) cc_final: 0.6153 (t80) REVERT: B 248 MET cc_start: 0.7665 (mmm) cc_final: 0.6856 (mmm) REVERT: B 249 TYR cc_start: 0.8208 (m-80) cc_final: 0.7654 (m-10) REVERT: B 252 MET cc_start: 0.8745 (mmp) cc_final: 0.7951 (pmm) REVERT: B 275 PHE cc_start: 0.3208 (p90) cc_final: 0.2884 (p90) REVERT: B 325 ASN cc_start: 0.8635 (t0) cc_final: 0.8297 (t0) REVERT: B 335 MET cc_start: 0.9214 (tpp) cc_final: 0.8712 (tpp) REVERT: B 437 TYR cc_start: 0.7455 (m-80) cc_final: 0.7213 (m-80) REVERT: B 450 LEU cc_start: 0.8243 (mt) cc_final: 0.8001 (pp) REVERT: C 43 LEU cc_start: 0.8846 (mt) cc_final: 0.8338 (mt) REVERT: C 55 GLN cc_start: 0.9296 (tt0) cc_final: 0.8840 (tp40) REVERT: C 63 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9324 (mm) REVERT: C 68 ILE cc_start: 0.9183 (pt) cc_final: 0.8686 (pt) REVERT: C 178 ASN cc_start: 0.9099 (m-40) cc_final: 0.8730 (m110) REVERT: C 195 GLU cc_start: 0.9315 (tp30) cc_final: 0.8925 (tp30) REVERT: C 265 VAL cc_start: 0.9540 (m) cc_final: 0.9265 (p) REVERT: C 269 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8705 (mtmm) REVERT: C 343 LEU cc_start: 0.9405 (tp) cc_final: 0.9165 (tt) REVERT: C 379 ASN cc_start: 0.9163 (p0) cc_final: 0.8936 (p0) REVERT: C 383 ASP cc_start: 0.9191 (t70) cc_final: 0.8990 (t0) REVERT: C 414 ASP cc_start: 0.8791 (m-30) cc_final: 0.8375 (p0) REVERT: C 469 ARG cc_start: 0.8806 (ttp80) cc_final: 0.8205 (ttp80) REVERT: C 564 ILE cc_start: 0.9381 (mt) cc_final: 0.8912 (mm) REVERT: C 565 ASN cc_start: 0.8066 (t0) cc_final: 0.7732 (t0) REVERT: C 579 MET cc_start: 0.9640 (mmm) cc_final: 0.9371 (mmm) REVERT: C 601 GLU cc_start: 0.9479 (tp30) cc_final: 0.8723 (pp20) REVERT: C 648 ASN cc_start: 0.9179 (m-40) cc_final: 0.8823 (p0) REVERT: C 652 ILE cc_start: 0.9361 (mm) cc_final: 0.9159 (mp) REVERT: C 661 LYS cc_start: 0.9356 (ptpp) cc_final: 0.9141 (ptpp) REVERT: C 664 ARG cc_start: 0.9425 (mmm-85) cc_final: 0.9199 (mmp80) REVERT: C 677 GLU cc_start: 0.8571 (pp20) cc_final: 0.8257 (pp20) REVERT: C 700 PHE cc_start: 0.9313 (m-80) cc_final: 0.9048 (m-80) REVERT: C 708 LYS cc_start: 0.8600 (pttt) cc_final: 0.8205 (tptt) REVERT: D 187 TYR cc_start: 0.9393 (m-80) cc_final: 0.9140 (m-80) REVERT: D 237 LYS cc_start: 0.9413 (mmtt) cc_final: 0.8742 (mttt) REVERT: D 243 MET cc_start: 0.8920 (tpp) cc_final: 0.8507 (mmm) REVERT: D 312 PHE cc_start: 0.9144 (m-80) cc_final: 0.8847 (m-80) REVERT: D 337 SER cc_start: 0.9069 (m) cc_final: 0.8681 (t) REVERT: D 338 MET cc_start: 0.8922 (mtp) cc_final: 0.8565 (mtp) REVERT: D 361 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7000 (tp30) REVERT: D 400 TYR cc_start: 0.8504 (t80) cc_final: 0.8101 (t80) REVERT: D 414 LYS cc_start: 0.9468 (tppt) cc_final: 0.9232 (tmtt) REVERT: D 488 PHE cc_start: 0.9448 (t80) cc_final: 0.9131 (t80) REVERT: D 492 LEU cc_start: 0.9321 (mt) cc_final: 0.8897 (mt) REVERT: D 526 ARG cc_start: 0.9272 (ptt-90) cc_final: 0.8976 (ptp90) REVERT: D 558 PHE cc_start: 0.8486 (t80) cc_final: 0.7776 (t80) REVERT: D 564 LEU cc_start: 0.9132 (tp) cc_final: 0.8843 (tp) REVERT: D 587 PHE cc_start: 0.9244 (t80) cc_final: 0.8700 (t80) REVERT: D 649 GLU cc_start: 0.9167 (tt0) cc_final: 0.8952 (tt0) REVERT: D 662 LYS cc_start: 0.9425 (mttt) cc_final: 0.9218 (mmmm) REVERT: D 664 MET cc_start: 0.8646 (ptm) cc_final: 0.8409 (ptm) REVERT: D 667 LYS cc_start: 0.9819 (mttt) cc_final: 0.9418 (mtpt) REVERT: D 679 PHE cc_start: 0.6994 (m-10) cc_final: 0.6516 (m-10) REVERT: D 723 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8674 (mt-10) REVERT: D 725 GLU cc_start: 0.9300 (tt0) cc_final: 0.8844 (tt0) REVERT: D 808 ASN cc_start: 0.8762 (m-40) cc_final: 0.8353 (m-40) REVERT: U 131 LYS cc_start: 0.9457 (mtpp) cc_final: 0.9136 (mtpp) outliers start: 52 outliers final: 27 residues processed: 630 average time/residue: 0.1402 time to fit residues: 134.3894 Evaluate side-chains 518 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 489 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 617 TYR Chi-restraints excluded: chain C residue 663 TYR Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 573 ASN Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain U residue 127 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 9.9990 chunk 92 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 142 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 HIS ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN C 497 HIS C 696 GLN D 387 GLN D 534 ASN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 669 GLN D 729 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.094327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.069908 restraints weight = 69488.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.072490 restraints weight = 34076.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.074161 restraints weight = 20770.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.075289 restraints weight = 14431.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076016 restraints weight = 11049.894| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 19090 Z= 0.196 Angle : 0.733 11.586 25841 Z= 0.385 Chirality : 0.046 0.241 2876 Planarity : 0.005 0.070 3326 Dihedral : 6.102 108.615 2528 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 2.70 % Allowed : 14.75 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.59 (0.17), residues: 2271 helix: 0.92 (0.14), residues: 1299 sheet: -0.89 (0.41), residues: 166 loop : 0.02 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 630 TYR 0.038 0.002 TYR D 345 PHE 0.040 0.002 PHE D 411 TRP 0.014 0.002 TRP B 105 HIS 0.010 0.001 HIS U 127 Details of bonding type rmsd covalent geometry : bond 0.00416 (19090) covalent geometry : angle 0.73304 (25841) hydrogen bonds : bond 0.05572 ( 1061) hydrogen bonds : angle 5.31486 ( 3081) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 519 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8333 (mt-10) REVERT: A 69 MET cc_start: 0.8926 (mtm) cc_final: 0.8677 (mtt) REVERT: A 225 GLN cc_start: 0.8103 (mt0) cc_final: 0.7898 (mm-40) REVERT: A 239 THR cc_start: 0.9411 (m) cc_final: 0.9117 (t) REVERT: A 310 MET cc_start: 0.7314 (tpt) cc_final: 0.7007 (mmp) REVERT: A 314 THR cc_start: 0.9024 (m) cc_final: 0.8692 (p) REVERT: A 320 ASN cc_start: 0.9167 (p0) cc_final: 0.8611 (p0) REVERT: A 322 ILE cc_start: 0.9564 (mm) cc_final: 0.9154 (mm) REVERT: A 333 ARG cc_start: 0.8958 (mtm-85) cc_final: 0.8634 (mtm-85) REVERT: A 335 MET cc_start: 0.8904 (mmp) cc_final: 0.8643 (mmp) REVERT: A 338 LEU cc_start: 0.9585 (mt) cc_final: 0.9220 (mt) REVERT: A 416 MET cc_start: 0.8565 (mmp) cc_final: 0.8180 (mmp) REVERT: A 448 ASP cc_start: 0.8399 (m-30) cc_final: 0.8048 (m-30) REVERT: B 28 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8907 (mt-10) REVERT: B 68 MET cc_start: 0.7528 (mtt) cc_final: 0.6987 (mtt) REVERT: B 132 ASN cc_start: 0.8404 (t0) cc_final: 0.7804 (t0) REVERT: B 160 ASP cc_start: 0.8530 (t0) cc_final: 0.8239 (p0) REVERT: B 162 TYR cc_start: 0.7872 (m-80) cc_final: 0.7659 (m-80) REVERT: B 252 MET cc_start: 0.8423 (mmp) cc_final: 0.7985 (pmm) REVERT: B 325 ASN cc_start: 0.8739 (t0) cc_final: 0.8509 (t0) REVERT: B 335 MET cc_start: 0.9242 (tpp) cc_final: 0.8852 (tpp) REVERT: B 369 GLU cc_start: 0.7990 (tp30) cc_final: 0.7568 (tp30) REVERT: B 370 ASN cc_start: 0.7705 (t0) cc_final: 0.7318 (m-40) REVERT: B 375 MET cc_start: 0.6813 (mmm) cc_final: 0.5999 (mmm) REVERT: B 423 PHE cc_start: 0.6030 (t80) cc_final: 0.5800 (t80) REVERT: C 43 LEU cc_start: 0.8931 (mt) cc_final: 0.8531 (mt) REVERT: C 55 GLN cc_start: 0.9246 (tt0) cc_final: 0.8880 (tp40) REVERT: C 63 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9391 (mm) REVERT: C 133 MET cc_start: 0.9359 (ptt) cc_final: 0.9084 (ptt) REVERT: C 164 LYS cc_start: 0.9383 (mmmm) cc_final: 0.9070 (mmmm) REVERT: C 174 GLU cc_start: 0.8864 (tp30) cc_final: 0.7929 (tp30) REVERT: C 178 ASN cc_start: 0.9227 (m-40) cc_final: 0.8721 (m110) REVERT: C 195 GLU cc_start: 0.9413 (tp30) cc_final: 0.9018 (tp30) REVERT: C 266 MET cc_start: 0.9115 (tmm) cc_final: 0.8842 (tmm) REVERT: C 269 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8652 (mtmm) REVERT: C 277 GLN cc_start: 0.9253 (tt0) cc_final: 0.9009 (tt0) REVERT: C 340 ASP cc_start: 0.9347 (m-30) cc_final: 0.8576 (p0) REVERT: C 379 ASN cc_start: 0.9228 (p0) cc_final: 0.8980 (p0) REVERT: C 430 GLN cc_start: 0.9031 (tm-30) cc_final: 0.8522 (tm-30) REVERT: C 459 ASP cc_start: 0.9232 (OUTLIER) cc_final: 0.8951 (m-30) REVERT: C 469 ARG cc_start: 0.8696 (ttp80) cc_final: 0.8262 (ttp80) REVERT: C 499 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8358 (tt) REVERT: C 562 PHE cc_start: 0.8504 (m-10) cc_final: 0.8269 (m-10) REVERT: C 565 ASN cc_start: 0.8167 (t0) cc_final: 0.7712 (t0) REVERT: C 597 ARG cc_start: 0.9487 (tpp80) cc_final: 0.9045 (tpp80) REVERT: C 601 GLU cc_start: 0.9445 (tp30) cc_final: 0.8723 (pp20) REVERT: C 604 MET cc_start: 0.8676 (mmm) cc_final: 0.8387 (mmm) REVERT: C 636 MET cc_start: 0.9261 (mmm) cc_final: 0.8967 (mmm) REVERT: C 641 LYS cc_start: 0.9515 (mmmt) cc_final: 0.9287 (mmmm) REVERT: C 648 ASN cc_start: 0.9232 (m-40) cc_final: 0.8808 (p0) REVERT: C 652 ILE cc_start: 0.9347 (mm) cc_final: 0.9142 (mp) REVERT: C 664 ARG cc_start: 0.9478 (mmm-85) cc_final: 0.9215 (mmp80) REVERT: C 674 ASN cc_start: 0.8904 (t0) cc_final: 0.8467 (t0) REVERT: C 677 GLU cc_start: 0.8424 (pp20) cc_final: 0.8073 (pp20) REVERT: C 700 PHE cc_start: 0.9384 (m-80) cc_final: 0.9063 (m-80) REVERT: C 708 LYS cc_start: 0.8668 (pttt) cc_final: 0.8143 (tptt) REVERT: C 782 PHE cc_start: 0.9339 (t80) cc_final: 0.8874 (m-80) REVERT: D 167 LEU cc_start: 0.9338 (mt) cc_final: 0.9097 (mt) REVERT: D 187 TYR cc_start: 0.9371 (m-80) cc_final: 0.9036 (m-80) REVERT: D 217 GLU cc_start: 0.8530 (mp0) cc_final: 0.7779 (mp0) REVERT: D 220 LEU cc_start: 0.9718 (tp) cc_final: 0.9512 (tp) REVERT: D 225 PHE cc_start: 0.9652 (m-10) cc_final: 0.9342 (m-80) REVERT: D 237 LYS cc_start: 0.9386 (mmtt) cc_final: 0.8985 (mmtp) REVERT: D 249 MET cc_start: 0.9339 (mmp) cc_final: 0.9091 (mmp) REVERT: D 251 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7516 (tttm) REVERT: D 281 LYS cc_start: 0.9454 (mttp) cc_final: 0.9248 (mttt) REVERT: D 312 PHE cc_start: 0.9162 (m-80) cc_final: 0.8700 (m-80) REVERT: D 337 SER cc_start: 0.9170 (m) cc_final: 0.8880 (t) REVERT: D 338 MET cc_start: 0.8896 (mtp) cc_final: 0.8599 (mtp) REVERT: D 400 TYR cc_start: 0.8665 (t80) cc_final: 0.8328 (t80) REVERT: D 414 LYS cc_start: 0.9384 (tppt) cc_final: 0.8961 (tppt) REVERT: D 478 LYS cc_start: 0.9422 (tmtt) cc_final: 0.9194 (tmmt) REVERT: D 488 PHE cc_start: 0.9437 (t80) cc_final: 0.9189 (t80) REVERT: D 492 LEU cc_start: 0.9215 (mt) cc_final: 0.8646 (mt) REVERT: D 529 MET cc_start: 0.9435 (tpp) cc_final: 0.9231 (tpp) REVERT: D 546 LEU cc_start: 0.8496 (tp) cc_final: 0.8258 (tp) REVERT: D 558 PHE cc_start: 0.8518 (t80) cc_final: 0.7803 (t80) REVERT: D 604 MET cc_start: 0.8006 (tpp) cc_final: 0.7693 (mmm) REVERT: D 662 LYS cc_start: 0.9450 (mttt) cc_final: 0.9242 (mmmm) REVERT: D 664 MET cc_start: 0.8857 (ptm) cc_final: 0.8522 (ptm) REVERT: D 667 LYS cc_start: 0.9778 (mttt) cc_final: 0.9383 (mtpt) REVERT: D 679 PHE cc_start: 0.6987 (m-80) cc_final: 0.6622 (m-10) REVERT: D 689 ILE cc_start: 0.8521 (mm) cc_final: 0.7849 (tp) REVERT: D 717 LYS cc_start: 0.8518 (tppt) cc_final: 0.8221 (tppt) REVERT: D 725 GLU cc_start: 0.9293 (tt0) cc_final: 0.8872 (tt0) REVERT: D 808 ASN cc_start: 0.8780 (m-40) cc_final: 0.8384 (m-40) REVERT: U 117 GLN cc_start: 0.8400 (pm20) cc_final: 0.7852 (pm20) REVERT: U 121 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8632 (tm-30) REVERT: U 131 LYS cc_start: 0.9474 (mtpp) cc_final: 0.9111 (mtpp) REVERT: U 132 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8943 (tm-30) REVERT: U 141 LYS cc_start: 0.8389 (tppt) cc_final: 0.7922 (mmtp) outliers start: 57 outliers final: 31 residues processed: 547 average time/residue: 0.1350 time to fit residues: 113.8992 Evaluate side-chains 502 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 466 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 354 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 269 LYS Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 397 CYS Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 617 TYR Chi-restraints excluded: chain C residue 663 TYR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 483 MET Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 624 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 129 optimal weight: 9.9990 chunk 197 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 201 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 122 GLN ** 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 = 0.3816 r_free = 0.3816 target = 0.095539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.070772 restraints weight = 68572.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.073410 restraints weight = 33754.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075104 restraints weight = 20591.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076266 restraints weight = 14375.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.077037 restraints weight = 11033.721| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19090 Z= 0.154 Angle : 0.690 10.871 25841 Z= 0.355 Chirality : 0.044 0.309 2876 Planarity : 0.004 0.072 3326 Dihedral : 5.830 103.599 2528 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.43 % Favored : 96.48 % Rotamer: Outliers : 2.47 % Allowed : 15.75 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.68 (0.18), residues: 2271 helix: 1.01 (0.14), residues: 1305 sheet: -1.04 (0.40), residues: 176 loop : 0.07 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG U 125 TYR 0.039 0.002 TYR D 345 PHE 0.028 0.002 PHE D 411 TRP 0.019 0.002 TRP A 347 HIS 0.009 0.001 HIS U 127 Details of bonding type rmsd covalent geometry : bond 0.00333 (19090) covalent geometry : angle 0.69031 (25841) hydrogen bonds : bond 0.05104 ( 1061) hydrogen bonds : angle 5.14892 ( 3081) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 523 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8317 (mt-10) REVERT: A 69 MET cc_start: 0.8765 (mtm) cc_final: 0.8488 (mtt) REVERT: A 121 ASN cc_start: 0.9005 (m-40) cc_final: 0.8741 (m110) REVERT: A 212 ILE cc_start: 0.9252 (tp) cc_final: 0.8929 (mm) REVERT: A 314 THR cc_start: 0.8944 (m) cc_final: 0.8675 (p) REVERT: A 416 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8222 (mmp) REVERT: B 28 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8700 (mt-10) REVERT: B 68 MET cc_start: 0.7480 (mtt) cc_final: 0.7022 (mtt) REVERT: B 132 ASN cc_start: 0.8462 (t0) cc_final: 0.7804 (t0) REVERT: B 160 ASP cc_start: 0.8525 (t0) cc_final: 0.8243 (p0) REVERT: B 252 MET cc_start: 0.8263 (mmp) cc_final: 0.7902 (pmm) REVERT: B 335 MET cc_start: 0.9340 (tpp) cc_final: 0.8786 (tpp) REVERT: B 369 GLU cc_start: 0.8103 (tp30) cc_final: 0.7648 (tp30) REVERT: B 370 ASN cc_start: 0.7761 (t0) cc_final: 0.7464 (m-40) REVERT: B 423 PHE cc_start: 0.6021 (t80) cc_final: 0.5820 (t80) REVERT: C 43 LEU cc_start: 0.8868 (mt) cc_final: 0.8519 (mp) REVERT: C 55 GLN cc_start: 0.9133 (tt0) cc_final: 0.8842 (tp40) REVERT: C 63 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9310 (mm) REVERT: C 147 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8681 (tm-30) REVERT: C 164 LYS cc_start: 0.9287 (mmmm) cc_final: 0.9012 (mmmm) REVERT: C 178 ASN cc_start: 0.9163 (m-40) cc_final: 0.8850 (m110) REVERT: C 195 GLU cc_start: 0.9281 (tp30) cc_final: 0.8871 (tp30) REVERT: C 266 MET cc_start: 0.9106 (tmm) cc_final: 0.8755 (tmm) REVERT: C 277 GLN cc_start: 0.9157 (tt0) cc_final: 0.8880 (tt0) REVERT: C 331 LEU cc_start: 0.9517 (mt) cc_final: 0.9047 (mt) REVERT: C 340 ASP cc_start: 0.9383 (m-30) cc_final: 0.8563 (p0) REVERT: C 379 ASN cc_start: 0.9224 (p0) cc_final: 0.8971 (p0) REVERT: C 430 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8365 (tm-30) REVERT: C 469 ARG cc_start: 0.8753 (ttp80) cc_final: 0.7779 (ptm-80) REVERT: C 479 ARG cc_start: 0.9216 (mmm-85) cc_final: 0.8752 (mmm160) REVERT: C 499 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8550 (tt) REVERT: C 558 TYR cc_start: 0.6820 (m-10) cc_final: 0.6390 (m-10) REVERT: C 565 ASN cc_start: 0.8220 (t0) cc_final: 0.7720 (t0) REVERT: C 597 ARG cc_start: 0.9499 (tpp80) cc_final: 0.9249 (tpp80) REVERT: C 636 MET cc_start: 0.9220 (mmm) cc_final: 0.8867 (mmm) REVERT: C 644 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9143 (mmp) REVERT: C 648 ASN cc_start: 0.9203 (m-40) cc_final: 0.8766 (p0) REVERT: C 664 ARG cc_start: 0.9446 (mmm-85) cc_final: 0.9210 (mmp80) REVERT: C 674 ASN cc_start: 0.8800 (t0) cc_final: 0.8347 (t0) REVERT: C 677 GLU cc_start: 0.8278 (pp20) cc_final: 0.7992 (pp20) REVERT: C 700 PHE cc_start: 0.9394 (m-10) cc_final: 0.9009 (m-80) REVERT: C 708 LYS cc_start: 0.8228 (pttt) cc_final: 0.7920 (pttm) REVERT: C 782 PHE cc_start: 0.9314 (t80) cc_final: 0.8811 (m-80) REVERT: D 187 TYR cc_start: 0.9255 (m-80) cc_final: 0.8864 (m-10) REVERT: D 225 PHE cc_start: 0.9627 (m-10) cc_final: 0.9343 (m-80) REVERT: D 236 TYR cc_start: 0.8199 (m-10) cc_final: 0.7988 (m-80) REVERT: D 237 LYS cc_start: 0.9454 (mmtt) cc_final: 0.9133 (mmtp) REVERT: D 249 MET cc_start: 0.9354 (mmp) cc_final: 0.9123 (mmp) REVERT: D 251 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7041 (tttm) REVERT: D 289 GLU cc_start: 0.8462 (tp30) cc_final: 0.8145 (tp30) REVERT: D 312 PHE cc_start: 0.9117 (m-80) cc_final: 0.8600 (m-80) REVERT: D 337 SER cc_start: 0.9223 (m) cc_final: 0.8906 (t) REVERT: D 338 MET cc_start: 0.8797 (mtp) cc_final: 0.8546 (mtp) REVERT: D 354 LEU cc_start: 0.9202 (mt) cc_final: 0.8936 (mt) REVERT: D 361 GLU cc_start: 0.8264 (mt-10) cc_final: 0.6921 (tp30) REVERT: D 400 TYR cc_start: 0.8604 (t80) cc_final: 0.8005 (t80) REVERT: D 414 LYS cc_start: 0.9361 (tppt) cc_final: 0.9139 (ttmm) REVERT: D 492 LEU cc_start: 0.9194 (mt) cc_final: 0.8599 (mt) REVERT: D 526 ARG cc_start: 0.9438 (ptt90) cc_final: 0.8934 (ptp90) REVERT: D 546 LEU cc_start: 0.8377 (tp) cc_final: 0.8152 (tp) REVERT: D 558 PHE cc_start: 0.8511 (t80) cc_final: 0.7569 (t80) REVERT: D 564 LEU cc_start: 0.9191 (tp) cc_final: 0.8991 (tp) REVERT: D 587 PHE cc_start: 0.9364 (t80) cc_final: 0.8753 (t80) REVERT: D 604 MET cc_start: 0.7955 (tpp) cc_final: 0.6888 (mmm) REVERT: D 656 ILE cc_start: 0.8578 (mt) cc_final: 0.8042 (mm) REVERT: D 661 PHE cc_start: 0.9461 (t80) cc_final: 0.9246 (t80) REVERT: D 664 MET cc_start: 0.8880 (ptm) cc_final: 0.8491 (ptm) REVERT: D 689 ILE cc_start: 0.8480 (mm) cc_final: 0.7683 (tp) REVERT: D 717 LYS cc_start: 0.8448 (tppt) cc_final: 0.8215 (tppt) REVERT: D 723 GLU cc_start: 0.9587 (mm-30) cc_final: 0.9214 (mm-30) REVERT: D 725 GLU cc_start: 0.9299 (tt0) cc_final: 0.8756 (tp30) REVERT: D 808 ASN cc_start: 0.8826 (m-40) cc_final: 0.8371 (m-40) REVERT: U 125 ARG cc_start: 0.9478 (mmm160) cc_final: 0.9271 (mmm160) REVERT: U 126 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8885 (mm-30) REVERT: U 131 LYS cc_start: 0.9502 (mtpp) cc_final: 0.9057 (mmmt) REVERT: U 132 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8866 (mt-10) outliers start: 52 outliers final: 23 residues processed: 549 average time/residue: 0.1339 time to fit residues: 114.0334 Evaluate side-chains 498 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 469 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 397 CYS Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain C residue 617 TYR Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain U residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 138 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 208 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 14 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 832 ASN ** U 122 GLN ** 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 = 0.3817 r_free = 0.3817 target = 0.095616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.071163 restraints weight = 68191.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.073747 restraints weight = 33700.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.075459 restraints weight = 20689.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.076609 restraints weight = 14434.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.077372 restraints weight = 11051.432| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 19090 Z= 0.147 Angle : 0.701 12.516 25841 Z= 0.355 Chirality : 0.045 0.392 2876 Planarity : 0.004 0.075 3326 Dihedral : 5.684 97.699 2528 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.43 % Rotamer: Outliers : 2.66 % Allowed : 17.13 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.80 (0.18), residues: 2271 helix: 1.13 (0.14), residues: 1296 sheet: -1.08 (0.39), residues: 176 loop : 0.11 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 806 TYR 0.052 0.002 TYR D 345 PHE 0.023 0.002 PHE D 679 TRP 0.019 0.001 TRP A 347 HIS 0.009 0.001 HIS U 127 Details of bonding type rmsd covalent geometry : bond 0.00317 (19090) covalent geometry : angle 0.70063 (25841) hydrogen bonds : bond 0.04911 ( 1061) hydrogen bonds : angle 5.09909 ( 3081) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 512 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8755 (mtm) cc_final: 0.8534 (mtt) REVERT: A 165 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7365 (mmtm) REVERT: A 212 ILE cc_start: 0.9248 (tp) cc_final: 0.8931 (mm) REVERT: A 310 MET cc_start: 0.7702 (tpp) cc_final: 0.7461 (mmt) REVERT: A 314 THR cc_start: 0.8959 (m) cc_final: 0.8734 (p) REVERT: A 320 ASN cc_start: 0.9275 (p0) cc_final: 0.8830 (p0) REVERT: A 416 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7992 (mmp) REVERT: B 28 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8649 (mt-10) REVERT: B 50 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8378 (m) REVERT: B 132 ASN cc_start: 0.8439 (t0) cc_final: 0.7785 (t0) REVERT: B 160 ASP cc_start: 0.8485 (t0) cc_final: 0.8253 (p0) REVERT: B 320 ASN cc_start: 0.8562 (p0) cc_final: 0.8277 (p0) REVERT: B 323 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8862 (tp) REVERT: B 335 MET cc_start: 0.9483 (tpp) cc_final: 0.9005 (tpp) REVERT: B 352 MET cc_start: 0.8539 (mpp) cc_final: 0.8015 (mpp) REVERT: B 423 PHE cc_start: 0.6046 (t80) cc_final: 0.5833 (t80) REVERT: C 8 ASP cc_start: 0.8668 (t70) cc_final: 0.8414 (t70) REVERT: C 43 LEU cc_start: 0.8887 (mt) cc_final: 0.8549 (mp) REVERT: C 55 GLN cc_start: 0.9146 (tt0) cc_final: 0.8916 (tp40) REVERT: C 63 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9271 (mm) REVERT: C 115 GLN cc_start: 0.9227 (mt0) cc_final: 0.8763 (mt0) REVERT: C 118 ILE cc_start: 0.9574 (mm) cc_final: 0.9164 (tt) REVERT: C 133 MET cc_start: 0.9341 (ptp) cc_final: 0.8313 (ptt) REVERT: C 164 LYS cc_start: 0.9239 (mmmm) cc_final: 0.8948 (mmmm) REVERT: C 178 ASN cc_start: 0.9219 (m-40) cc_final: 0.8854 (m110) REVERT: C 195 GLU cc_start: 0.9253 (tp30) cc_final: 0.8866 (tp30) REVERT: C 231 MET cc_start: 0.7347 (mtm) cc_final: 0.6975 (ptp) REVERT: C 266 MET cc_start: 0.9110 (tmm) cc_final: 0.8888 (tmm) REVERT: C 277 GLN cc_start: 0.9051 (tt0) cc_final: 0.8822 (tt0) REVERT: C 278 ASP cc_start: 0.8706 (p0) cc_final: 0.7969 (p0) REVERT: C 340 ASP cc_start: 0.9383 (m-30) cc_final: 0.8501 (p0) REVERT: C 379 ASN cc_start: 0.9262 (p0) cc_final: 0.9041 (p0) REVERT: C 430 GLN cc_start: 0.8729 (tm-30) cc_final: 0.7994 (tm-30) REVERT: C 469 ARG cc_start: 0.8759 (ttp80) cc_final: 0.8192 (ptm-80) REVERT: C 499 LEU cc_start: 0.8882 (mm) cc_final: 0.8452 (tt) REVERT: C 636 MET cc_start: 0.9220 (mmm) cc_final: 0.8855 (mmm) REVERT: C 646 TYR cc_start: 0.9044 (t80) cc_final: 0.8726 (t80) REVERT: C 648 ASN cc_start: 0.9214 (m-40) cc_final: 0.8737 (p0) REVERT: C 664 ARG cc_start: 0.9440 (mmm-85) cc_final: 0.9224 (mmp80) REVERT: C 674 ASN cc_start: 0.8800 (t0) cc_final: 0.8313 (t0) REVERT: C 677 GLU cc_start: 0.8197 (pp20) cc_final: 0.7930 (pp20) REVERT: C 684 MET cc_start: 0.9382 (mmp) cc_final: 0.8887 (mmm) REVERT: C 700 PHE cc_start: 0.9413 (m-10) cc_final: 0.8990 (m-80) REVERT: C 708 LYS cc_start: 0.7854 (pttt) cc_final: 0.7548 (pttm) REVERT: C 782 PHE cc_start: 0.9316 (t80) cc_final: 0.8857 (m-80) REVERT: C 806 ARG cc_start: 0.8864 (ttm110) cc_final: 0.8661 (ttm110) REVERT: D 167 LEU cc_start: 0.9324 (mt) cc_final: 0.9017 (mt) REVERT: D 187 TYR cc_start: 0.9298 (m-80) cc_final: 0.8394 (m-80) REVERT: D 225 PHE cc_start: 0.9620 (m-10) cc_final: 0.9369 (m-80) REVERT: D 236 TYR cc_start: 0.8158 (m-10) cc_final: 0.7870 (m-80) REVERT: D 237 LYS cc_start: 0.9418 (mmtt) cc_final: 0.9143 (mmtp) REVERT: D 242 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8423 (ttp80) REVERT: D 251 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.7030 (tttm) REVERT: D 289 GLU cc_start: 0.8444 (tp30) cc_final: 0.8072 (tp30) REVERT: D 312 PHE cc_start: 0.9092 (m-80) cc_final: 0.8524 (m-80) REVERT: D 337 SER cc_start: 0.9256 (m) cc_final: 0.8932 (t) REVERT: D 338 MET cc_start: 0.8841 (mtp) cc_final: 0.8522 (mtp) REVERT: D 400 TYR cc_start: 0.8667 (t80) cc_final: 0.7968 (t80) REVERT: D 414 LYS cc_start: 0.9436 (tppt) cc_final: 0.9042 (tppt) REVERT: D 471 ARG cc_start: 0.9216 (ptp-110) cc_final: 0.8352 (ttm170) REVERT: D 492 LEU cc_start: 0.9097 (mt) cc_final: 0.8839 (mt) REVERT: D 526 ARG cc_start: 0.9394 (ptt90) cc_final: 0.8916 (ptp90) REVERT: D 529 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.9096 (tpt) REVERT: D 546 LEU cc_start: 0.8380 (tp) cc_final: 0.8144 (tp) REVERT: D 558 PHE cc_start: 0.8555 (t80) cc_final: 0.7760 (t80) REVERT: D 564 LEU cc_start: 0.9146 (tp) cc_final: 0.8925 (tp) REVERT: D 587 PHE cc_start: 0.9358 (t80) cc_final: 0.8789 (t80) REVERT: D 661 PHE cc_start: 0.9445 (t80) cc_final: 0.9166 (t80) REVERT: D 664 MET cc_start: 0.8961 (ptm) cc_final: 0.8439 (ptm) REVERT: D 667 LYS cc_start: 0.9752 (mttt) cc_final: 0.9345 (mtmm) REVERT: D 689 ILE cc_start: 0.8627 (mm) cc_final: 0.7819 (tp) REVERT: D 723 GLU cc_start: 0.9668 (mm-30) cc_final: 0.9280 (mm-30) REVERT: D 725 GLU cc_start: 0.9302 (tt0) cc_final: 0.8894 (tt0) REVERT: D 741 PHE cc_start: 0.7856 (m-80) cc_final: 0.6975 (m-80) REVERT: D 808 ASN cc_start: 0.8901 (m-40) cc_final: 0.8438 (m-40) REVERT: U 126 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8932 (mm-30) REVERT: U 131 LYS cc_start: 0.9475 (mtpp) cc_final: 0.9192 (mtpp) outliers start: 56 outliers final: 35 residues processed: 541 average time/residue: 0.1344 time to fit residues: 112.3169 Evaluate side-chains 517 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 476 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 407 TYR Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 397 CYS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 617 TYR Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 529 MET Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain U residue 119 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 124 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 182 optimal weight: 0.6980 chunk 156 optimal weight: 0.0980 chunk 58 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 223 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 GLN C 696 GLN ** U 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.096466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.071874 restraints weight = 67623.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.074484 restraints weight = 33763.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.076174 restraints weight = 20785.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.077329 restraints weight = 14580.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.078109 restraints weight = 11206.840| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19090 Z= 0.139 Angle : 0.712 16.488 25841 Z= 0.354 Chirality : 0.045 0.372 2876 Planarity : 0.004 0.075 3326 Dihedral : 5.543 91.410 2528 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 2.75 % Allowed : 18.22 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.77 (0.18), residues: 2271 helix: 1.14 (0.14), residues: 1292 sheet: -1.25 (0.40), residues: 166 loop : 0.06 (0.23), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 14 TYR 0.040 0.002 TYR D 345 PHE 0.023 0.002 PHE D 679 TRP 0.021 0.001 TRP A 347 HIS 0.008 0.001 HIS U 127 Details of bonding type rmsd covalent geometry : bond 0.00299 (19090) covalent geometry : angle 0.71162 (25841) hydrogen bonds : bond 0.04715 ( 1061) hydrogen bonds : angle 5.00767 ( 3081) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 516 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8744 (mtm) cc_final: 0.8502 (mtt) REVERT: A 126 GLU cc_start: 0.8362 (tp30) cc_final: 0.7970 (tp30) REVERT: A 165 LYS cc_start: 0.7843 (mmtt) cc_final: 0.7493 (mmtm) REVERT: A 212 ILE cc_start: 0.9160 (tp) cc_final: 0.8867 (mm) REVERT: A 239 THR cc_start: 0.9479 (m) cc_final: 0.9215 (t) REVERT: A 314 THR cc_start: 0.8982 (m) cc_final: 0.8728 (p) REVERT: A 375 MET cc_start: 0.8588 (ttp) cc_final: 0.8366 (ttm) REVERT: A 416 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7977 (mmp) REVERT: B 28 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8652 (mt-10) REVERT: B 49 ASP cc_start: 0.9196 (t0) cc_final: 0.8893 (t0) REVERT: B 132 ASN cc_start: 0.8444 (t0) cc_final: 0.7781 (t0) REVERT: B 169 THR cc_start: 0.9521 (m) cc_final: 0.9196 (p) REVERT: B 248 MET cc_start: 0.7489 (tpt) cc_final: 0.6844 (tpp) REVERT: B 320 ASN cc_start: 0.8662 (p0) cc_final: 0.8319 (p0) REVERT: B 335 MET cc_start: 0.9488 (tpp) cc_final: 0.8972 (tpp) REVERT: B 352 MET cc_start: 0.8478 (mpp) cc_final: 0.7990 (mpp) REVERT: B 380 MET cc_start: 0.4005 (OUTLIER) cc_final: 0.3130 (mtt) REVERT: B 423 PHE cc_start: 0.6032 (t80) cc_final: 0.5801 (t80) REVERT: C 8 ASP cc_start: 0.8569 (t70) cc_final: 0.8301 (t70) REVERT: C 63 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9215 (mm) REVERT: C 114 LYS cc_start: 0.9411 (tttt) cc_final: 0.9164 (tptt) REVERT: C 115 GLN cc_start: 0.9157 (mt0) cc_final: 0.8679 (mt0) REVERT: C 118 ILE cc_start: 0.9590 (mm) cc_final: 0.9227 (tt) REVERT: C 133 MET cc_start: 0.9300 (ptp) cc_final: 0.8216 (ptt) REVERT: C 164 LYS cc_start: 0.9170 (mmmm) cc_final: 0.8878 (mmmm) REVERT: C 174 GLU cc_start: 0.8821 (tp30) cc_final: 0.8514 (tp30) REVERT: C 179 GLU cc_start: 0.9152 (tt0) cc_final: 0.8881 (tt0) REVERT: C 195 GLU cc_start: 0.9244 (tp30) cc_final: 0.8106 (tp30) REVERT: C 266 MET cc_start: 0.9123 (tmm) cc_final: 0.8843 (tmm) REVERT: C 277 GLN cc_start: 0.9048 (tt0) cc_final: 0.8841 (tt0) REVERT: C 278 ASP cc_start: 0.8706 (p0) cc_final: 0.7962 (p0) REVERT: C 331 LEU cc_start: 0.9504 (tp) cc_final: 0.9126 (tp) REVERT: C 340 ASP cc_start: 0.9375 (m-30) cc_final: 0.8551 (p0) REVERT: C 379 ASN cc_start: 0.9224 (p0) cc_final: 0.8973 (p0) REVERT: C 430 GLN cc_start: 0.8826 (tm-30) cc_final: 0.7816 (tm-30) REVERT: C 469 ARG cc_start: 0.8749 (ttp80) cc_final: 0.7888 (ptm-80) REVERT: C 479 ARG cc_start: 0.9213 (mmm-85) cc_final: 0.8701 (mmm160) REVERT: C 483 MET cc_start: 0.7673 (ppp) cc_final: 0.7347 (ppp) REVERT: C 579 MET cc_start: 0.9695 (mmp) cc_final: 0.9453 (mmm) REVERT: C 592 LEU cc_start: 0.9689 (mt) cc_final: 0.9024 (tt) REVERT: C 606 LEU cc_start: 0.7029 (mm) cc_final: 0.6773 (mm) REVERT: C 636 MET cc_start: 0.9180 (mmm) cc_final: 0.8772 (mmm) REVERT: C 646 TYR cc_start: 0.8955 (t80) cc_final: 0.8656 (t80) REVERT: C 648 ASN cc_start: 0.9259 (m-40) cc_final: 0.8823 (p0) REVERT: C 664 ARG cc_start: 0.9445 (mmm-85) cc_final: 0.9225 (mmp80) REVERT: C 684 MET cc_start: 0.9474 (mmp) cc_final: 0.9192 (mmm) REVERT: C 700 PHE cc_start: 0.9421 (m-10) cc_final: 0.8948 (m-80) REVERT: C 708 LYS cc_start: 0.7780 (pttt) cc_final: 0.7456 (pttm) REVERT: C 782 PHE cc_start: 0.9313 (t80) cc_final: 0.8891 (m-80) REVERT: D 167 LEU cc_start: 0.9306 (mt) cc_final: 0.9000 (mt) REVERT: D 225 PHE cc_start: 0.9604 (m-10) cc_final: 0.9263 (m-80) REVERT: D 236 TYR cc_start: 0.8121 (m-10) cc_final: 0.7813 (m-80) REVERT: D 237 LYS cc_start: 0.9423 (mmtt) cc_final: 0.9217 (mmtp) REVERT: D 251 LYS cc_start: 0.7053 (OUTLIER) cc_final: 0.6613 (tttm) REVERT: D 289 GLU cc_start: 0.8402 (tp30) cc_final: 0.8079 (tp30) REVERT: D 312 PHE cc_start: 0.9076 (m-80) cc_final: 0.8489 (m-80) REVERT: D 337 SER cc_start: 0.9312 (m) cc_final: 0.8935 (t) REVERT: D 361 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8027 (tt0) REVERT: D 396 LYS cc_start: 0.9112 (mmmm) cc_final: 0.8399 (mmmm) REVERT: D 400 TYR cc_start: 0.8558 (t80) cc_final: 0.7856 (t80) REVERT: D 413 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8392 (pp20) REVERT: D 452 GLN cc_start: 0.9336 (tt0) cc_final: 0.8999 (tt0) REVERT: D 471 ARG cc_start: 0.9036 (ptp-110) cc_final: 0.8234 (ttm170) REVERT: D 492 LEU cc_start: 0.9178 (mt) cc_final: 0.8859 (mt) REVERT: D 526 ARG cc_start: 0.9385 (ptt90) cc_final: 0.8943 (ptp90) REVERT: D 546 LEU cc_start: 0.8277 (tp) cc_final: 0.8048 (tp) REVERT: D 558 PHE cc_start: 0.8479 (t80) cc_final: 0.7576 (t80) REVERT: D 564 LEU cc_start: 0.9145 (tp) cc_final: 0.8933 (tp) REVERT: D 624 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7882 (tp) REVERT: D 649 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8414 (mt-10) REVERT: D 652 TYR cc_start: 0.8745 (m-80) cc_final: 0.7968 (t80) REVERT: D 661 PHE cc_start: 0.9446 (t80) cc_final: 0.9155 (t80) REVERT: D 664 MET cc_start: 0.8969 (ptm) cc_final: 0.8526 (ptm) REVERT: D 689 ILE cc_start: 0.8389 (mm) cc_final: 0.7554 (tp) REVERT: D 723 GLU cc_start: 0.9671 (mm-30) cc_final: 0.9274 (mm-30) REVERT: D 725 GLU cc_start: 0.9317 (tt0) cc_final: 0.8941 (tp30) REVERT: D 741 PHE cc_start: 0.7753 (m-80) cc_final: 0.6859 (m-80) REVERT: D 808 ASN cc_start: 0.8880 (m-40) cc_final: 0.8393 (m-40) REVERT: U 117 GLN cc_start: 0.8503 (pm20) cc_final: 0.8131 (mp10) REVERT: U 126 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8936 (mm-30) REVERT: U 131 LYS cc_start: 0.9489 (mtpp) cc_final: 0.9234 (mmmt) outliers start: 58 outliers final: 35 residues processed: 547 average time/residue: 0.1331 time to fit residues: 112.5925 Evaluate side-chains 520 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 479 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 416 MET Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain B residue 7 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 272 PHE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 397 CYS Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 617 TYR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 529 MET Chi-restraints excluded: chain D residue 571 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 845 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 145 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN B 29 HIS ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 342 ASN ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 GLN ** U 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.096271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071721 restraints weight = 68557.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.074294 restraints weight = 34148.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.075992 restraints weight = 21007.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.077100 restraints weight = 14676.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.077891 restraints weight = 11292.676| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19090 Z= 0.148 Angle : 0.717 14.757 25841 Z= 0.358 Chirality : 0.045 0.391 2876 Planarity : 0.005 0.077 3326 Dihedral : 5.457 85.279 2528 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.52 % Favored : 96.35 % Rotamer: Outliers : 2.56 % Allowed : 19.92 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.79 (0.18), residues: 2271 helix: 1.14 (0.14), residues: 1294 sheet: -1.23 (0.39), residues: 176 loop : 0.11 (0.24), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 638 TYR 0.033 0.002 TYR C 568 PHE 0.023 0.002 PHE D 679 TRP 0.021 0.001 TRP A 347 HIS 0.007 0.001 HIS U 127 Details of bonding type rmsd covalent geometry : bond 0.00325 (19090) covalent geometry : angle 0.71674 (25841) hydrogen bonds : bond 0.04626 ( 1061) hydrogen bonds : angle 4.99142 ( 3081) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 493 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8797 (mtm) cc_final: 0.8570 (mtt) REVERT: A 126 GLU cc_start: 0.8498 (tp30) cc_final: 0.8156 (tp30) REVERT: A 165 LYS cc_start: 0.7940 (mmtt) cc_final: 0.7704 (mmtp) REVERT: A 212 ILE cc_start: 0.9176 (tp) cc_final: 0.8883 (mm) REVERT: A 239 THR cc_start: 0.9436 (m) cc_final: 0.9174 (t) REVERT: A 314 THR cc_start: 0.8985 (m) cc_final: 0.8656 (p) REVERT: A 375 MET cc_start: 0.8488 (ttp) cc_final: 0.8101 (ptm) REVERT: B 28 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8650 (mt-10) REVERT: B 132 ASN cc_start: 0.8453 (t0) cc_final: 0.7791 (t0) REVERT: B 162 TYR cc_start: 0.8409 (m-80) cc_final: 0.7725 (m-80) REVERT: B 169 THR cc_start: 0.9502 (m) cc_final: 0.9191 (p) REVERT: B 323 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8858 (tp) REVERT: B 335 MET cc_start: 0.9490 (tpp) cc_final: 0.8920 (tpp) REVERT: B 352 MET cc_start: 0.8464 (mpp) cc_final: 0.7921 (mpp) REVERT: B 423 PHE cc_start: 0.5846 (t80) cc_final: 0.5607 (t80) REVERT: C 8 ASP cc_start: 0.8614 (t70) cc_final: 0.8350 (t70) REVERT: C 63 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9176 (mm) REVERT: C 97 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8281 (mmmm) REVERT: C 114 LYS cc_start: 0.9366 (tttt) cc_final: 0.9075 (tptt) REVERT: C 115 GLN cc_start: 0.9068 (mt0) cc_final: 0.8478 (mt0) REVERT: C 118 ILE cc_start: 0.9639 (mm) cc_final: 0.9316 (tt) REVERT: C 133 MET cc_start: 0.9296 (ptp) cc_final: 0.8235 (ptt) REVERT: C 164 LYS cc_start: 0.9146 (mmmm) cc_final: 0.8862 (mmmm) REVERT: C 174 GLU cc_start: 0.8907 (tp30) cc_final: 0.8593 (tp30) REVERT: C 195 GLU cc_start: 0.9117 (tp30) cc_final: 0.8864 (tp30) REVERT: C 266 MET cc_start: 0.9143 (tmm) cc_final: 0.8858 (tmm) REVERT: C 277 GLN cc_start: 0.9021 (tt0) cc_final: 0.8810 (tt0) REVERT: C 278 ASP cc_start: 0.8738 (p0) cc_final: 0.8002 (p0) REVERT: C 331 LEU cc_start: 0.9498 (tp) cc_final: 0.9126 (tp) REVERT: C 379 ASN cc_start: 0.9250 (p0) cc_final: 0.9002 (p0) REVERT: C 430 GLN cc_start: 0.8661 (tm-30) cc_final: 0.7584 (tm-30) REVERT: C 441 LYS cc_start: 0.9281 (mmmm) cc_final: 0.8959 (mtmt) REVERT: C 469 ARG cc_start: 0.8699 (ttp80) cc_final: 0.8333 (ttp80) REVERT: C 483 MET cc_start: 0.7794 (ppp) cc_final: 0.7401 (ppp) REVERT: C 592 LEU cc_start: 0.9626 (mt) cc_final: 0.9041 (tt) REVERT: C 612 TRP cc_start: 0.8276 (p-90) cc_final: 0.7826 (p-90) REVERT: C 636 MET cc_start: 0.9186 (mmm) cc_final: 0.8729 (mmm) REVERT: C 646 TYR cc_start: 0.8983 (t80) cc_final: 0.8605 (t80) REVERT: C 661 LYS cc_start: 0.9368 (ptpp) cc_final: 0.9159 (ptpp) REVERT: C 664 ARG cc_start: 0.9437 (mmm-85) cc_final: 0.9227 (mmp80) REVERT: C 684 MET cc_start: 0.9522 (mmp) cc_final: 0.9236 (mmm) REVERT: C 700 PHE cc_start: 0.9429 (m-10) cc_final: 0.8943 (m-80) REVERT: C 708 LYS cc_start: 0.7827 (pttt) cc_final: 0.7494 (pttm) REVERT: C 782 PHE cc_start: 0.9299 (t80) cc_final: 0.8894 (m-80) REVERT: D 167 LEU cc_start: 0.9339 (mt) cc_final: 0.9021 (mt) REVERT: D 225 PHE cc_start: 0.9605 (m-10) cc_final: 0.9335 (m-80) REVERT: D 236 TYR cc_start: 0.8128 (m-10) cc_final: 0.7815 (m-80) REVERT: D 251 LYS cc_start: 0.7083 (OUTLIER) cc_final: 0.6520 (tttm) REVERT: D 312 PHE cc_start: 0.9039 (m-80) cc_final: 0.8486 (m-80) REVERT: D 337 SER cc_start: 0.9331 (m) cc_final: 0.8989 (t) REVERT: D 361 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8022 (tt0) REVERT: D 400 TYR cc_start: 0.8615 (t80) cc_final: 0.7996 (t80) REVERT: D 471 ARG cc_start: 0.9108 (ptp-110) cc_final: 0.8328 (ttm170) REVERT: D 478 LYS cc_start: 0.9296 (tmtt) cc_final: 0.9010 (ttpp) REVERT: D 492 LEU cc_start: 0.9205 (mt) cc_final: 0.8887 (mt) REVERT: D 518 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9141 (mp0) REVERT: D 529 MET cc_start: 0.9410 (OUTLIER) cc_final: 0.9048 (mmm) REVERT: D 546 LEU cc_start: 0.8145 (tp) cc_final: 0.7925 (tp) REVERT: D 558 PHE cc_start: 0.8513 (t80) cc_final: 0.7773 (t80) REVERT: D 564 LEU cc_start: 0.9127 (tp) cc_final: 0.8910 (tp) REVERT: D 604 MET cc_start: 0.8443 (tpp) cc_final: 0.7784 (tpp) REVERT: D 624 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7874 (tp) REVERT: D 649 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8606 (mt-10) REVERT: D 652 TYR cc_start: 0.8736 (m-80) cc_final: 0.7910 (t80) REVERT: D 661 PHE cc_start: 0.9452 (t80) cc_final: 0.8983 (t80) REVERT: D 664 MET cc_start: 0.9029 (ptm) cc_final: 0.8518 (ptm) REVERT: D 667 LYS cc_start: 0.9743 (mttt) cc_final: 0.9298 (mtpt) REVERT: D 723 GLU cc_start: 0.9688 (mm-30) cc_final: 0.9315 (mm-30) REVERT: D 741 PHE cc_start: 0.7943 (m-80) cc_final: 0.6912 (m-80) REVERT: D 808 ASN cc_start: 0.8906 (m-40) cc_final: 0.8459 (m-40) REVERT: D 843 LYS cc_start: 0.9687 (mtmt) cc_final: 0.9465 (ptpp) REVERT: U 117 GLN cc_start: 0.8494 (pm20) cc_final: 0.8119 (mp10) REVERT: U 126 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8925 (mm-30) REVERT: U 131 LYS cc_start: 0.9582 (mtpp) cc_final: 0.9294 (mmmt) REVERT: U 133 ARG cc_start: 0.9217 (ptp90) cc_final: 0.8790 (ptp90) outliers start: 54 outliers final: 38 residues processed: 518 average time/residue: 0.1290 time to fit residues: 103.5071 Evaluate side-chains 513 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 470 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 198 ARG Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 397 CYS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 617 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain D residue 179 ILE Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 529 MET Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 845 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 63 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 108 optimal weight: 7.9990 chunk 94 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 8.9990 overall best weight: 1.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 ASN B 29 HIS ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 GLN C 696 GLN ** U 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.096009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071599 restraints weight = 68465.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.074186 restraints weight = 34190.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.075869 restraints weight = 21041.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.076919 restraints weight = 14738.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.077729 restraints weight = 11468.449| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 19090 Z= 0.152 Angle : 0.739 15.206 25841 Z= 0.368 Chirality : 0.045 0.387 2876 Planarity : 0.005 0.122 3326 Dihedral : 5.416 80.216 2528 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.01 % Favored : 95.90 % Rotamer: Outliers : 2.23 % Allowed : 20.40 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.78 (0.18), residues: 2271 helix: 1.15 (0.14), residues: 1294 sheet: -1.30 (0.39), residues: 177 loop : 0.11 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 806 TYR 0.036 0.002 TYR C 568 PHE 0.040 0.002 PHE C 639 TRP 0.022 0.002 TRP A 347 HIS 0.007 0.001 HIS U 127 Details of bonding type rmsd covalent geometry : bond 0.00336 (19090) covalent geometry : angle 0.73883 (25841) hydrogen bonds : bond 0.04567 ( 1061) hydrogen bonds : angle 5.00094 ( 3081) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 491 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.8808 (mtm) cc_final: 0.8557 (mtt) REVERT: A 126 GLU cc_start: 0.8518 (tp30) cc_final: 0.8284 (tp30) REVERT: A 212 ILE cc_start: 0.9182 (tp) cc_final: 0.8887 (mm) REVERT: A 239 THR cc_start: 0.9357 (m) cc_final: 0.9060 (t) REVERT: A 314 THR cc_start: 0.8960 (m) cc_final: 0.8628 (p) REVERT: A 375 MET cc_start: 0.8416 (ttp) cc_final: 0.8089 (ptm) REVERT: A 416 MET cc_start: 0.7733 (mmp) cc_final: 0.7387 (mmp) REVERT: B 28 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8683 (mt-10) REVERT: B 132 ASN cc_start: 0.8457 (t0) cc_final: 0.7795 (t0) REVERT: B 162 TYR cc_start: 0.8371 (m-80) cc_final: 0.7587 (m-80) REVERT: B 169 THR cc_start: 0.9486 (m) cc_final: 0.9163 (p) REVERT: B 323 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8895 (tp) REVERT: B 335 MET cc_start: 0.9514 (tpp) cc_final: 0.8808 (tpp) REVERT: B 352 MET cc_start: 0.8467 (mpp) cc_final: 0.7800 (mpp) REVERT: B 423 PHE cc_start: 0.5849 (t80) cc_final: 0.5622 (t80) REVERT: C 8 ASP cc_start: 0.8568 (t70) cc_final: 0.8338 (t70) REVERT: C 63 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9201 (mm) REVERT: C 97 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8339 (mmmm) REVERT: C 114 LYS cc_start: 0.9396 (tttt) cc_final: 0.9087 (tptt) REVERT: C 115 GLN cc_start: 0.9044 (mt0) cc_final: 0.8474 (mt0) REVERT: C 118 ILE cc_start: 0.9654 (mm) cc_final: 0.9338 (tt) REVERT: C 133 MET cc_start: 0.9287 (ptp) cc_final: 0.8245 (ptt) REVERT: C 160 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7703 (ptt180) REVERT: C 164 LYS cc_start: 0.9085 (mmmm) cc_final: 0.8817 (mmmm) REVERT: C 195 GLU cc_start: 0.9094 (tp30) cc_final: 0.8779 (tp30) REVERT: C 266 MET cc_start: 0.9147 (tmm) cc_final: 0.8942 (tmm) REVERT: C 278 ASP cc_start: 0.8745 (p0) cc_final: 0.8050 (p0) REVERT: C 331 LEU cc_start: 0.9484 (tp) cc_final: 0.9097 (tp) REVERT: C 379 ASN cc_start: 0.9232 (p0) cc_final: 0.8985 (p0) REVERT: C 430 GLN cc_start: 0.8637 (tm-30) cc_final: 0.7554 (tm-30) REVERT: C 441 LYS cc_start: 0.9317 (mmmm) cc_final: 0.9003 (mtmt) REVERT: C 469 ARG cc_start: 0.8746 (ttp80) cc_final: 0.8313 (ttp80) REVERT: C 483 MET cc_start: 0.7817 (ppp) cc_final: 0.7421 (ppp) REVERT: C 579 MET cc_start: 0.9463 (mmp) cc_final: 0.9152 (mmp) REVERT: C 592 LEU cc_start: 0.9682 (mt) cc_final: 0.8943 (tt) REVERT: C 612 TRP cc_start: 0.8342 (p-90) cc_final: 0.7842 (p-90) REVERT: C 636 MET cc_start: 0.8986 (mmm) cc_final: 0.8641 (mmm) REVERT: C 646 TYR cc_start: 0.9004 (t80) cc_final: 0.8575 (t80) REVERT: C 661 LYS cc_start: 0.9364 (ptpp) cc_final: 0.9130 (ptpp) REVERT: C 664 ARG cc_start: 0.9481 (mmm-85) cc_final: 0.9229 (mmp80) REVERT: C 700 PHE cc_start: 0.9377 (m-10) cc_final: 0.8884 (m-80) REVERT: C 708 LYS cc_start: 0.7659 (pttt) cc_final: 0.7276 (pttm) REVERT: C 782 PHE cc_start: 0.9292 (t80) cc_final: 0.8898 (m-80) REVERT: D 167 LEU cc_start: 0.9375 (mt) cc_final: 0.9088 (mt) REVERT: D 225 PHE cc_start: 0.9629 (m-10) cc_final: 0.9308 (m-80) REVERT: D 236 TYR cc_start: 0.8161 (m-10) cc_final: 0.7847 (m-80) REVERT: D 251 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6533 (tttm) REVERT: D 334 LEU cc_start: 0.9433 (mm) cc_final: 0.9147 (mt) REVERT: D 337 SER cc_start: 0.9314 (m) cc_final: 0.8981 (p) REVERT: D 361 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7941 (tt0) REVERT: D 396 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8534 (mmmm) REVERT: D 400 TYR cc_start: 0.8666 (t80) cc_final: 0.8009 (t80) REVERT: D 471 ARG cc_start: 0.9089 (ptp-110) cc_final: 0.8336 (ttm170) REVERT: D 478 LYS cc_start: 0.9276 (tmtt) cc_final: 0.9032 (ttpp) REVERT: D 492 LEU cc_start: 0.9228 (mt) cc_final: 0.8929 (mt) REVERT: D 529 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.9054 (mmm) REVERT: D 546 LEU cc_start: 0.8140 (tp) cc_final: 0.7914 (tp) REVERT: D 558 PHE cc_start: 0.8519 (t80) cc_final: 0.7793 (t80) REVERT: D 564 LEU cc_start: 0.9146 (tp) cc_final: 0.8922 (tp) REVERT: D 624 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7837 (tp) REVERT: D 649 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8567 (mt-10) REVERT: D 652 TYR cc_start: 0.8702 (m-80) cc_final: 0.8027 (t80) REVERT: D 661 PHE cc_start: 0.9432 (t80) cc_final: 0.8981 (t80) REVERT: D 664 MET cc_start: 0.9037 (ptm) cc_final: 0.8527 (ptm) REVERT: D 667 LYS cc_start: 0.9734 (mttt) cc_final: 0.9279 (mtpt) REVERT: D 723 GLU cc_start: 0.9667 (mm-30) cc_final: 0.9290 (mm-30) REVERT: D 741 PHE cc_start: 0.7998 (m-80) cc_final: 0.6995 (m-80) REVERT: D 808 ASN cc_start: 0.8884 (m-40) cc_final: 0.8443 (m-40) REVERT: D 843 LYS cc_start: 0.9660 (mtmt) cc_final: 0.9398 (ptpp) REVERT: U 117 GLN cc_start: 0.8373 (pm20) cc_final: 0.7973 (mp10) REVERT: U 126 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8910 (mm-30) REVERT: U 131 LYS cc_start: 0.9588 (mtpp) cc_final: 0.9304 (mmmt) outliers start: 47 outliers final: 36 residues processed: 515 average time/residue: 0.1327 time to fit residues: 106.0929 Evaluate side-chains 504 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 463 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 397 CYS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 617 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain D residue 204 HIS Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 529 MET Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 809 LEU Chi-restraints excluded: chain D residue 845 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 95 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 185 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS ** C 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 GLN C 665 ASN ** U 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.096308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071859 restraints weight = 68519.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.074446 restraints weight = 34364.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.076143 restraints weight = 21115.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.077259 restraints weight = 14741.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.078013 restraints weight = 11324.516| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.6229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 19090 Z= 0.150 Angle : 0.758 15.471 25841 Z= 0.378 Chirality : 0.046 0.375 2876 Planarity : 0.005 0.100 3326 Dihedral : 5.385 74.772 2528 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 2.09 % Allowed : 21.58 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.71 (0.18), residues: 2271 helix: 1.11 (0.14), residues: 1302 sheet: -1.35 (0.39), residues: 181 loop : 0.05 (0.24), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 198 TYR 0.042 0.002 TYR C 568 PHE 0.034 0.002 PHE C 639 TRP 0.024 0.002 TRP A 347 HIS 0.008 0.001 HIS U 127 Details of bonding type rmsd covalent geometry : bond 0.00336 (19090) covalent geometry : angle 0.75777 (25841) hydrogen bonds : bond 0.04520 ( 1061) hydrogen bonds : angle 5.00421 ( 3081) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 489 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.7925 (ttp80) REVERT: A 69 MET cc_start: 0.8794 (mtm) cc_final: 0.8558 (mtt) REVERT: A 212 ILE cc_start: 0.9119 (tp) cc_final: 0.8839 (mm) REVERT: A 239 THR cc_start: 0.9345 (m) cc_final: 0.9065 (t) REVERT: A 247 TYR cc_start: 0.8589 (p90) cc_final: 0.7740 (p90) REVERT: A 314 THR cc_start: 0.8939 (m) cc_final: 0.8516 (p) REVERT: A 375 MET cc_start: 0.8432 (ttp) cc_final: 0.8132 (ptm) REVERT: A 416 MET cc_start: 0.7707 (mmp) cc_final: 0.7356 (mmp) REVERT: B 28 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8694 (mt-10) REVERT: B 132 ASN cc_start: 0.8487 (t0) cc_final: 0.7795 (t0) REVERT: B 169 THR cc_start: 0.9449 (m) cc_final: 0.9140 (p) REVERT: B 170 TYR cc_start: 0.8577 (m-80) cc_final: 0.8162 (m-80) REVERT: B 323 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8951 (tp) REVERT: B 335 MET cc_start: 0.9517 (tpp) cc_final: 0.8796 (tpp) REVERT: B 352 MET cc_start: 0.8479 (mpp) cc_final: 0.7828 (mpp) REVERT: B 423 PHE cc_start: 0.5847 (t80) cc_final: 0.5636 (t80) REVERT: C 8 ASP cc_start: 0.8521 (t70) cc_final: 0.8274 (t70) REVERT: C 63 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9182 (mm) REVERT: C 97 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8241 (mmmm) REVERT: C 114 LYS cc_start: 0.9377 (tttt) cc_final: 0.9106 (tptt) REVERT: C 115 GLN cc_start: 0.9041 (mt0) cc_final: 0.8503 (mt0) REVERT: C 118 ILE cc_start: 0.9671 (mm) cc_final: 0.9367 (tt) REVERT: C 133 MET cc_start: 0.9269 (ptp) cc_final: 0.8232 (ptt) REVERT: C 156 GLU cc_start: 0.8739 (tp30) cc_final: 0.8231 (tp30) REVERT: C 164 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8821 (mmmt) REVERT: C 195 GLU cc_start: 0.9254 (tp30) cc_final: 0.8738 (tp30) REVERT: C 278 ASP cc_start: 0.8756 (p0) cc_final: 0.8032 (p0) REVERT: C 331 LEU cc_start: 0.9471 (tp) cc_final: 0.9115 (tp) REVERT: C 379 ASN cc_start: 0.9209 (p0) cc_final: 0.8985 (p0) REVERT: C 430 GLN cc_start: 0.8648 (tm-30) cc_final: 0.7627 (tm-30) REVERT: C 469 ARG cc_start: 0.8774 (ttp80) cc_final: 0.8358 (ttp80) REVERT: C 483 MET cc_start: 0.7838 (ppp) cc_final: 0.7440 (ppp) REVERT: C 579 MET cc_start: 0.9416 (mmp) cc_final: 0.8578 (mmp) REVERT: C 592 LEU cc_start: 0.9678 (mt) cc_final: 0.9414 (mm) REVERT: C 612 TRP cc_start: 0.8347 (p-90) cc_final: 0.7875 (p-90) REVERT: C 636 MET cc_start: 0.8960 (mmm) cc_final: 0.8560 (mmm) REVERT: C 646 TYR cc_start: 0.9045 (t80) cc_final: 0.8606 (t80) REVERT: C 647 PHE cc_start: 0.9381 (t80) cc_final: 0.9172 (t80) REVERT: C 648 ASN cc_start: 0.9350 (t0) cc_final: 0.9062 (t0) REVERT: C 661 LYS cc_start: 0.9348 (ptpp) cc_final: 0.9111 (ptpp) REVERT: C 664 ARG cc_start: 0.9468 (mmm-85) cc_final: 0.9212 (mmp80) REVERT: C 684 MET cc_start: 0.9385 (mmm) cc_final: 0.8957 (mmp) REVERT: C 700 PHE cc_start: 0.9376 (m-10) cc_final: 0.8850 (m-80) REVERT: C 708 LYS cc_start: 0.7702 (pttt) cc_final: 0.7297 (pttm) REVERT: C 782 PHE cc_start: 0.9263 (t80) cc_final: 0.8881 (m-80) REVERT: D 167 LEU cc_start: 0.9387 (mt) cc_final: 0.9147 (mt) REVERT: D 187 TYR cc_start: 0.9270 (m-80) cc_final: 0.8673 (m-80) REVERT: D 225 PHE cc_start: 0.9611 (m-10) cc_final: 0.9295 (m-80) REVERT: D 230 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9347 (tp) REVERT: D 236 TYR cc_start: 0.8172 (m-10) cc_final: 0.7876 (m-80) REVERT: D 251 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6536 (tttm) REVERT: D 334 LEU cc_start: 0.9461 (mm) cc_final: 0.9172 (mt) REVERT: D 337 SER cc_start: 0.9327 (m) cc_final: 0.8999 (p) REVERT: D 400 TYR cc_start: 0.8676 (t80) cc_final: 0.7948 (t80) REVERT: D 471 ARG cc_start: 0.9038 (ptp-110) cc_final: 0.8321 (ttm170) REVERT: D 478 LYS cc_start: 0.9234 (tmtt) cc_final: 0.8995 (ttpp) REVERT: D 492 LEU cc_start: 0.9212 (mt) cc_final: 0.8663 (mt) REVERT: D 558 PHE cc_start: 0.8542 (t80) cc_final: 0.7651 (t80) REVERT: D 564 LEU cc_start: 0.9170 (tp) cc_final: 0.8959 (tp) REVERT: D 649 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8584 (mt-10) REVERT: D 652 TYR cc_start: 0.8737 (m-80) cc_final: 0.8091 (t80) REVERT: D 661 PHE cc_start: 0.9431 (t80) cc_final: 0.9088 (t80) REVERT: D 667 LYS cc_start: 0.9733 (mttt) cc_final: 0.9327 (mtpt) REVERT: D 723 GLU cc_start: 0.9643 (mm-30) cc_final: 0.9268 (mm-30) REVERT: D 741 PHE cc_start: 0.8052 (m-80) cc_final: 0.7075 (m-80) REVERT: D 808 ASN cc_start: 0.8896 (m-40) cc_final: 0.8461 (m-40) REVERT: D 843 LYS cc_start: 0.9604 (mtmt) cc_final: 0.9365 (ptpp) REVERT: U 117 GLN cc_start: 0.8277 (pm20) cc_final: 0.7882 (mp10) REVERT: U 126 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8888 (mm-30) REVERT: U 131 LYS cc_start: 0.9588 (mtpp) cc_final: 0.9315 (mmmt) REVERT: U 141 LYS cc_start: 0.8207 (tppt) cc_final: 0.7968 (mmtt) outliers start: 44 outliers final: 35 residues processed: 509 average time/residue: 0.1323 time to fit residues: 104.9671 Evaluate side-chains 507 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 468 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 436 ASP Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 127 SER Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 397 CYS Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 617 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 665 ASN Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 529 MET Chi-restraints excluded: chain D residue 702 LEU Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 809 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 95 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 208 optimal weight: 0.0570 chunk 2 optimal weight: 0.9980 chunk 221 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 216 optimal weight: 0.1980 chunk 107 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 198 optimal weight: 0.0470 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS ** C 583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 GLN C 665 ASN ** U 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.097411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072426 restraints weight = 67686.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075020 restraints weight = 34034.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076726 restraints weight = 21144.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.077863 restraints weight = 14897.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.078637 restraints weight = 11518.955| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.6422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 19090 Z= 0.146 Angle : 0.783 15.270 25841 Z= 0.387 Chirality : 0.046 0.371 2876 Planarity : 0.005 0.084 3326 Dihedral : 5.343 69.913 2528 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 1.47 % Allowed : 23.06 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.74 (0.18), residues: 2271 helix: 1.14 (0.14), residues: 1296 sheet: -1.25 (0.40), residues: 171 loop : -0.00 (0.24), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 198 TYR 0.042 0.002 TYR C 568 PHE 0.046 0.002 PHE D 411 TRP 0.023 0.002 TRP A 347 HIS 0.008 0.001 HIS U 127 Details of bonding type rmsd covalent geometry : bond 0.00320 (19090) covalent geometry : angle 0.78337 (25841) hydrogen bonds : bond 0.04474 ( 1061) hydrogen bonds : angle 5.02307 ( 3081) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 488 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ARG cc_start: 0.8235 (mmm-85) cc_final: 0.7901 (ttp80) REVERT: A 69 MET cc_start: 0.8778 (mtm) cc_final: 0.8573 (mtt) REVERT: A 212 ILE cc_start: 0.9166 (tp) cc_final: 0.8866 (mm) REVERT: A 239 THR cc_start: 0.9308 (m) cc_final: 0.9035 (t) REVERT: A 247 TYR cc_start: 0.8629 (p90) cc_final: 0.7645 (p90) REVERT: A 314 THR cc_start: 0.9031 (m) cc_final: 0.8647 (p) REVERT: A 355 ASN cc_start: 0.8357 (t0) cc_final: 0.7696 (p0) REVERT: A 375 MET cc_start: 0.8391 (ttp) cc_final: 0.8136 (ptm) REVERT: A 416 MET cc_start: 0.8106 (mmp) cc_final: 0.7749 (mmp) REVERT: B 28 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8700 (mt-10) REVERT: B 132 ASN cc_start: 0.8575 (t0) cc_final: 0.7895 (t0) REVERT: B 162 TYR cc_start: 0.8212 (m-80) cc_final: 0.7353 (m-80) REVERT: B 169 THR cc_start: 0.9476 (m) cc_final: 0.9268 (p) REVERT: B 170 TYR cc_start: 0.8606 (m-80) cc_final: 0.8175 (m-80) REVERT: B 323 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8905 (tp) REVERT: B 329 ARG cc_start: 0.8796 (tpt170) cc_final: 0.8564 (tpp80) REVERT: B 335 MET cc_start: 0.9509 (tpp) cc_final: 0.8805 (tpp) REVERT: B 352 MET cc_start: 0.8454 (mpp) cc_final: 0.7792 (mpp) REVERT: B 423 PHE cc_start: 0.5840 (t80) cc_final: 0.5639 (t80) REVERT: B 434 MET cc_start: 0.8896 (mtp) cc_final: 0.8670 (mpp) REVERT: C 63 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9219 (mm) REVERT: C 97 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8263 (mmmm) REVERT: C 114 LYS cc_start: 0.9391 (tttt) cc_final: 0.9103 (tptt) REVERT: C 115 GLN cc_start: 0.8972 (mt0) cc_final: 0.8427 (mt0) REVERT: C 118 ILE cc_start: 0.9648 (mm) cc_final: 0.9316 (tt) REVERT: C 133 MET cc_start: 0.9395 (ptp) cc_final: 0.8387 (ptt) REVERT: C 195 GLU cc_start: 0.9060 (tp30) cc_final: 0.8540 (tp30) REVERT: C 278 ASP cc_start: 0.8769 (p0) cc_final: 0.8032 (p0) REVERT: C 331 LEU cc_start: 0.9474 (tp) cc_final: 0.9114 (tp) REVERT: C 379 ASN cc_start: 0.9224 (p0) cc_final: 0.8996 (p0) REVERT: C 397 CYS cc_start: 0.9465 (OUTLIER) cc_final: 0.9079 (t) REVERT: C 430 GLN cc_start: 0.8523 (tm-30) cc_final: 0.7508 (tm-30) REVERT: C 443 MET cc_start: 0.8232 (tpt) cc_final: 0.7927 (tpt) REVERT: C 469 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8307 (ttp80) REVERT: C 483 MET cc_start: 0.7869 (ppp) cc_final: 0.7432 (ppp) REVERT: C 579 MET cc_start: 0.9378 (mmp) cc_final: 0.8484 (mmp) REVERT: C 612 TRP cc_start: 0.8145 (p-90) cc_final: 0.7745 (p-90) REVERT: C 636 MET cc_start: 0.8981 (mmm) cc_final: 0.8614 (mmm) REVERT: C 644 MET cc_start: 0.9332 (tpp) cc_final: 0.9029 (mmm) REVERT: C 646 TYR cc_start: 0.8905 (t80) cc_final: 0.8533 (t80) REVERT: C 648 ASN cc_start: 0.9381 (t0) cc_final: 0.9062 (t0) REVERT: C 661 LYS cc_start: 0.9360 (ptpp) cc_final: 0.9116 (ptpp) REVERT: C 664 ARG cc_start: 0.9413 (mmm-85) cc_final: 0.9184 (mmp80) REVERT: C 700 PHE cc_start: 0.9380 (m-10) cc_final: 0.8848 (m-80) REVERT: C 782 PHE cc_start: 0.9295 (t80) cc_final: 0.8890 (m-80) REVERT: D 167 LEU cc_start: 0.9364 (mt) cc_final: 0.9110 (mt) REVERT: D 181 GLU cc_start: 0.9359 (pm20) cc_final: 0.9159 (pm20) REVERT: D 187 TYR cc_start: 0.9259 (m-80) cc_final: 0.8660 (m-80) REVERT: D 225 PHE cc_start: 0.9605 (m-10) cc_final: 0.9273 (m-80) REVERT: D 230 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9366 (tp) REVERT: D 236 TYR cc_start: 0.8170 (m-10) cc_final: 0.7846 (m-80) REVERT: D 251 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6466 (tttm) REVERT: D 334 LEU cc_start: 0.9449 (mm) cc_final: 0.9161 (mt) REVERT: D 337 SER cc_start: 0.9366 (m) cc_final: 0.9031 (p) REVERT: D 361 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7753 (mt-10) REVERT: D 400 TYR cc_start: 0.8697 (t80) cc_final: 0.7962 (t80) REVERT: D 471 ARG cc_start: 0.9066 (ptp-110) cc_final: 0.8338 (ttm170) REVERT: D 478 LYS cc_start: 0.9243 (tmtt) cc_final: 0.9004 (ttpp) REVERT: D 492 LEU cc_start: 0.9197 (mt) cc_final: 0.8900 (mt) REVERT: D 529 MET cc_start: 0.9468 (OUTLIER) cc_final: 0.9031 (mmm) REVERT: D 558 PHE cc_start: 0.8389 (t80) cc_final: 0.7558 (t80) REVERT: D 564 LEU cc_start: 0.9142 (tp) cc_final: 0.8941 (tp) REVERT: D 652 TYR cc_start: 0.8741 (m-80) cc_final: 0.8142 (t80) REVERT: D 661 PHE cc_start: 0.9493 (t80) cc_final: 0.9138 (t80) REVERT: D 662 LYS cc_start: 0.9470 (mmmm) cc_final: 0.9174 (ptpp) REVERT: D 667 LYS cc_start: 0.9727 (mttt) cc_final: 0.9339 (mtpt) REVERT: D 681 LEU cc_start: 0.9089 (mt) cc_final: 0.8815 (mm) REVERT: D 723 GLU cc_start: 0.9646 (mm-30) cc_final: 0.9283 (mm-30) REVERT: D 741 PHE cc_start: 0.8080 (m-80) cc_final: 0.7144 (m-80) REVERT: D 808 ASN cc_start: 0.8883 (m-40) cc_final: 0.8387 (m110) REVERT: D 843 LYS cc_start: 0.9555 (mtmt) cc_final: 0.9309 (ptpp) REVERT: U 117 GLN cc_start: 0.8250 (pm20) cc_final: 0.7860 (mp10) REVERT: U 126 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8935 (mm-30) REVERT: U 131 LYS cc_start: 0.9576 (mtpp) cc_final: 0.9311 (mmmt) REVERT: U 141 LYS cc_start: 0.8138 (tppt) cc_final: 0.7657 (mttm) outliers start: 31 outliers final: 21 residues processed: 500 average time/residue: 0.1361 time to fit residues: 105.1604 Evaluate side-chains 491 residues out of total 2108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 464 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 TRP Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 323 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 125 LYS Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 282 MET Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 397 CYS Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 617 TYR Chi-restraints excluded: chain C residue 662 CYS Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 529 MET Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 809 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 24 optimal weight: 0.0010 chunk 8 optimal weight: 0.0370 chunk 182 optimal weight: 0.9980 chunk 159 optimal weight: 0.4980 chunk 150 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 overall best weight: 0.5064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 HIS ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 GLN C 665 ASN C 696 GLN D 832 ASN ** U 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.097575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072692 restraints weight = 67445.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.075327 restraints weight = 33839.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.077031 restraints weight = 20899.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.078197 restraints weight = 14689.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.078981 restraints weight = 11269.040| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 19090 Z= 0.147 Angle : 0.803 15.157 25841 Z= 0.392 Chirality : 0.047 0.350 2876 Planarity : 0.005 0.072 3326 Dihedral : 5.294 66.054 2528 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 1.52 % Allowed : 23.62 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % 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: 0.70 (0.18), residues: 2271 helix: 1.11 (0.14), residues: 1306 sheet: -1.27 (0.41), residues: 171 loop : -0.02 (0.24), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 806 TYR 0.054 0.002 TYR A 292 PHE 0.038 0.002 PHE D 411 TRP 0.042 0.002 TRP D 555 HIS 0.007 0.001 HIS U 127 Details of bonding type rmsd covalent geometry : bond 0.00332 (19090) covalent geometry : angle 0.80286 (25841) hydrogen bonds : bond 0.04460 ( 1061) hydrogen bonds : angle 5.02743 ( 3081) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4302.53 seconds wall clock time: 75 minutes 3.13 seconds (4503.13 seconds total)