Starting phenix.real_space_refine on Fri Nov 15 15:17:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4b_36882/11_2024/8k4b_36882.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4b_36882/11_2024/8k4b_36882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4b_36882/11_2024/8k4b_36882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4b_36882/11_2024/8k4b_36882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4b_36882/11_2024/8k4b_36882.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4b_36882/11_2024/8k4b_36882.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 S 28 5.16 5 C 5732 2.51 5 N 1462 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "B" Number of atoms: 4427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4427 Classifications: {'peptide': 563} Link IDs: {'PTRANS': 12, 'TRANS': 550} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.38, per 1000 atoms: 0.60 Number of scatterers: 8918 At special positions: 0 Unit cell: (77.35, 90.61, 142.545, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 28 16.00 P 6 15.00 O 1688 8.00 N 1462 7.00 C 5732 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: 2.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 67.2% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 168 through 195 removed outlier: 4.394A pdb=" N VAL A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 192 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 251 removed outlier: 4.448A pdb=" N LEU A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLN A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.906A pdb=" N PHE A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 271 removed outlier: 3.766A pdb=" N ARG A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 292 removed outlier: 4.431A pdb=" N ASP A 277 " --> pdb=" O ASN A 273 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A 278 " --> pdb=" O SER A 274 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 304 removed outlier: 3.716A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.662A pdb=" N THR A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 323 removed outlier: 3.758A pdb=" N TYR A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 353 removed outlier: 4.698A pdb=" N GLU A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N MET A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.137A pdb=" N ILE A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 416 removed outlier: 4.226A pdb=" N ARG A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL A 412 " --> pdb=" O TRP A 408 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU A 413 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N VAL A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 443 removed outlier: 3.929A pdb=" N TYR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 444 through 463 removed outlier: 3.843A pdb=" N LEU A 448 " --> pdb=" O LEU A 444 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.573A pdb=" N ASN A 577 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 598 Processing helix chain 'A' and resid 623 through 638 removed outlier: 4.011A pdb=" N THR A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 664 Processing helix chain 'A' and resid 677 through 684 removed outlier: 4.233A pdb=" N ALA A 681 " --> pdb=" O ARG A 677 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 684 " --> pdb=" O ILE A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 707 Processing helix chain 'A' and resid 709 through 716 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 168 through 195 removed outlier: 4.409A pdb=" N VAL B 172 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 192 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 251 removed outlier: 4.447A pdb=" N LEU B 218 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN B 220 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL B 232 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N TYR B 245 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE B 246 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.905A pdb=" N PHE B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 271 removed outlier: 3.946A pdb=" N ARG B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 292 removed outlier: 4.067A pdb=" N ALA B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N VAL B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 304 removed outlier: 3.718A pdb=" N LEU B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 removed outlier: 3.660A pdb=" N THR B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 313 " --> pdb=" O PHE B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 323 removed outlier: 3.719A pdb=" N TYR B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 353 removed outlier: 4.698A pdb=" N GLU B 330 " --> pdb=" O MET B 326 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LYS B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N MET B 332 " --> pdb=" O PRO B 328 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY B 353 " --> pdb=" O GLU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 4.136A pdb=" N ILE B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 416 removed outlier: 4.228A pdb=" N ARG B 366 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL B 412 " --> pdb=" O TRP B 408 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU B 413 " --> pdb=" O MET B 409 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 443 removed outlier: 3.842A pdb=" N TYR B 433 " --> pdb=" O THR B 429 " (cutoff:3.500A) Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 444 through 463 removed outlier: 3.842A pdb=" N LEU B 448 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 450 " --> pdb=" O THR B 446 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 Processing helix chain 'B' and resid 552 through 559 Processing helix chain 'B' and resid 573 through 579 removed outlier: 3.567A pdb=" N ASN B 577 " --> pdb=" O THR B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 598 Processing helix chain 'B' and resid 623 through 638 removed outlier: 4.011A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 664 Processing helix chain 'B' and resid 677 through 684 removed outlier: 4.231A pdb=" N ALA B 681 " --> pdb=" O ARG B 677 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG B 683 " --> pdb=" O THR B 679 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR B 684 " --> pdb=" O ILE B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 707 Processing helix chain 'B' and resid 709 through 716 Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 503 removed outlier: 6.124A pdb=" N SER A 501 " --> pdb=" O TYR A 491 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N TYR A 491 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N PHE A 486 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER A 542 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN A 488 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU A 540 " --> pdb=" O GLN A 488 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 560 through 561 removed outlier: 6.291A pdb=" N ASN A 561 " --> pdb=" O ILE A 644 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 672 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 513 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ALA A 675 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE A 515 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 686 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 688 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 687 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU A 698 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 689 " --> pdb=" O VAL A 696 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 500 through 503 removed outlier: 6.125A pdb=" N SER B 501 " --> pdb=" O TYR B 491 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N TYR B 491 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N PHE B 486 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER B 542 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN B 488 " --> pdb=" O GLU B 540 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU B 540 " --> pdb=" O GLN B 488 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 560 through 561 removed outlier: 6.291A pdb=" N ASN B 561 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 672 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 513 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA B 675 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N PHE B 515 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS B 512 " --> pdb=" O LYS B 686 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N VAL B 688 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA B 514 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU B 690 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 516 " --> pdb=" O LEU B 690 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 687 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU B 698 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 689 " --> pdb=" O VAL B 696 " (cutoff:3.500A) 481 hydrogen bonds defined for protein. 1437 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2788 1.34 - 1.47: 1960 1.47 - 1.59: 4236 1.59 - 1.71: 10 1.71 - 1.83: 56 Bond restraints: 9050 Sorted by residual: bond pdb=" C5 ATP B 801 " pdb=" C6 ATP B 801 " ideal model delta sigma weight residual 1.409 1.308 0.101 1.00e-02 1.00e+04 1.02e+02 bond pdb=" C5 ATP A 801 " pdb=" C6 ATP A 801 " ideal model delta sigma weight residual 1.409 1.308 0.101 1.00e-02 1.00e+04 1.01e+02 bond pdb=" C2 ATP A 801 " pdb=" N1 ATP A 801 " ideal model delta sigma weight residual 1.334 1.420 -0.086 1.00e-02 1.00e+04 7.35e+01 bond pdb=" C2 ATP B 801 " pdb=" N1 ATP B 801 " ideal model delta sigma weight residual 1.334 1.419 -0.085 1.00e-02 1.00e+04 7.26e+01 bond pdb=" C1' ATP A 801 " pdb=" C2' ATP A 801 " ideal model delta sigma weight residual 1.531 1.434 0.097 1.20e-02 6.94e+03 6.54e+01 ... (remaining 9045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 11809 3.28 - 6.55: 381 6.55 - 9.83: 73 9.83 - 13.10: 13 13.10 - 16.38: 2 Bond angle restraints: 12278 Sorted by residual: angle pdb=" PA ATP B 801 " pdb=" O3A ATP B 801 " pdb=" PB ATP B 801 " ideal model delta sigma weight residual 136.83 120.45 16.38 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 120.48 16.35 1.00e+00 1.00e+00 2.67e+02 angle pdb=" N1 ATP A 801 " pdb=" C2 ATP A 801 " pdb=" N3 ATP A 801 " ideal model delta sigma weight residual 128.69 117.41 11.28 1.00e+00 1.00e+00 1.27e+02 angle pdb=" N1 ATP B 801 " pdb=" C2 ATP B 801 " pdb=" N3 ATP B 801 " ideal model delta sigma weight residual 128.69 117.43 11.26 1.00e+00 1.00e+00 1.27e+02 angle pdb=" PB ATP B 801 " pdb=" O3B ATP B 801 " pdb=" PG ATP B 801 " ideal model delta sigma weight residual 139.87 129.76 10.11 1.00e+00 1.00e+00 1.02e+02 ... (remaining 12273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4874 17.62 - 35.23: 492 35.23 - 52.85: 115 52.85 - 70.46: 23 70.46 - 88.08: 14 Dihedral angle restraints: 5518 sinusoidal: 2224 harmonic: 3294 Sorted by residual: dihedral pdb=" CA ILE B 622 " pdb=" C ILE B 622 " pdb=" N SER B 623 " pdb=" CA SER B 623 " ideal model delta harmonic sigma weight residual -180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA ILE A 622 " pdb=" C ILE A 622 " pdb=" N SER A 623 " pdb=" CA SER A 623 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ASP B 653 " pdb=" C ASP B 653 " pdb=" N ILE B 654 " pdb=" CA ILE B 654 " ideal model delta harmonic sigma weight residual -180.00 -159.81 -20.19 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 5515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1219 0.075 - 0.150: 233 0.150 - 0.225: 26 0.225 - 0.300: 12 0.300 - 0.375: 8 Chirality restraints: 1498 Sorted by residual: chirality pdb=" CB ILE A 622 " pdb=" CA ILE A 622 " pdb=" CG1 ILE A 622 " pdb=" CG2 ILE A 622 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB ILE B 622 " pdb=" CA ILE B 622 " pdb=" CG1 ILE B 622 " pdb=" CG2 ILE B 622 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CB VAL B 531 " pdb=" CA VAL B 531 " pdb=" CG1 VAL B 531 " pdb=" CG2 VAL B 531 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 1495 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 252 " -0.064 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO A 253 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 252 " 0.064 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO B 253 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 253 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 253 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 614 " 0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" CD GLU A 614 " -0.052 2.00e-02 2.50e+03 pdb=" OE1 GLU A 614 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU A 614 " 0.018 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 72 2.59 - 3.17: 7257 3.17 - 3.74: 14121 3.74 - 4.32: 17989 4.32 - 4.90: 28464 Nonbonded interactions: 67903 Sorted by model distance: nonbonded pdb=" O3G ATP B 801 " pdb="ZN ZN B 802 " model vdw 2.010 2.230 nonbonded pdb=" O3G ATP A 801 " pdb="ZN ZN A 802 " model vdw 2.010 2.230 nonbonded pdb=" O2B ATP A 801 " pdb="ZN ZN A 802 " model vdw 2.072 2.230 nonbonded pdb=" O2B ATP B 801 " pdb="ZN ZN B 802 " model vdw 2.072 2.230 nonbonded pdb=" OG SER A 385 " pdb=" CD2 LEU B 231 " model vdw 2.265 3.460 ... (remaining 67898 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' } 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.810 Find NCS groups from input model: 0.250 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: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 : 0.007 0.101 9050 Z= 0.465 Angle : 1.397 16.379 12278 Z= 0.795 Chirality : 0.067 0.375 1498 Planarity : 0.008 0.098 1522 Dihedral : 15.605 88.080 3394 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.04 % Favored : 92.78 % Rotamer: Outliers : 0.91 % Allowed : 1.92 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.20), residues: 1122 helix: -2.28 (0.15), residues: 710 sheet: -0.52 (0.73), residues: 68 loop : -3.15 (0.25), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP A 408 HIS 0.003 0.001 HIS A 490 PHE 0.022 0.002 PHE A 434 TYR 0.034 0.002 TYR B 188 ARG 0.007 0.001 ARG B 627 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 255 time to evaluate : 1.036 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: A 201 MET cc_start: 0.8531 (ppp) cc_final: 0.8172 (tmm) REVERT: A 247 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8862 (tptt) REVERT: A 271 ASP cc_start: 0.8026 (t0) cc_final: 0.7665 (t70) REVERT: A 310 MET cc_start: 0.8639 (pmm) cc_final: 0.7999 (mmt) REVERT: A 312 LEU cc_start: 0.9177 (tp) cc_final: 0.8742 (pp) REVERT: A 409 MET cc_start: 0.6014 (mmp) cc_final: 0.5775 (tmm) REVERT: A 492 LYS cc_start: 0.8580 (tppt) cc_final: 0.8139 (mmtt) REVERT: A 609 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6848 (pp) REVERT: B 309 PHE cc_start: 0.5798 (t80) cc_final: 0.5391 (t80) REVERT: B 561 ASN cc_start: 0.7874 (p0) cc_final: 0.7429 (m-40) REVERT: B 690 LEU cc_start: 0.8382 (tp) cc_final: 0.7896 (tp) outliers start: 9 outliers final: 2 residues processed: 261 average time/residue: 0.2451 time to fit residues: 84.2497 Evaluate side-chains 162 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 158 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 GLN Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 219 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 101 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A 455 ASN ** A 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN B 455 ASN B 550 GLN ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9050 Z= 0.192 Angle : 0.745 13.116 12278 Z= 0.373 Chirality : 0.041 0.177 1498 Planarity : 0.005 0.075 1522 Dihedral : 8.731 79.064 1292 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.64 % Allowed : 12.02 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.24), residues: 1122 helix: -0.57 (0.19), residues: 712 sheet: 0.32 (0.95), residues: 46 loop : -2.72 (0.26), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 408 HIS 0.003 0.001 HIS A 490 PHE 0.020 0.002 PHE B 434 TYR 0.024 0.002 TYR A 216 ARG 0.005 0.001 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7709 (t80) REVERT: A 326 MET cc_start: 0.7832 (tmm) cc_final: 0.7114 (tmm) REVERT: A 409 MET cc_start: 0.6468 (mmp) cc_final: 0.6156 (tpp) REVERT: A 468 PHE cc_start: 0.8380 (m-10) cc_final: 0.8091 (m-80) REVERT: A 627 ARG cc_start: 0.7904 (mmp80) cc_final: 0.7599 (mmp80) REVERT: B 231 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.6055 (mp) REVERT: B 326 MET cc_start: 0.6856 (tpt) cc_final: 0.6459 (tpt) REVERT: B 503 ILE cc_start: 0.8786 (mm) cc_final: 0.8494 (mp) REVERT: B 550 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8373 (tm-30) REVERT: B 657 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8465 (mp0) REVERT: B 690 LEU cc_start: 0.8744 (tp) cc_final: 0.8292 (tp) REVERT: B 711 TYR cc_start: 0.8537 (t80) cc_final: 0.8240 (t80) outliers start: 36 outliers final: 19 residues processed: 192 average time/residue: 0.2026 time to fit residues: 53.8774 Evaluate side-chains 170 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 559 TYR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 657 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 0.0970 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 455 ASN B 550 GLN ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9050 Z= 0.183 Angle : 0.709 11.935 12278 Z= 0.351 Chirality : 0.041 0.194 1498 Planarity : 0.005 0.064 1522 Dihedral : 8.019 87.868 1283 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.64 % Allowed : 14.44 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.25), residues: 1122 helix: -0.02 (0.20), residues: 716 sheet: 0.44 (0.95), residues: 46 loop : -2.51 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 408 HIS 0.004 0.001 HIS A 490 PHE 0.027 0.001 PHE B 308 TYR 0.026 0.001 TYR A 216 ARG 0.005 0.001 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8628 (ppp) cc_final: 0.8231 (ppp) REVERT: A 323 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7727 (t80) REVERT: A 326 MET cc_start: 0.7967 (tmm) cc_final: 0.7254 (tmm) REVERT: A 409 MET cc_start: 0.6583 (mmp) cc_final: 0.6133 (tpp) REVERT: A 431 LEU cc_start: 0.9563 (tp) cc_final: 0.9229 (tp) REVERT: A 468 PHE cc_start: 0.8469 (m-10) cc_final: 0.8146 (m-80) REVERT: A 627 ARG cc_start: 0.7735 (mmp80) cc_final: 0.7508 (mmp80) REVERT: B 188 TYR cc_start: 0.4704 (t80) cc_final: 0.4466 (t80) REVERT: B 196 TYR cc_start: 0.5045 (t80) cc_final: 0.4300 (t80) REVERT: B 201 MET cc_start: 0.9030 (mpp) cc_final: 0.8379 (mpp) REVERT: B 326 MET cc_start: 0.6858 (tpt) cc_final: 0.6419 (tpt) REVERT: B 503 ILE cc_start: 0.8769 (mm) cc_final: 0.8476 (mp) REVERT: B 550 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8517 (tm-30) REVERT: B 690 LEU cc_start: 0.8916 (tp) cc_final: 0.8532 (tp) REVERT: B 701 HIS cc_start: 0.9270 (OUTLIER) cc_final: 0.8470 (t-170) REVERT: B 711 TYR cc_start: 0.8656 (t80) cc_final: 0.8242 (t80) outliers start: 36 outliers final: 24 residues processed: 174 average time/residue: 0.2016 time to fit residues: 49.1997 Evaluate side-chains 161 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 701 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.0870 chunk 48 optimal weight: 0.0770 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN B 612 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9050 Z= 0.200 Angle : 0.702 11.892 12278 Z= 0.342 Chirality : 0.040 0.200 1498 Planarity : 0.004 0.057 1522 Dihedral : 7.526 89.925 1283 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.84 % Allowed : 17.68 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.25), residues: 1122 helix: 0.15 (0.20), residues: 726 sheet: 0.51 (0.92), residues: 46 loop : -2.53 (0.27), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 408 HIS 0.004 0.001 HIS A 490 PHE 0.029 0.001 PHE B 308 TYR 0.028 0.001 TYR A 216 ARG 0.004 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.993 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: A 201 MET cc_start: 0.8716 (ppp) cc_final: 0.8438 (ppp) REVERT: A 312 LEU cc_start: 0.9228 (tt) cc_final: 0.8749 (pp) REVERT: A 323 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7773 (t80) REVERT: A 326 MET cc_start: 0.8075 (tmm) cc_final: 0.7483 (tmm) REVERT: A 468 PHE cc_start: 0.8463 (m-10) cc_final: 0.8172 (m-80) REVERT: A 607 MET cc_start: 0.6603 (mpp) cc_final: 0.6374 (mpp) REVERT: B 196 TYR cc_start: 0.5011 (t80) cc_final: 0.4300 (t80) REVERT: B 326 MET cc_start: 0.6830 (tpt) cc_final: 0.6371 (tpt) REVERT: B 407 LEU cc_start: 0.9472 (tp) cc_final: 0.9005 (pp) REVERT: B 419 MET cc_start: 0.7964 (mmp) cc_final: 0.7693 (mmp) REVERT: B 484 MET cc_start: 0.8333 (mmm) cc_final: 0.7904 (mmm) REVERT: B 503 ILE cc_start: 0.8797 (mm) cc_final: 0.8521 (mp) REVERT: B 550 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8667 (tm-30) REVERT: B 657 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8424 (pm20) REVERT: B 690 LEU cc_start: 0.8935 (tp) cc_final: 0.8531 (tp) outliers start: 38 outliers final: 26 residues processed: 170 average time/residue: 0.1978 time to fit residues: 47.5043 Evaluate side-chains 163 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 684 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS A 352 ASN B 219 GLN B 550 GLN ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9050 Z= 0.243 Angle : 0.738 11.914 12278 Z= 0.364 Chirality : 0.042 0.191 1498 Planarity : 0.004 0.054 1522 Dihedral : 7.535 89.866 1283 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.15 % Allowed : 19.49 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.25), residues: 1122 helix: 0.19 (0.20), residues: 716 sheet: 0.53 (0.92), residues: 46 loop : -2.36 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 408 HIS 0.005 0.001 HIS B 713 PHE 0.029 0.001 PHE B 308 TYR 0.027 0.002 TYR A 216 ARG 0.006 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 150 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8768 (ppp) cc_final: 0.8312 (ppp) REVERT: A 312 LEU cc_start: 0.9226 (tt) cc_final: 0.8739 (pp) REVERT: A 606 ARG cc_start: 0.8267 (ptp90) cc_final: 0.8015 (mtm-85) REVERT: A 607 MET cc_start: 0.6978 (mpp) cc_final: 0.6636 (mpp) REVERT: B 260 ARG cc_start: 0.7599 (tpp80) cc_final: 0.7353 (tpp80) REVERT: B 291 SER cc_start: 0.8226 (OUTLIER) cc_final: 0.8003 (p) REVERT: B 497 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6674 (ptp-170) REVERT: B 503 ILE cc_start: 0.8832 (mm) cc_final: 0.8551 (mp) REVERT: B 550 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8676 (tm-30) REVERT: B 657 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8457 (pm20) REVERT: B 690 LEU cc_start: 0.8991 (tp) cc_final: 0.8662 (tp) outliers start: 51 outliers final: 30 residues processed: 180 average time/residue: 0.1943 time to fit residues: 49.6296 Evaluate side-chains 168 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 371 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 283 ILE Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 684 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS B 550 GLN ** B 571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9050 Z= 0.207 Angle : 0.739 12.180 12278 Z= 0.356 Chirality : 0.042 0.204 1498 Planarity : 0.004 0.052 1522 Dihedral : 7.288 88.135 1280 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.04 % Allowed : 21.82 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.24), residues: 1122 helix: 0.21 (0.20), residues: 714 sheet: 0.28 (0.89), residues: 46 loop : -2.40 (0.27), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 408 HIS 0.008 0.001 HIS B 701 PHE 0.030 0.001 PHE B 308 TYR 0.031 0.001 TYR A 216 ARG 0.006 0.001 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 140 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8668 (ppp) cc_final: 0.7517 (ppp) REVERT: A 312 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8720 (pp) REVERT: A 323 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7860 (t80) REVERT: A 326 MET cc_start: 0.8281 (tmm) cc_final: 0.7810 (tmm) REVERT: A 433 TYR cc_start: 0.6929 (m-80) cc_final: 0.6661 (m-80) REVERT: A 607 MET cc_start: 0.7068 (mpp) cc_final: 0.6813 (mpp) REVERT: B 196 TYR cc_start: 0.5161 (t80) cc_final: 0.4583 (t80) REVERT: B 201 MET cc_start: 0.9156 (mpp) cc_final: 0.8470 (mpp) REVERT: B 260 ARG cc_start: 0.7520 (tpp80) cc_final: 0.7295 (tpp80) REVERT: B 291 SER cc_start: 0.8358 (OUTLIER) cc_final: 0.8104 (p) REVERT: B 326 MET cc_start: 0.6731 (tpt) cc_final: 0.6430 (tpt) REVERT: B 407 LEU cc_start: 0.9537 (tp) cc_final: 0.9059 (pp) REVERT: B 419 MET cc_start: 0.7896 (mmp) cc_final: 0.7691 (mmp) REVERT: B 497 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6613 (ptp-170) REVERT: B 503 ILE cc_start: 0.8791 (mm) cc_final: 0.8525 (mp) REVERT: B 550 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8591 (tm-30) REVERT: B 690 LEU cc_start: 0.9107 (tp) cc_final: 0.8769 (tp) outliers start: 40 outliers final: 25 residues processed: 162 average time/residue: 0.2198 time to fit residues: 50.2443 Evaluate side-chains 161 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 291 SER Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 684 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.0050 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS B 549 ASN B 550 GLN B 701 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9050 Z= 0.168 Angle : 0.725 12.512 12278 Z= 0.345 Chirality : 0.041 0.215 1498 Planarity : 0.004 0.050 1522 Dihedral : 7.035 88.974 1280 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.33 % Allowed : 24.14 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.25), residues: 1122 helix: 0.34 (0.20), residues: 714 sheet: 0.23 (0.89), residues: 46 loop : -2.43 (0.27), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 408 HIS 0.009 0.001 HIS B 701 PHE 0.029 0.001 PHE B 308 TYR 0.030 0.001 TYR A 216 ARG 0.010 0.001 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8631 (ppp) cc_final: 0.7436 (ppp) REVERT: A 312 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8706 (pp) REVERT: A 323 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7867 (t80) REVERT: A 326 MET cc_start: 0.8265 (tmm) cc_final: 0.7718 (tmm) REVERT: A 433 TYR cc_start: 0.6841 (m-80) cc_final: 0.6565 (m-80) REVERT: A 568 TYR cc_start: 0.9049 (t80) cc_final: 0.8733 (t80) REVERT: A 607 MET cc_start: 0.6801 (mpp) cc_final: 0.6538 (mpp) REVERT: B 196 TYR cc_start: 0.5036 (t80) cc_final: 0.4547 (t80) REVERT: B 326 MET cc_start: 0.6862 (tpt) cc_final: 0.6647 (tpt) REVERT: B 407 LEU cc_start: 0.9560 (tp) cc_final: 0.9101 (pp) REVERT: B 497 ARG cc_start: 0.6782 (OUTLIER) cc_final: 0.6435 (ptp-170) REVERT: B 503 ILE cc_start: 0.8814 (mm) cc_final: 0.8551 (mp) REVERT: B 550 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8491 (tm-30) REVERT: B 690 LEU cc_start: 0.9111 (tp) cc_final: 0.8789 (tp) outliers start: 33 outliers final: 26 residues processed: 163 average time/residue: 0.2120 time to fit residues: 48.6660 Evaluate side-chains 164 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 684 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 0.1980 chunk 103 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS B 550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9050 Z= 0.177 Angle : 0.733 12.860 12278 Z= 0.347 Chirality : 0.041 0.205 1498 Planarity : 0.004 0.048 1522 Dihedral : 6.857 89.483 1280 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.13 % Allowed : 24.95 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1122 helix: 0.38 (0.20), residues: 714 sheet: 0.27 (0.91), residues: 46 loop : -2.37 (0.27), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 408 HIS 0.003 0.001 HIS A 490 PHE 0.029 0.001 PHE B 308 TYR 0.029 0.001 TYR A 216 ARG 0.009 0.001 ARG A 627 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8601 (ppp) cc_final: 0.7383 (ppp) REVERT: A 312 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8707 (pp) REVERT: A 326 MET cc_start: 0.8176 (tmm) cc_final: 0.7881 (tpp) REVERT: A 392 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8761 (tmtt) REVERT: A 419 MET cc_start: 0.8300 (mmp) cc_final: 0.7492 (ttt) REVERT: A 433 TYR cc_start: 0.6823 (m-80) cc_final: 0.6508 (m-10) REVERT: A 568 TYR cc_start: 0.9059 (t80) cc_final: 0.8737 (t80) REVERT: A 607 MET cc_start: 0.6766 (mpp) cc_final: 0.6496 (mpp) REVERT: B 196 TYR cc_start: 0.5024 (t80) cc_final: 0.4525 (t80) REVERT: B 326 MET cc_start: 0.6856 (tpt) cc_final: 0.6629 (tpt) REVERT: B 338 GLU cc_start: 0.8785 (tp30) cc_final: 0.8428 (tp30) REVERT: B 407 LEU cc_start: 0.9564 (tp) cc_final: 0.9119 (pp) REVERT: B 419 MET cc_start: 0.7738 (mmp) cc_final: 0.7526 (mmp) REVERT: B 430 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8387 (pp) REVERT: B 497 ARG cc_start: 0.6776 (OUTLIER) cc_final: 0.6446 (ptp-170) REVERT: B 503 ILE cc_start: 0.8809 (mm) cc_final: 0.8554 (mp) REVERT: B 550 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8495 (tm-30) REVERT: B 657 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8476 (mp0) REVERT: B 690 LEU cc_start: 0.9092 (tp) cc_final: 0.8774 (tp) outliers start: 31 outliers final: 25 residues processed: 150 average time/residue: 0.1890 time to fit residues: 40.4709 Evaluate side-chains 158 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 684 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 6.9990 chunk 100 optimal weight: 0.0470 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS B 550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9050 Z= 0.171 Angle : 0.736 13.221 12278 Z= 0.346 Chirality : 0.041 0.208 1498 Planarity : 0.004 0.048 1522 Dihedral : 6.702 89.539 1280 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.64 % Allowed : 24.85 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.25), residues: 1122 helix: 0.46 (0.20), residues: 706 sheet: 0.22 (0.91), residues: 46 loop : -2.27 (0.27), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 408 HIS 0.003 0.001 HIS A 490 PHE 0.020 0.001 PHE B 434 TYR 0.028 0.001 TYR A 216 ARG 0.011 0.001 ARG A 593 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8582 (ppp) cc_final: 0.7324 (ppp) REVERT: A 312 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8712 (pp) REVERT: A 326 MET cc_start: 0.8172 (tmm) cc_final: 0.7872 (tpp) REVERT: A 392 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8764 (tmtt) REVERT: A 409 MET cc_start: 0.6279 (mmp) cc_final: 0.5896 (tpp) REVERT: A 419 MET cc_start: 0.8277 (mmp) cc_final: 0.7306 (ttt) REVERT: A 433 TYR cc_start: 0.6710 (m-80) cc_final: 0.6381 (m-10) REVERT: A 495 TYR cc_start: 0.7339 (OUTLIER) cc_final: 0.6307 (m-80) REVERT: A 607 MET cc_start: 0.6746 (mpp) cc_final: 0.6531 (mpp) REVERT: B 196 TYR cc_start: 0.5024 (t80) cc_final: 0.4540 (t80) REVERT: B 326 MET cc_start: 0.6877 (tpt) cc_final: 0.6632 (tpt) REVERT: B 338 GLU cc_start: 0.8757 (tp30) cc_final: 0.8423 (tp30) REVERT: B 407 LEU cc_start: 0.9557 (tp) cc_final: 0.9102 (pp) REVERT: B 497 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6308 (ptp-170) REVERT: B 503 ILE cc_start: 0.8799 (mm) cc_final: 0.8546 (mp) REVERT: B 550 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8448 (tm-30) REVERT: B 678 LEU cc_start: 0.8855 (tp) cc_final: 0.8627 (tp) REVERT: B 690 LEU cc_start: 0.9091 (tp) cc_final: 0.8776 (tp) outliers start: 36 outliers final: 26 residues processed: 159 average time/residue: 0.2213 time to fit residues: 50.5765 Evaluate side-chains 162 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 657 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 0.0060 chunk 88 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 HIS B 550 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9050 Z= 0.189 Angle : 0.760 13.784 12278 Z= 0.361 Chirality : 0.042 0.348 1498 Planarity : 0.005 0.120 1522 Dihedral : 6.667 86.759 1280 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.23 % Allowed : 26.16 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.25), residues: 1122 helix: 0.42 (0.20), residues: 706 sheet: 0.26 (0.92), residues: 46 loop : -2.23 (0.28), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 408 HIS 0.003 0.001 HIS A 490 PHE 0.022 0.001 PHE B 434 TYR 0.027 0.001 TYR A 216 ARG 0.015 0.001 ARG A 593 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8572 (ppp) cc_final: 0.7303 (ppp) REVERT: A 312 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8711 (pp) REVERT: A 326 MET cc_start: 0.8182 (tmm) cc_final: 0.7896 (tpp) REVERT: A 392 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8765 (tmtt) REVERT: A 409 MET cc_start: 0.6296 (mmp) cc_final: 0.5903 (tpp) REVERT: A 495 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6336 (m-80) REVERT: A 607 MET cc_start: 0.6776 (mpp) cc_final: 0.6560 (mpp) REVERT: B 196 TYR cc_start: 0.5153 (t80) cc_final: 0.4632 (t80) REVERT: B 326 MET cc_start: 0.6894 (tpt) cc_final: 0.6679 (tpt) REVERT: B 338 GLU cc_start: 0.8723 (tp30) cc_final: 0.8385 (tp30) REVERT: B 497 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.6274 (ptp-170) REVERT: B 503 ILE cc_start: 0.8815 (mm) cc_final: 0.8561 (mp) REVERT: B 550 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8435 (tm-30) REVERT: B 678 LEU cc_start: 0.8856 (tp) cc_final: 0.8646 (tp) REVERT: B 690 LEU cc_start: 0.9098 (tp) cc_final: 0.8797 (tp) outliers start: 32 outliers final: 26 residues processed: 147 average time/residue: 0.1920 time to fit residues: 40.3676 Evaluate side-chains 159 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 432 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 550 GLN Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 657 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.109261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.085499 restraints weight = 30755.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.088223 restraints weight = 17052.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.090011 restraints weight = 11569.880| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9050 Z= 0.176 Angle : 0.772 14.016 12278 Z= 0.362 Chirality : 0.042 0.306 1498 Planarity : 0.005 0.101 1522 Dihedral : 6.525 83.821 1280 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.43 % Allowed : 26.77 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.25), residues: 1122 helix: 0.40 (0.20), residues: 712 sheet: 0.20 (0.90), residues: 46 loop : -2.31 (0.27), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 408 HIS 0.003 0.001 HIS A 490 PHE 0.023 0.001 PHE B 434 TYR 0.025 0.001 TYR A 216 ARG 0.013 0.001 ARG A 627 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1919.75 seconds wall clock time: 36 minutes 5.92 seconds (2165.92 seconds total)