Starting phenix.real_space_refine on Thu Jan 18 14:46:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4b_36882/01_2024/8k4b_36882_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4b_36882/01_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_36882/01_2024/8k4b_36882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4b_36882/01_2024/8k4b_36882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4b_36882/01_2024/8k4b_36882_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k4b_36882/01_2024/8k4b_36882_updated.pdb" } 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 Residue "A GLU 227": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 388": "OE1" <-> "OE2" Residue "A TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B GLU 614": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 5.12, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 3.95 Conformation dependent library (CDL) restraints added in 1.9 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... running ksdssp... Secondary structure from input PDB file: 40 helices and 4 sheets defined 60.7% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 158 through 162 Processing helix chain 'A' and resid 167 through 194 removed outlier: 4.121A pdb=" N ILE A 171 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 172 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU A 173 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 175 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY A 185 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR A 188 " --> pdb=" O GLY A 185 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 189 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN A 190 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP A 194 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 250 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) Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 263 through 270 removed outlier: 3.766A pdb=" N ARG A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 303 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) removed outlier: 4.423A pdb=" N VAL A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ILE A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) 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) Processing helix chain 'A' and resid 306 through 322 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) removed outlier: 5.223A pdb=" N ALA A 314 " --> pdb=" O MET A 310 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LEU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 327 through 352 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) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 363 through 415 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 421 through 462 removed outlier: 3.929A pdb=" N TYR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix removed outlier: 4.188A pdb=" N LEU A 444 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR A 446 " --> pdb=" O ILE A 442 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LYS A 447 " --> pdb=" O ASN A 443 " (cutoff:3.500A) 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 523 through 531 Processing helix chain 'A' and resid 553 through 559 Processing helix chain 'A' and resid 574 through 578 Processing helix chain 'A' and resid 589 through 597 Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 654 through 664 Processing helix chain 'A' and resid 678 through 683 removed outlier: 4.374A pdb=" N ARG A 683 " --> pdb=" O THR A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 Processing helix chain 'A' and resid 710 through 715 Processing helix chain 'B' and resid 158 through 162 Processing helix chain 'B' and resid 167 through 194 removed outlier: 4.128A pdb=" N ILE B 171 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL B 172 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 173 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR B 175 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 178 " --> pdb=" O THR B 175 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY B 185 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N TYR B 188 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 189 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN B 190 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP B 194 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 250 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) Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 263 through 270 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 276 through 303 removed outlier: 5.331A pdb=" N VAL B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL B 293 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) 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) Processing helix chain 'B' and resid 306 through 322 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) removed outlier: 5.320A pdb=" N ALA B 314 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LEU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 351 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) Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 363 through 415 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 421 through 462 removed outlier: 3.842A pdb=" N TYR B 433 " --> pdb=" O THR B 429 " (cutoff:3.500A) Proline residue: B 437 - end of helix removed outlier: 4.186A pdb=" N LEU B 444 " --> pdb=" O ASN B 440 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLN B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N THR B 446 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N LYS B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) 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 523 through 531 Processing helix chain 'B' and resid 553 through 559 Processing helix chain 'B' and resid 574 through 578 Processing helix chain 'B' and resid 589 through 597 Processing helix chain 'B' and resid 624 through 637 Processing helix chain 'B' and resid 654 through 664 Processing helix chain 'B' and resid 678 through 683 removed outlier: 4.373A pdb=" N ARG B 683 " --> pdb=" O THR B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 706 Processing helix chain 'B' and resid 710 through 715 Processing sheet with id= A, first strand: chain 'A' and resid 485 through 487 removed outlier: 3.727A pdb=" N THR A 485 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 542 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 695 through 699 removed outlier: 6.821A pdb=" N VAL A 689 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU A 698 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 687 " --> pdb=" O GLU A 698 " (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: 7.149A pdb=" N LEU A 671 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N PHE A 515 " --> pdb=" O LEU A 671 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE A 673 " --> pdb=" O PHE A 515 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLY A 517 " --> pdb=" O PHE A 673 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 675 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 672 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 485 through 487 removed outlier: 3.729A pdb=" N THR B 485 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER B 542 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 695 through 699 removed outlier: 6.821A pdb=" N VAL B 689 " --> pdb=" O VAL B 696 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLU B 698 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL B 687 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 686 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 688 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU B 671 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N PHE B 515 " --> pdb=" O LEU B 671 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N PHE B 673 " --> pdb=" O PHE B 515 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N GLY B 517 " --> pdb=" O PHE B 673 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ALA B 675 " --> pdb=" O GLY B 517 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 672 " --> pdb=" O ILE B 643 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1197 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: 2.28 Time building geometry restraints manager: 4.26 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: 97.08 - 104.44: 104 104.44 - 111.80: 3899 111.80 - 119.17: 3652 119.17 - 126.53: 4563 126.53 - 133.89: 60 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: 7318 3.17 - 3.74: 14133 3.74 - 4.32: 18102 4.32 - 4.90: 28474 Nonbonded interactions: 68099 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 68094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.590 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: 2.870 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.010 Find NCS groups from input model: 0.470 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.140 ------------------------------------------------------------------------------- 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= 0.464 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 fitting. rotamer outliers: 9 poor density : 255 time to evaluate : 1.118 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: 84.0012 Evaluate side-chains 162 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 158 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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: 7.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 443 ASN A 455 ASN B 455 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3113 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= 0.216 Angle : 0.731 12.586 12278 Z= 0.369 Chirality : 0.041 0.199 1498 Planarity : 0.005 0.075 1522 Dihedral : 8.933 71.921 1292 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.84 % Allowed : 12.93 % Favored : 83.23 % 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: -2.01 (0.24), residues: 1122 helix: -0.61 (0.19), residues: 710 sheet: -0.57 (0.76), residues: 66 loop : -2.88 (0.26), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 408 HIS 0.003 0.001 HIS B 251 PHE 0.021 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 200 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 162 time to evaluate : 1.180 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: 0.8659 (ppp) cc_final: 0.8252 (tmm) REVERT: A 310 MET cc_start: 0.8582 (pmm) cc_final: 0.8380 (pmm) REVERT: A 326 MET cc_start: 0.7987 (tmm) cc_final: 0.7313 (tmm) REVERT: A 409 MET cc_start: 0.6625 (mmp) cc_final: 0.6320 (tpp) REVERT: A 468 PHE cc_start: 0.8475 (m-10) cc_final: 0.8139 (m-80) REVERT: B 254 MET cc_start: 0.8566 (tpt) cc_final: 0.8196 (tpp) REVERT: B 308 PHE cc_start: 0.7652 (t80) cc_final: 0.7424 (t80) REVERT: B 310 MET cc_start: 0.8978 (ppp) cc_final: 0.8775 (ppp) REVERT: B 395 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8505 (mtmt) REVERT: B 415 MET cc_start: 0.7940 (tpt) cc_final: 0.7574 (tpt) REVERT: B 455 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8692 (t0) REVERT: B 690 LEU cc_start: 0.8746 (tp) cc_final: 0.8376 (tp) REVERT: B 711 TYR cc_start: 0.8177 (t80) cc_final: 0.7592 (t80) outliers start: 38 outliers final: 26 residues processed: 182 average time/residue: 0.2077 time to fit residues: 52.4457 Evaluate side-chains 170 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 1.098 ------------------------------------------------------------------------------- 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 348 ILE Chi-restraints excluded: chain A residue 354 ILE 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 239 ILE Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 250 PHE Chi-restraints excluded: chain B residue 291 SER 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 412 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 455 ASN Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 644 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 0.0980 chunk 110 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 0.0570 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 HIS ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3765 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= 0.176 Angle : 0.679 11.960 12278 Z= 0.331 Chirality : 0.040 0.187 1498 Planarity : 0.004 0.064 1522 Dihedral : 8.072 79.886 1283 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.74 % Allowed : 16.46 % Favored : 79.80 % 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: -1.28 (0.25), residues: 1122 helix: -0.00 (0.20), residues: 706 sheet: 0.48 (0.95), residues: 46 loop : -2.66 (0.27), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 408 HIS 0.002 0.001 HIS A 248 PHE 0.019 0.001 PHE B 434 TYR 0.025 0.001 TYR A 216 ARG 0.004 0.000 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 188 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 1.128 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: 0.8708 (ppp) cc_final: 0.8431 (ppp) REVERT: A 312 LEU cc_start: 0.9227 (tt) cc_final: 0.8757 (pp) REVERT: A 326 MET cc_start: 0.8022 (tmm) cc_final: 0.7371 (tmm) REVERT: A 468 PHE cc_start: 0.8567 (m-10) cc_final: 0.8197 (m-80) REVERT: B 196 TYR cc_start: 0.5036 (t80) cc_final: 0.4150 (t80) REVERT: B 201 MET cc_start: 0.9090 (mpp) cc_final: 0.8268 (mpp) REVERT: B 254 MET cc_start: 0.8613 (tpt) cc_final: 0.8403 (tpp) REVERT: B 310 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8743 (ppp) REVERT: B 413 LEU cc_start: 0.9241 (mm) cc_final: 0.8932 (pp) REVERT: B 657 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: B 690 LEU cc_start: 0.8825 (tp) cc_final: 0.8492 (tp) REVERT: B 711 TYR cc_start: 0.8342 (t80) cc_final: 0.7805 (t80) outliers start: 37 outliers final: 26 residues processed: 171 average time/residue: 0.1984 time to fit residues: 47.5924 Evaluate side-chains 166 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 578 LEU 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 310 MET Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 425 ILE 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 617 SER Chi-restraints excluded: chain B residue 657 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9050 Z= 0.168 Angle : 0.657 12.046 12278 Z= 0.319 Chirality : 0.039 0.185 1498 Planarity : 0.004 0.057 1522 Dihedral : 7.582 87.827 1283 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.55 % Allowed : 18.99 % Favored : 76.46 % 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: -1.08 (0.25), residues: 1122 helix: 0.14 (0.20), residues: 712 sheet: 0.52 (0.93), residues: 46 loop : -2.57 (0.27), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 408 HIS 0.002 0.001 HIS A 490 PHE 0.026 0.001 PHE B 308 TYR 0.027 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 201 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 156 time to evaluate : 1.103 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: 0.8815 (ppp) cc_final: 0.8334 (ppp) REVERT: A 312 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8659 (pp) REVERT: A 326 MET cc_start: 0.7992 (tmm) cc_final: 0.7431 (tmm) REVERT: B 196 TYR cc_start: 0.4825 (t80) cc_final: 0.4107 (t80) REVERT: B 201 MET cc_start: 0.9085 (mpp) cc_final: 0.8322 (mpp) REVERT: B 413 LEU cc_start: 0.9236 (mm) cc_final: 0.8894 (pp) REVERT: B 419 MET cc_start: 0.8080 (mmp) cc_final: 0.7809 (mmp) REVERT: B 484 MET cc_start: 0.8568 (mmm) cc_final: 0.8058 (mmm) REVERT: B 503 ILE cc_start: 0.9132 (mm) cc_final: 0.8911 (mp) REVERT: B 657 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8519 (mp0) REVERT: B 690 LEU cc_start: 0.8857 (tp) cc_final: 0.8520 (tp) REVERT: B 701 HIS cc_start: 0.9205 (OUTLIER) cc_final: 0.8686 (t-170) REVERT: B 711 TYR cc_start: 0.8342 (t80) cc_final: 0.7669 (t80) outliers start: 45 outliers final: 29 residues processed: 181 average time/residue: 0.2043 time to fit residues: 51.6366 Evaluate side-chains 171 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 184 VAL 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 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 563 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 176 LEU 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 304 ASN Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 406 ILE 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 617 SER Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 701 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 443 ASN ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9050 Z= 0.156 Angle : 0.658 12.221 12278 Z= 0.317 Chirality : 0.039 0.192 1498 Planarity : 0.004 0.054 1522 Dihedral : 7.394 89.015 1283 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.94 % Allowed : 21.01 % Favored : 75.05 % 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: 0.21 (0.20), residues: 712 sheet: 0.69 (0.93), residues: 46 loop : -2.43 (0.27), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 408 HIS 0.002 0.000 HIS A 490 PHE 0.027 0.001 PHE B 308 TYR 0.030 0.001 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 189 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 150 time to evaluate : 1.096 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: 0.8810 (ppp) cc_final: 0.7782 (ppp) REVERT: A 312 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8624 (pp) REVERT: A 326 MET cc_start: 0.7980 (tmm) cc_final: 0.7434 (tmm) REVERT: A 392 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8892 (ptmm) REVERT: A 409 MET cc_start: 0.6722 (mmp) cc_final: 0.6329 (tpp) REVERT: B 196 TYR cc_start: 0.4506 (t80) cc_final: 0.3465 (t80) REVERT: B 260 ARG cc_start: 0.7770 (tpp80) cc_final: 0.7561 (tpp80) REVERT: B 407 LEU cc_start: 0.9481 (tp) cc_final: 0.9032 (pp) REVERT: B 413 LEU cc_start: 0.9247 (mm) cc_final: 0.8914 (pp) REVERT: B 419 MET cc_start: 0.8079 (mmp) cc_final: 0.7795 (mmp) REVERT: B 431 LEU cc_start: 0.8528 (mt) cc_final: 0.8229 (mt) REVERT: B 484 MET cc_start: 0.8580 (mmm) cc_final: 0.8236 (mmp) REVERT: B 503 ILE cc_start: 0.8935 (mm) cc_final: 0.8682 (mp) REVERT: B 593 ARG cc_start: 0.8720 (mmt-90) cc_final: 0.8441 (mmt-90) REVERT: B 657 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: B 690 LEU cc_start: 0.8880 (tp) cc_final: 0.8488 (tp) REVERT: B 701 HIS cc_start: 0.9208 (OUTLIER) cc_final: 0.8725 (t-170) REVERT: B 711 TYR cc_start: 0.8324 (t80) cc_final: 0.7673 (t80) outliers start: 39 outliers final: 25 residues processed: 172 average time/residue: 0.2169 time to fit residues: 52.3289 Evaluate side-chains 170 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE 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 438 LEU Chi-restraints excluded: chain A residue 439 GLU Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 657 GLU 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 250 PHE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 402 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 617 SER Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 701 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.0470 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- 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** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9050 Z= 0.181 Angle : 0.661 12.240 12278 Z= 0.322 Chirality : 0.039 0.197 1498 Planarity : 0.004 0.051 1522 Dihedral : 7.177 84.648 1283 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 4.55 % Allowed : 22.63 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.73 (0.25), residues: 1122 helix: 0.37 (0.21), residues: 694 sheet: 0.80 (0.94), residues: 46 loop : -2.24 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 408 HIS 0.002 0.001 HIS A 490 PHE 0.029 0.001 PHE B 308 TYR 0.024 0.001 TYR A 216 ARG 0.005 0.001 ARG B 260 *********************** 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 194 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 149 time to evaluate : 1.187 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: 0.8835 (ppp) cc_final: 0.7669 (ppp) REVERT: A 312 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8657 (pp) REVERT: A 392 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8840 (ptmm) REVERT: B 196 TYR cc_start: 0.4581 (t80) cc_final: 0.3401 (t80) REVERT: B 260 ARG cc_start: 0.7783 (tpp80) cc_final: 0.7566 (tpp80) REVERT: B 310 MET cc_start: 0.9086 (ppp) cc_final: 0.8637 (ppp) REVERT: B 413 LEU cc_start: 0.9281 (mm) cc_final: 0.8937 (pp) REVERT: B 419 MET cc_start: 0.7895 (mmp) cc_final: 0.7593 (mmp) REVERT: B 657 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: B 690 LEU cc_start: 0.8977 (tp) cc_final: 0.8652 (tp) REVERT: B 701 HIS cc_start: 0.9213 (OUTLIER) cc_final: 0.8792 (t70) REVERT: B 711 TYR cc_start: 0.8298 (t80) cc_final: 0.7721 (t80) outliers start: 45 outliers final: 31 residues processed: 177 average time/residue: 0.1997 time to fit residues: 49.8795 Evaluate side-chains 171 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 PHE 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 507 VAL Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 176 LEU 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 304 ASN Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 381 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 406 ILE 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 617 SER Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 701 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 0.3980 chunk 107 optimal weight: 0.0870 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 49 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9050 Z= 0.147 Angle : 0.675 12.803 12278 Z= 0.319 Chirality : 0.040 0.203 1498 Planarity : 0.004 0.050 1522 Dihedral : 6.921 86.593 1283 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 3.54 % Allowed : 25.05 % Favored : 71.41 % 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: -0.69 (0.26), residues: 1122 helix: 0.37 (0.21), residues: 698 sheet: 0.82 (0.94), residues: 46 loop : -2.16 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 408 HIS 0.002 0.000 HIS B 490 PHE 0.028 0.001 PHE B 308 TYR 0.026 0.001 TYR A 216 ARG 0.005 0.000 ARG B 260 *********************** 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 188 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 1.019 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: 0.8813 (ppp) cc_final: 0.7695 (ppp) REVERT: A 312 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8731 (pp) REVERT: A 326 MET cc_start: 0.8141 (tmm) cc_final: 0.7707 (tmm) REVERT: A 392 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8815 (tmtt) REVERT: A 409 MET cc_start: 0.6597 (mmp) cc_final: 0.6177 (tpp) REVERT: A 606 ARG cc_start: 0.7865 (ptp90) cc_final: 0.6148 (ptt-90) REVERT: A 664 LEU cc_start: 0.9470 (tp) cc_final: 0.9150 (pp) REVERT: B 196 TYR cc_start: 0.4510 (t80) cc_final: 0.3421 (t80) REVERT: B 326 MET cc_start: 0.6505 (tpt) cc_final: 0.5827 (tpt) REVERT: B 407 LEU cc_start: 0.9469 (tp) cc_final: 0.9002 (pp) REVERT: B 408 TRP cc_start: 0.5866 (t60) cc_final: 0.5573 (t60) REVERT: B 413 LEU cc_start: 0.9231 (mm) cc_final: 0.8794 (pp) REVERT: B 419 MET cc_start: 0.7735 (mmp) cc_final: 0.7440 (mmp) REVERT: B 503 ILE cc_start: 0.9208 (mm) cc_final: 0.8987 (mp) REVERT: B 657 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: B 690 LEU cc_start: 0.8978 (tp) cc_final: 0.8651 (tp) REVERT: B 701 HIS cc_start: 0.9168 (OUTLIER) cc_final: 0.8904 (t-90) REVERT: B 711 TYR cc_start: 0.8329 (t80) cc_final: 0.7808 (t80) outliers start: 35 outliers final: 27 residues processed: 172 average time/residue: 0.1882 time to fit residues: 46.0636 Evaluate side-chains 174 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 312 LEU 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 A residue 578 LEU Chi-restraints excluded: chain A residue 657 GLU 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 250 PHE Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 406 ILE 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 495 TYR Chi-restraints excluded: chain B residue 617 SER Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 657 GLU Chi-restraints excluded: chain B residue 701 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 0.0470 chunk 53 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9050 Z= 0.150 Angle : 0.673 12.688 12278 Z= 0.318 Chirality : 0.040 0.207 1498 Planarity : 0.004 0.048 1522 Dihedral : 6.720 85.804 1283 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.64 % Allowed : 25.56 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.61 (0.26), residues: 1122 helix: 0.43 (0.21), residues: 692 sheet: 0.79 (0.93), residues: 46 loop : -2.07 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 408 HIS 0.002 0.000 HIS B 490 PHE 0.029 0.001 PHE B 308 TYR 0.025 0.001 TYR A 216 ARG 0.005 0.000 ARG B 260 *********************** 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 185 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8791 (ppp) cc_final: 0.7633 (ppp) REVERT: A 312 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8745 (pp) REVERT: A 326 MET cc_start: 0.8148 (tmm) cc_final: 0.7749 (tmm) REVERT: A 409 MET cc_start: 0.6444 (mmp) cc_final: 0.6018 (tpp) REVERT: A 606 ARG cc_start: 0.7816 (ptp90) cc_final: 0.6048 (ptt-90) REVERT: A 664 LEU cc_start: 0.9500 (tp) cc_final: 0.9199 (pp) REVERT: B 254 MET cc_start: 0.8560 (tpp) cc_final: 0.8226 (tpp) REVERT: B 338 GLU cc_start: 0.8756 (tp30) cc_final: 0.8427 (tp30) REVERT: B 407 LEU cc_start: 0.9458 (tp) cc_final: 0.8985 (pp) REVERT: B 408 TRP cc_start: 0.5930 (t60) cc_final: 0.5642 (t60) REVERT: B 413 LEU cc_start: 0.9215 (mm) cc_final: 0.8787 (pp) REVERT: B 419 MET cc_start: 0.7676 (mmp) cc_final: 0.7379 (mmp) REVERT: B 503 ILE cc_start: 0.9064 (mm) cc_final: 0.8822 (mp) REVERT: B 657 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8315 (mp0) REVERT: B 690 LEU cc_start: 0.8998 (tp) cc_final: 0.8686 (tp) REVERT: B 711 TYR cc_start: 0.8283 (t80) cc_final: 0.7838 (t80) outliers start: 36 outliers final: 26 residues processed: 171 average time/residue: 0.1904 time to fit residues: 46.3570 Evaluate side-chains 170 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 PHE 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 392 LYS 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 A residue 573 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 657 GLU 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 346 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 406 ILE 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 617 SER Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 657 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 43 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 90 optimal weight: 0.2980 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 B 352 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9050 Z= 0.224 Angle : 0.715 12.528 12278 Z= 0.350 Chirality : 0.041 0.224 1498 Planarity : 0.004 0.063 1522 Dihedral : 6.854 80.518 1283 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.84 % Allowed : 25.76 % Favored : 70.40 % 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: -0.83 (0.25), residues: 1122 helix: 0.23 (0.20), residues: 694 sheet: 0.76 (0.93), residues: 46 loop : -2.14 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 408 HIS 0.003 0.001 HIS A 248 PHE 0.029 0.001 PHE B 308 TYR 0.024 0.001 TYR A 216 ARG 0.007 0.001 ARG B 386 *********************** 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 174 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8732 (ppp) cc_final: 0.7512 (ppp) REVERT: A 312 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8640 (pp) REVERT: A 392 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8689 (ptmm) REVERT: A 606 ARG cc_start: 0.8157 (ptp90) cc_final: 0.6359 (ptt-90) REVERT: B 196 TYR cc_start: 0.4722 (t80) cc_final: 0.3503 (t80) REVERT: B 250 PHE cc_start: 0.8383 (m-10) cc_final: 0.8176 (m-10) REVERT: B 254 MET cc_start: 0.8738 (tpp) cc_final: 0.8516 (tpp) REVERT: B 304 ASN cc_start: 0.6673 (OUTLIER) cc_final: 0.5710 (p0) REVERT: B 413 LEU cc_start: 0.9320 (mm) cc_final: 0.8935 (pp) REVERT: B 419 MET cc_start: 0.7665 (mmp) cc_final: 0.7268 (mmp) REVERT: B 607 MET cc_start: 0.8166 (mtt) cc_final: 0.7891 (mmm) REVERT: B 657 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: B 690 LEU cc_start: 0.9027 (tp) cc_final: 0.8754 (tp) REVERT: B 711 TYR cc_start: 0.8173 (t80) cc_final: 0.7904 (t80) outliers start: 38 outliers final: 29 residues processed: 160 average time/residue: 0.1819 time to fit residues: 42.1471 Evaluate side-chains 164 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 312 LEU 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 559 TYR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 304 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 402 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 617 SER 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: 3.9990 chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 0.0870 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.0060 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.1778 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9050 Z= 0.184 Angle : 0.727 13.158 12278 Z= 0.343 Chirality : 0.041 0.219 1498 Planarity : 0.004 0.055 1522 Dihedral : 6.745 80.382 1283 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % 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: -0.84 (0.25), residues: 1122 helix: 0.25 (0.20), residues: 698 sheet: 0.77 (0.94), residues: 46 loop : -2.22 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 408 HIS 0.002 0.001 HIS A 248 PHE 0.021 0.001 PHE B 434 TYR 0.025 0.001 TYR A 216 ARG 0.008 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 175 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 141 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 MET cc_start: 0.8709 (ppp) cc_final: 0.7492 (ppp) REVERT: A 312 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8677 (pp) REVERT: A 326 MET cc_start: 0.8195 (tmm) cc_final: 0.7712 (tmm) REVERT: A 495 TYR cc_start: 0.7380 (OUTLIER) cc_final: 0.6495 (m-80) REVERT: A 589 GLU cc_start: 0.8740 (pm20) cc_final: 0.8379 (pm20) REVERT: A 606 ARG cc_start: 0.8100 (ptp90) cc_final: 0.6379 (ptt-90) REVERT: B 196 TYR cc_start: 0.4550 (t80) cc_final: 0.3365 (t80) REVERT: B 338 GLU cc_start: 0.8736 (tp30) cc_final: 0.8401 (tp30) REVERT: B 413 LEU cc_start: 0.9330 (mm) cc_final: 0.8919 (pp) REVERT: B 419 MET cc_start: 0.7566 (mmp) cc_final: 0.7316 (mmp) REVERT: B 607 MET cc_start: 0.8113 (mtt) cc_final: 0.7832 (mmm) REVERT: B 657 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8338 (pm20) REVERT: B 690 LEU cc_start: 0.9022 (tp) cc_final: 0.8738 (tp) REVERT: B 711 TYR cc_start: 0.8268 (t80) cc_final: 0.7683 (t80) outliers start: 34 outliers final: 27 residues processed: 160 average time/residue: 0.1788 time to fit residues: 41.1526 Evaluate side-chains 167 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 137 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 PHE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 312 LEU 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 495 TYR Chi-restraints excluded: chain A residue 559 TYR Chi-restraints excluded: chain A residue 573 THR Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 402 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 617 SER 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: 0.5980 chunk 81 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.107911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.083754 restraints weight = 31321.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.086493 restraints weight = 17750.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.088212 restraints weight = 12157.954| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5620 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= 0.179 Angle : 0.707 13.114 12278 Z= 0.337 Chirality : 0.041 0.214 1498 Planarity : 0.004 0.054 1522 Dihedral : 6.634 78.938 1283 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.54 % Allowed : 26.36 % Favored : 70.10 % 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: -0.85 (0.25), residues: 1122 helix: 0.23 (0.20), residues: 700 sheet: 0.85 (0.95), residues: 46 loop : -2.22 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 408 HIS 0.002 0.001 HIS B 676 PHE 0.022 0.001 PHE B 434 TYR 0.024 0.001 TYR A 216 ARG 0.005 0.000 ARG B 386 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1951.12 seconds wall clock time: 36 minutes 15.04 seconds (2175.04 seconds total)