Starting phenix.real_space_refine on Sat Jul 4 00:28:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7obq_12799/07_2026/7obq_12799_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7obq_12799/07_2026/7obq_12799.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 { model { file = "/net/cci-nas-00/data/ceres_data/7obq_12799/07_2026/7obq_12799_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7obq_12799/07_2026/7obq_12799_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7obq_12799/07_2026/7obq_12799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7obq_12799/07_2026/7obq_12799.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 P 174 5.49 5 Mg 3 5.21 5 S 67 5.16 5 C 9823 2.51 5 N 2979 2.21 5 O 3622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16668 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3542 Classifications: {'RNA': 165} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 11, 'rna3p_pur': 79, 'rna3p_pyr': 61} Link IDs: {'rna2p': 24, 'rna3p': 140} Chain: "q" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 842 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "s" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "u" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3431 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 420} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'TYR:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 45 Chain: "u" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Chain: "v" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1563 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain breaks: 1 Chain: "x" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3049 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 10, 'TRANS': 382} Chain breaks: 2 Chain: "y" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3483 Classifications: {'peptide': 454} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 443} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "z" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "v" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "y" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.56, per 1000 atoms: 0.21 Number of scatterers: 16668 At special positions: 0 Unit cell: (118.77, 117.7, 189.39, 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) S 67 16.00 P 174 15.00 Mg 3 11.99 O 3622 8.00 N 2979 7.00 C 9823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 473.8 milliseconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 5 sheets defined 61.5% alpha, 7.9% beta 39 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'q' and resid 19 through 24 removed outlier: 3.504A pdb=" N ASN q 24 " --> pdb=" O ALA q 21 " (cutoff:3.500A) Processing helix chain 'q' and resid 45 through 55 removed outlier: 3.534A pdb=" N ALA q 55 " --> pdb=" O ASP q 51 " (cutoff:3.500A) Processing helix chain 'q' and resid 100 through 117 removed outlier: 3.546A pdb=" N VAL q 104 " --> pdb=" O SER q 100 " (cutoff:3.500A) Proline residue: q 113 - end of helix Processing helix chain 's' and resid 2 through 20 removed outlier: 3.503A pdb=" N UNK s 20 " --> pdb=" O UNK s 16 " (cutoff:3.500A) Processing helix chain 'u' and resid 58 through 68 Processing helix chain 'u' and resid 77 through 96 Processing helix chain 'u' and resid 113 through 118 removed outlier: 4.013A pdb=" N THR u 116 " --> pdb=" O ASP u 113 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP u 117 " --> pdb=" O LEU u 114 " (cutoff:3.500A) Processing helix chain 'u' and resid 119 through 142 removed outlier: 3.506A pdb=" N LEU u 123 " --> pdb=" O ARG u 119 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL u 124 " --> pdb=" O TYR u 120 " (cutoff:3.500A) Processing helix chain 'u' and resid 143 through 145 No H-bonds generated for 'chain 'u' and resid 143 through 145' Processing helix chain 'u' and resid 146 through 170 removed outlier: 4.193A pdb=" N PHE u 150 " --> pdb=" O PRO u 146 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS u 151 " --> pdb=" O ARG u 147 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS u 161 " --> pdb=" O ARG u 157 " (cutoff:3.500A) Processing helix chain 'u' and resid 176 through 198 Processing helix chain 'u' and resid 200 through 222 Processing helix chain 'u' and resid 223 through 249 removed outlier: 3.502A pdb=" N VAL u 228 " --> pdb=" O GLU u 224 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU u 229 " --> pdb=" O GLU u 225 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR u 230 " --> pdb=" O GLN u 226 " (cutoff:3.500A) Proline residue: u 239 - end of helix Processing helix chain 'u' and resid 252 through 267 removed outlier: 3.541A pdb=" N LEU u 262 " --> pdb=" O MET u 258 " (cutoff:3.500A) Processing helix chain 'u' and resid 268 through 290 Processing helix chain 'u' and resid 304 through 320 removed outlier: 3.888A pdb=" N ARG u 308 " --> pdb=" O ILE u 304 " (cutoff:3.500A) Processing helix chain 'u' and resid 330 through 362 removed outlier: 3.715A pdb=" N GLU u 351 " --> pdb=" O ALA u 347 " (cutoff:3.500A) Proline residue: u 354 - end of helix removed outlier: 3.515A pdb=" N THR u 362 " --> pdb=" O GLN u 358 " (cutoff:3.500A) Processing helix chain 'u' and resid 373 through 399 removed outlier: 3.562A pdb=" N HIS u 377 " --> pdb=" O LEU u 373 " (cutoff:3.500A) Processing helix chain 'u' and resid 415 through 443 removed outlier: 3.994A pdb=" N GLN u 419 " --> pdb=" O SER u 415 " (cutoff:3.500A) Proline residue: u 439 - end of helix Processing helix chain 'u' and resid 446 through 468 Processing helix chain 'u' and resid 478 through 494 removed outlier: 3.803A pdb=" N LYS u 488 " --> pdb=" O ASP u 484 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR u 489 " --> pdb=" O ARG u 485 " (cutoff:3.500A) Processing helix chain 'u' and resid 512 through 523 Processing helix chain 'v' and resid 76 through 87 Processing helix chain 'v' and resid 124 through 132 removed outlier: 3.501A pdb=" N PHE v 128 " --> pdb=" O LEU v 124 " (cutoff:3.500A) Processing helix chain 'v' and resid 151 through 168 removed outlier: 3.537A pdb=" N SER v 168 " --> pdb=" O ILE v 164 " (cutoff:3.500A) Processing helix chain 'v' and resid 189 through 208 removed outlier: 3.835A pdb=" N THR v 203 " --> pdb=" O LYS v 199 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG v 205 " --> pdb=" O LEU v 201 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL v 206 " --> pdb=" O ASN v 202 " (cutoff:3.500A) Processing helix chain 'v' and resid 260 through 271 Processing helix chain 'x' and resid 21 through 42 removed outlier: 3.803A pdb=" N GLU x 26 " --> pdb=" O ILE x 22 " (cutoff:3.500A) Processing helix chain 'x' and resid 45 through 64 Processing helix chain 'x' and resid 72 through 88 removed outlier: 3.951A pdb=" N ASP x 88 " --> pdb=" O VAL x 84 " (cutoff:3.500A) Processing helix chain 'x' and resid 113 through 128 Processing helix chain 'x' and resid 144 through 156 Processing helix chain 'x' and resid 167 through 182 Processing helix chain 'x' and resid 198 through 213 removed outlier: 3.679A pdb=" N PHE x 202 " --> pdb=" O GLU x 198 " (cutoff:3.500A) Processing helix chain 'x' and resid 228 through 240 removed outlier: 4.243A pdb=" N GLN x 232 " --> pdb=" O ALA x 228 " (cutoff:3.500A) Processing helix chain 'x' and resid 258 through 267 removed outlier: 3.606A pdb=" N ALA x 262 " --> pdb=" O GLY x 258 " (cutoff:3.500A) Processing helix chain 'x' and resid 286 through 296 removed outlier: 3.624A pdb=" N PHE x 290 " --> pdb=" O LYS x 286 " (cutoff:3.500A) Processing helix chain 'x' and resid 317 through 325 Processing helix chain 'x' and resid 328 through 343 Processing helix chain 'x' and resid 344 through 350 removed outlier: 4.267A pdb=" N ILE x 348 " --> pdb=" O PRO x 344 " (cutoff:3.500A) Processing helix chain 'x' and resid 365 through 382 removed outlier: 4.043A pdb=" N MET x 382 " --> pdb=" O ILE x 378 " (cutoff:3.500A) Processing helix chain 'x' and resid 383 through 388 Processing helix chain 'x' and resid 391 through 399 removed outlier: 3.523A pdb=" N VAL x 395 " --> pdb=" O ASP x 391 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN x 399 " --> pdb=" O VAL x 395 " (cutoff:3.500A) Processing helix chain 'x' and resid 399 through 410 removed outlier: 3.974A pdb=" N ILE x 403 " --> pdb=" O GLN x 399 " (cutoff:3.500A) Processing helix chain 'x' and resid 415 through 437 Processing helix chain 'y' and resid 27 through 38 removed outlier: 3.507A pdb=" N ALA y 31 " --> pdb=" O GLY y 27 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU y 32 " --> pdb=" O PRO y 28 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 94 removed outlier: 4.357A pdb=" N LYS y 81 " --> pdb=" O THR y 77 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N HIS y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'y' and resid 94 through 99 Processing helix chain 'y' and resid 103 through 109 Processing helix chain 'y' and resid 113 through 130 removed outlier: 3.984A pdb=" N ILE y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) Processing helix chain 'y' and resid 133 through 147 Processing helix chain 'y' and resid 333 through 351 removed outlier: 4.565A pdb=" N SER y 339 " --> pdb=" O GLU y 335 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL y 340 " --> pdb=" O ASP y 336 " (cutoff:3.500A) Processing helix chain 'y' and resid 354 through 369 Processing helix chain 'y' and resid 379 through 397 Processing helix chain 'y' and resid 403 through 414 removed outlier: 3.571A pdb=" N ASP y 407 " --> pdb=" O ASP y 403 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET y 409 " --> pdb=" O LEU y 405 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP y 410 " --> pdb=" O ARG y 406 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARG y 414 " --> pdb=" O ASP y 410 " (cutoff:3.500A) Processing helix chain 'y' and resid 429 through 445 Processing helix chain 'y' and resid 459 through 475 Processing helix chain 'y' and resid 496 through 512 Processing helix chain 'y' and resid 527 through 542 Processing helix chain 'y' and resid 557 through 572 removed outlier: 3.554A pdb=" N HIS y 572 " --> pdb=" O ALA y 568 " (cutoff:3.500A) Processing helix chain 'y' and resid 588 through 592 removed outlier: 3.697A pdb=" N THR y 591 " --> pdb=" O LYS y 588 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE y 592 " --> pdb=" O PHE y 589 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 588 through 592' Processing helix chain 'y' and resid 596 through 606 removed outlier: 3.923A pdb=" N ILE y 600 " --> pdb=" O VAL y 596 " (cutoff:3.500A) Processing helix chain 'y' and resid 626 through 636 Processing helix chain 'z' and resid 561 through 567 Processing helix chain 'z' and resid 579 through 583 Processing helix chain 'z' and resid 593 through 600 Processing sheet with id=AA1, first strand: chain 'q' and resid 16 through 18 removed outlier: 8.769A pdb=" N ARG q 79 " --> pdb=" O ASN q 65 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASN q 65 " --> pdb=" O ARG q 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'v' and resid 99 through 104 removed outlier: 6.022A pdb=" N VAL v 67 " --> pdb=" O ILE v 116 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA v 66 " --> pdb=" O ARG v 137 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL v 139 " --> pdb=" O ALA v 66 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU v 68 " --> pdb=" O VAL v 139 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N PHE v 141 " --> pdb=" O LEU v 68 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU v 70 " --> pdb=" O PHE v 141 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL v 143 " --> pdb=" O LEU v 70 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N SER v 174 " --> pdb=" O ARG v 137 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU v 176 " --> pdb=" O VAL v 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU v 244 " --> pdb=" O ILE v 177 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N CYS v 179 " --> pdb=" O LEU v 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'x' and resid 159 through 160 removed outlier: 9.081A pdb=" N TYR x 160 " --> pdb=" O THR x 132 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LEU x 134 " --> pdb=" O TYR x 160 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS x 133 " --> pdb=" O ILE x 188 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASP x 190 " --> pdb=" O CYS x 133 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE x 135 " --> pdb=" O ASP x 190 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ASN x 102 " --> pdb=" O ILE x 187 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N VAL x 189 " --> pdb=" O ASN x 102 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE x 104 " --> pdb=" O VAL x 189 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ILE x 246 " --> pdb=" O ILE x 217 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR x 219 " --> pdb=" O ILE x 246 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N THR x 248 " --> pdb=" O TYR x 219 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N MET x 221 " --> pdb=" O THR x 248 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL x 245 " --> pdb=" O ILE x 270 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE x 272 " --> pdb=" O VAL x 245 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL x 247 " --> pdb=" O PHE x 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'y' and resid 14 through 17 removed outlier: 6.202A pdb=" N VAL y 14 " --> pdb=" O SER y 9 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SER y 9 " --> pdb=" O VAL y 14 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'y' and resid 486 through 489 removed outlier: 7.055A pdb=" N VAL y 448 " --> pdb=" O GLN y 487 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N PHE y 489 " --> pdb=" O VAL y 448 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE y 450 " --> pdb=" O PHE y 489 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU y 449 " --> pdb=" O LEU y 517 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ASP y 519 " --> pdb=" O LEU y 449 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA y 451 " --> pdb=" O ASP y 519 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR y 418 " --> pdb=" O VAL y 516 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL y 518 " --> pdb=" O TYR y 418 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL y 420 " --> pdb=" O VAL y 518 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR y 520 " --> pdb=" O VAL y 420 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE y 422 " --> pdb=" O THR y 520 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE y 584 " --> pdb=" O PHE y 612 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY y 614 " --> pdb=" O ILE y 584 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU y 586 " --> pdb=" O GLY y 614 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 152 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.92 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: 4456 1.34 - 1.45: 3604 1.45 - 1.57: 8760 1.57 - 1.69: 341 1.69 - 1.81: 113 Bond restraints: 17274 Sorted by residual: bond pdb=" N3B GNP y 701 " pdb=" PG GNP y 701 " ideal model delta sigma weight residual 1.801 1.705 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N3B GNP x 601 " pdb=" PG GNP x 601 " ideal model delta sigma weight residual 1.801 1.706 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O5' GNP x 601 " pdb=" PA GNP x 601 " ideal model delta sigma weight residual 1.660 1.571 0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" O5' GNP y 701 " pdb=" PA GNP y 701 " ideal model delta sigma weight residual 1.660 1.572 0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" N PRO y 133 " pdb=" CA PRO y 133 " ideal model delta sigma weight residual 1.474 1.456 0.018 7.40e-03 1.83e+04 5.93e+00 ... (remaining 17269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 23926 2.02 - 4.03: 135 4.03 - 6.05: 41 6.05 - 8.06: 9 8.06 - 10.08: 6 Bond angle restraints: 24117 Sorted by residual: angle pdb=" N PRO y 133 " pdb=" CA PRO y 133 " pdb=" CB PRO y 133 " ideal model delta sigma weight residual 101.83 110.21 -8.38 8.40e-01 1.42e+00 9.95e+01 angle pdb=" C3' C 1 99 " pdb=" O3' C 1 99 " pdb=" P C 1 100 " ideal model delta sigma weight residual 120.20 125.60 -5.40 1.50e+00 4.44e-01 1.30e+01 angle pdb=" O1B GNP y 701 " pdb=" PB GNP y 701 " pdb=" O2B GNP y 701 " ideal model delta sigma weight residual 119.66 109.58 10.08 3.00e+00 1.11e-01 1.13e+01 angle pdb=" O3' C 1 99 " pdb=" C3' C 1 99 " pdb=" C2' C 1 99 " ideal model delta sigma weight residual 109.50 114.39 -4.89 1.50e+00 4.44e-01 1.06e+01 angle pdb=" O1B GNP x 601 " pdb=" PB GNP x 601 " pdb=" O2B GNP x 601 " ideal model delta sigma weight residual 119.66 109.88 9.78 3.00e+00 1.11e-01 1.06e+01 ... (remaining 24112 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 10258 35.69 - 71.39: 486 71.39 - 107.08: 70 107.08 - 142.77: 0 142.77 - 178.47: 3 Dihedral angle restraints: 10817 sinusoidal: 5956 harmonic: 4861 Sorted by residual: dihedral pdb=" O4' C 1 242 " pdb=" C1' C 1 242 " pdb=" N1 C 1 242 " pdb=" C2 C 1 242 " ideal model delta sinusoidal sigma weight residual -128.00 50.47 -178.47 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O3B GTP v 301 " pdb=" O3A GTP v 301 " pdb=" PB GTP v 301 " pdb=" PA GTP v 301 " ideal model delta sinusoidal sigma weight residual -68.92 -171.58 102.66 1 2.00e+01 2.50e-03 2.93e+01 dihedral pdb=" O3A GTP v 301 " pdb=" O3B GTP v 301 " pdb=" PB GTP v 301 " pdb=" PG GTP v 301 " ideal model delta sinusoidal sigma weight residual -56.21 -151.21 95.01 1 2.00e+01 2.50e-03 2.61e+01 ... (remaining 10814 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2575 0.052 - 0.103: 260 0.103 - 0.155: 28 0.155 - 0.207: 2 0.207 - 0.258: 1 Chirality restraints: 2866 Sorted by residual: chirality pdb=" CA PRO y 133 " pdb=" N PRO y 133 " pdb=" C PRO y 133 " pdb=" CB PRO y 133 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C3' C 1 99 " pdb=" C4' C 1 99 " pdb=" O3' C 1 99 " pdb=" C2' C 1 99 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" C3' U 1 236 " pdb=" C4' U 1 236 " pdb=" O3' U 1 236 " pdb=" C2' U 1 236 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 2863 not shown) Planarity restraints: 2459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS y 343 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.12e+00 pdb=" C LYS y 343 " -0.025 2.00e-02 2.50e+03 pdb=" O LYS y 343 " 0.009 2.00e-02 2.50e+03 pdb=" N MET y 344 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU y 82 " -0.007 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C LEU y 82 " 0.022 2.00e-02 2.50e+03 pdb=" O LEU y 82 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE y 83 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU u 314 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C LEU u 314 " 0.021 2.00e-02 2.50e+03 pdb=" O LEU u 314 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA u 315 " -0.007 2.00e-02 2.50e+03 ... (remaining 2456 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 376 2.66 - 3.22: 16164 3.22 - 3.78: 28910 3.78 - 4.34: 36732 4.34 - 4.90: 55806 Nonbonded interactions: 137988 Sorted by model distance: nonbonded pdb=" OG1 THR v 78 " pdb="MG MG v 300 " model vdw 2.106 2.170 nonbonded pdb=" O1B GNP x 601 " pdb="MG MG x 602 " model vdw 2.107 2.170 nonbonded pdb=" OG SER v 95 " pdb="MG MG v 300 " model vdw 2.114 2.170 nonbonded pdb=" O1G GNP x 601 " pdb="MG MG x 602 " model vdw 2.114 2.170 nonbonded pdb=" OG1 THR x 115 " pdb="MG MG x 602 " model vdw 2.120 2.170 ... (remaining 137983 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.57 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.810 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.750 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.003 0.096 17274 Z= 0.141 Angle : 0.483 10.077 24117 Z= 0.264 Chirality : 0.032 0.258 2866 Planarity : 0.003 0.030 2459 Dihedral : 17.779 178.468 7661 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.63 % Allowed : 6.29 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.21), residues: 1620 helix: 2.22 (0.18), residues: 905 sheet: 0.41 (0.39), residues: 166 loop : -0.83 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG q 74 TYR 0.006 0.001 TYR u 379 PHE 0.012 0.001 PHE y 8 TRP 0.005 0.001 TRP y 440 HIS 0.004 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (17274) covalent geometry : angle 0.48348 / 0.26 (24117) hydrogen bonds : bond 0.15862 / 14.14 ( 842) hydrogen bonds : angle 6.03003 / 7.73 ( 2339) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 400 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 48 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8633 (tt0) REVERT: q 68 TYR cc_start: 0.6149 (t80) cc_final: 0.5360 (t80) REVERT: q 75 ASP cc_start: 0.6167 (m-30) cc_final: 0.4865 (m-30) REVERT: q 77 GLN cc_start: 0.8182 (pm20) cc_final: 0.7767 (pm20) REVERT: q 102 LYS cc_start: 0.9357 (tptt) cc_final: 0.9087 (tppt) REVERT: q 107 TYR cc_start: 0.7416 (t80) cc_final: 0.7185 (t80) REVERT: u 260 MET cc_start: -0.0498 (tpt) cc_final: -0.0770 (mtm) REVERT: u 274 LYS cc_start: 0.9181 (ptpt) cc_final: 0.8929 (ptpt) REVERT: u 350 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8495 (mt-10) REVERT: u 375 TYR cc_start: 0.6252 (m-10) cc_final: 0.6008 (m-10) REVERT: u 433 VAL cc_start: 0.8747 (t) cc_final: 0.8456 (t) REVERT: u 449 LYS cc_start: 0.7139 (mppt) cc_final: 0.6436 (tmmt) REVERT: v 74 ASP cc_start: 0.8289 (t0) cc_final: 0.8080 (t70) REVERT: v 90 ARG cc_start: 0.8518 (tpp80) cc_final: 0.8307 (ttt90) REVERT: v 98 ASP cc_start: 0.8793 (p0) cc_final: 0.8583 (p0) REVERT: x 33 LYS cc_start: 0.9124 (tppt) cc_final: 0.8881 (mmtm) REVERT: x 41 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8401 (mm-30) REVERT: x 126 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8314 (tm-30) REVERT: x 151 ASN cc_start: 0.8787 (m-40) cc_final: 0.8558 (m110) REVERT: x 329 LEU cc_start: 0.9188 (mm) cc_final: 0.8798 (mm) REVERT: x 374 LYS cc_start: 0.9426 (pptt) cc_final: 0.9173 (pttm) REVERT: x 396 PHE cc_start: 0.8081 (m-80) cc_final: 0.7673 (m-80) REVERT: y 40 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5285 (mp0) REVERT: y 396 LEU cc_start: 0.8419 (tt) cc_final: 0.8131 (tt) REVERT: y 397 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6359 (tm-30) REVERT: y 405 LEU cc_start: 0.9247 (tp) cc_final: 0.8629 (tt) REVERT: y 409 MET cc_start: 0.8545 (mpp) cc_final: 0.8311 (mpp) REVERT: y 524 MET cc_start: 0.8553 (mmm) cc_final: 0.8179 (mmt) REVERT: y 556 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7345 (t0) REVERT: y 612 PHE cc_start: 0.8552 (m-80) cc_final: 0.8227 (m-80) outliers start: 36 outliers final: 8 residues processed: 426 average time/residue: 0.1230 time to fit residues: 77.0767 Evaluate side-chains 281 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 270 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 397 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 556 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 247 ASN u 346 GLN ** u 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 431 ASN u 468 GLN v 161 GLN v 182 GLN ** x 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 60 ASN y 61 GLN y 71 GLN y 444 ASN y 541 ASN y 617 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.088992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.068822 restraints weight = 69086.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.070733 restraints weight = 39221.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.071988 restraints weight = 26874.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.072830 restraints weight = 20751.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073244 restraints weight = 17469.471| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17274 Z= 0.158 Angle : 0.607 8.332 24117 Z= 0.317 Chirality : 0.038 0.217 2866 Planarity : 0.004 0.046 2459 Dihedral : 20.399 179.313 4505 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.78 % Allowed : 15.20 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.21), residues: 1620 helix: 2.10 (0.17), residues: 915 sheet: 0.46 (0.40), residues: 159 loop : -0.91 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG u 391 TYR 0.017 0.002 TYR u 186 PHE 0.023 0.002 PHE y 70 TRP 0.006 0.001 TRP u 295 HIS 0.005 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (17274) covalent geometry : angle 0.60715 / 0.32 (24117) hydrogen bonds : bond 0.06437 / 6.02 ( 842) hydrogen bonds : angle 4.35354 / 5.48 ( 2339) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 282 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 68 TYR cc_start: 0.6129 (t80) cc_final: 0.5508 (t80) REVERT: q 75 ASP cc_start: 0.6674 (m-30) cc_final: 0.6024 (m-30) REVERT: q 77 GLN cc_start: 0.8243 (pm20) cc_final: 0.7990 (pm20) REVERT: q 102 LYS cc_start: 0.9425 (tptt) cc_final: 0.9142 (tppt) REVERT: u 260 MET cc_start: -0.0468 (tpt) cc_final: -0.0710 (mtm) REVERT: u 330 LYS cc_start: 0.8865 (tmtt) cc_final: 0.8332 (tptt) REVERT: u 431 ASN cc_start: 0.8837 (m110) cc_final: 0.8601 (m-40) REVERT: u 449 LYS cc_start: 0.6925 (mppt) cc_final: 0.6335 (tmmt) REVERT: v 90 ARG cc_start: 0.8693 (tpp80) cc_final: 0.8489 (tpp80) REVERT: v 98 ASP cc_start: 0.8855 (p0) cc_final: 0.8615 (p0) REVERT: v 130 GLU cc_start: 0.8446 (pp20) cc_final: 0.8216 (pp20) REVERT: v 152 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8235 (p) REVERT: x 33 LYS cc_start: 0.9139 (tppt) cc_final: 0.8608 (mmtm) REVERT: x 204 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7937 (mp0) REVERT: x 338 ASN cc_start: 0.8925 (m-40) cc_final: 0.8717 (m110) REVERT: y 40 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.5482 (mp0) REVERT: y 128 SER cc_start: 0.7625 (m) cc_final: 0.7410 (p) REVERT: y 397 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6203 (tm-30) REVERT: y 405 LEU cc_start: 0.9096 (tp) cc_final: 0.8696 (tp) REVERT: y 409 MET cc_start: 0.8697 (mpp) cc_final: 0.8374 (mpp) REVERT: y 524 MET cc_start: 0.8678 (mmm) cc_final: 0.8226 (mpp) REVERT: y 560 ASP cc_start: 0.8704 (t70) cc_final: 0.8444 (t0) REVERT: y 612 PHE cc_start: 0.8592 (m-80) cc_final: 0.8312 (m-80) outliers start: 38 outliers final: 14 residues processed: 310 average time/residue: 0.1166 time to fit residues: 55.5476 Evaluate side-chains 258 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain v residue 152 VAL Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain y residue 14 VAL Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 397 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 605 ILE Chi-restraints excluded: chain z residue 590 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 52 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 18 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... u 247 ASN v 93 GLN x 195 HIS y 412 GLN y 541 ASN y 556 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.089304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.069187 restraints weight = 69330.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.071113 restraints weight = 39308.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.072386 restraints weight = 26918.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073072 restraints weight = 20861.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.073625 restraints weight = 17732.325| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17274 Z= 0.131 Angle : 0.606 13.091 24117 Z= 0.311 Chirality : 0.038 0.216 2866 Planarity : 0.004 0.052 2459 Dihedral : 20.364 179.844 4502 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.00 % Allowed : 14.84 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.21), residues: 1620 helix: 1.95 (0.17), residues: 921 sheet: 0.39 (0.41), residues: 159 loop : -1.07 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG u 342 TYR 0.016 0.001 TYR y 78 PHE 0.021 0.002 PHE x 106 TRP 0.017 0.001 TRP v 266 HIS 0.004 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (17274) covalent geometry : angle 0.60587 / 0.31 (24117) hydrogen bonds : bond 0.05394 / 5.18 ( 842) hydrogen bonds : angle 4.15335 / 5.25 ( 2339) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 0.506 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: q 48 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8419 (pp20) REVERT: q 68 TYR cc_start: 0.6113 (t80) cc_final: 0.5650 (t80) REVERT: q 75 ASP cc_start: 0.6563 (m-30) cc_final: 0.6032 (m-30) REVERT: q 102 LYS cc_start: 0.9452 (tptt) cc_final: 0.9119 (tppt) REVERT: u 260 MET cc_start: -0.0681 (tpt) cc_final: -0.0915 (mtm) REVERT: u 312 LEU cc_start: 0.8160 (pp) cc_final: 0.7719 (mp) REVERT: u 340 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8830 (mp0) REVERT: u 449 LYS cc_start: 0.6910 (mppt) cc_final: 0.6259 (tmmt) REVERT: u 453 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7574 (pp) REVERT: v 90 ARG cc_start: 0.8721 (tpp80) cc_final: 0.8520 (tpp80) REVERT: v 98 ASP cc_start: 0.8831 (p0) cc_final: 0.8610 (p0) REVERT: v 130 GLU cc_start: 0.8411 (pp20) cc_final: 0.8207 (pp20) REVERT: x 204 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7923 (mp0) REVERT: x 396 PHE cc_start: 0.8305 (m-80) cc_final: 0.7728 (m-80) REVERT: x 424 TYR cc_start: 0.8014 (t80) cc_final: 0.7600 (t80) REVERT: y 40 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5424 (mp0) REVERT: y 128 SER cc_start: 0.7433 (m) cc_final: 0.7189 (p) REVERT: y 130 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8673 (pt) REVERT: y 397 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6270 (tm-30) REVERT: y 405 LEU cc_start: 0.9050 (tp) cc_final: 0.8631 (tp) REVERT: y 409 MET cc_start: 0.8715 (mpp) cc_final: 0.8347 (mpp) REVERT: y 503 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7784 (mt-10) REVERT: y 524 MET cc_start: 0.8624 (mmm) cc_final: 0.8240 (mmt) REVERT: y 560 ASP cc_start: 0.8657 (t70) cc_final: 0.8396 (t0) REVERT: y 602 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8542 (ttm) REVERT: y 612 PHE cc_start: 0.8546 (m-80) cc_final: 0.8271 (m-80) outliers start: 41 outliers final: 16 residues processed: 292 average time/residue: 0.1125 time to fit residues: 50.3657 Evaluate side-chains 264 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 340 GLU Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 130 ILE Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 397 GLN Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 516 VAL Chi-restraints excluded: chain y residue 602 MET Chi-restraints excluded: chain z residue 590 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 1 optimal weight: 30.0000 chunk 115 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 87 optimal weight: 0.4980 chunk 59 optimal weight: 0.0980 chunk 105 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... y 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.088192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.068026 restraints weight = 69574.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.069872 restraints weight = 39607.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.071130 restraints weight = 27253.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.071948 restraints weight = 21129.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072488 restraints weight = 17783.515| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17274 Z= 0.148 Angle : 0.597 11.396 24117 Z= 0.310 Chirality : 0.038 0.217 2866 Planarity : 0.003 0.043 2459 Dihedral : 20.348 179.689 4501 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.36 % Allowed : 15.28 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.21), residues: 1620 helix: 1.98 (0.17), residues: 915 sheet: 0.32 (0.41), residues: 159 loop : -1.15 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG z 576 TYR 0.017 0.002 TYR y 78 PHE 0.018 0.002 PHE y 8 TRP 0.010 0.001 TRP v 266 HIS 0.004 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (17274) covalent geometry : angle 0.59707 / 0.31 (24117) hydrogen bonds : bond 0.04986 / 4.84 ( 842) hydrogen bonds : angle 4.12053 / 5.11 ( 2339) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 68 TYR cc_start: 0.6508 (t80) cc_final: 0.5920 (t80) REVERT: q 75 ASP cc_start: 0.6935 (m-30) cc_final: 0.6603 (m-30) REVERT: q 83 ARG cc_start: 0.8748 (mmp80) cc_final: 0.8541 (mmp80) REVERT: q 102 LYS cc_start: 0.9444 (tptt) cc_final: 0.9120 (tppt) REVERT: u 260 MET cc_start: -0.0516 (tpt) cc_final: -0.0789 (mtm) REVERT: u 449 LYS cc_start: 0.6923 (mppt) cc_final: 0.6369 (tmmt) REVERT: v 98 ASP cc_start: 0.8883 (p0) cc_final: 0.8594 (p0) REVERT: v 117 ASP cc_start: 0.8332 (t70) cc_final: 0.8128 (t0) REVERT: v 130 GLU cc_start: 0.8475 (pp20) cc_final: 0.8236 (pp20) REVERT: x 106 PHE cc_start: 0.8843 (m-80) cc_final: 0.8356 (m-10) REVERT: x 221 MET cc_start: 0.7975 (ppp) cc_final: 0.7530 (ppp) REVERT: x 332 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8044 (mtt) REVERT: x 379 MET cc_start: 0.8971 (ptm) cc_final: 0.8718 (ppp) REVERT: x 424 TYR cc_start: 0.8074 (t80) cc_final: 0.7694 (t80) REVERT: y 40 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5373 (mp0) REVERT: y 397 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6667 (tm-30) REVERT: y 405 LEU cc_start: 0.9104 (tp) cc_final: 0.8688 (tp) REVERT: y 409 MET cc_start: 0.8736 (mpp) cc_final: 0.8361 (mpp) REVERT: y 418 TYR cc_start: 0.8973 (t80) cc_final: 0.8742 (t80) REVERT: y 503 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7799 (mt-10) REVERT: y 524 MET cc_start: 0.8654 (mmm) cc_final: 0.8370 (mmt) REVERT: y 560 ASP cc_start: 0.8624 (t70) cc_final: 0.8360 (t0) REVERT: y 612 PHE cc_start: 0.8588 (m-80) cc_final: 0.8282 (m-80) outliers start: 46 outliers final: 27 residues processed: 283 average time/residue: 0.1205 time to fit residues: 52.6381 Evaluate side-chains 260 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 340 GLU Chi-restraints excluded: chain u residue 437 GLN Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 197 LEU Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 77 HIS Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 332 MET Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 130 ILE Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 397 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 516 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 13 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 0.0050 chunk 6 optimal weight: 20.0000 chunk 132 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... u 78 GLN x 151 ASN y 399 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.088442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.068334 restraints weight = 69408.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070226 restraints weight = 39345.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.071481 restraints weight = 27025.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.072307 restraints weight = 20979.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.072829 restraints weight = 17622.442| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17274 Z= 0.126 Angle : 0.597 10.526 24117 Z= 0.308 Chirality : 0.037 0.214 2866 Planarity : 0.003 0.062 2459 Dihedral : 20.354 179.715 4501 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.92 % Allowed : 17.25 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.21), residues: 1620 helix: 1.93 (0.17), residues: 917 sheet: 0.29 (0.42), residues: 157 loop : -1.14 (0.24), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG q 81 TYR 0.017 0.001 TYR y 78 PHE 0.019 0.001 PHE y 70 TRP 0.007 0.001 TRP u 132 HIS 0.004 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (17274) covalent geometry : angle 0.59732 / 0.31 (24117) hydrogen bonds : bond 0.04718 / 4.57 ( 842) hydrogen bonds : angle 4.08275 / 5.01 ( 2339) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 68 TYR cc_start: 0.6571 (t80) cc_final: 0.6017 (t80) REVERT: q 83 ARG cc_start: 0.8682 (mmp80) cc_final: 0.8130 (mpp-170) REVERT: q 102 LYS cc_start: 0.9430 (tptt) cc_final: 0.9129 (tppt) REVERT: u 260 MET cc_start: -0.0803 (tpt) cc_final: -0.1030 (mtm) REVERT: u 449 LYS cc_start: 0.6926 (mppt) cc_final: 0.6283 (tmmt) REVERT: u 453 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7633 (pp) REVERT: v 98 ASP cc_start: 0.8874 (p0) cc_final: 0.8588 (p0) REVERT: v 117 ASP cc_start: 0.8332 (t70) cc_final: 0.8118 (t0) REVERT: v 130 GLU cc_start: 0.8488 (pp20) cc_final: 0.8249 (pp20) REVERT: x 106 PHE cc_start: 0.8880 (m-80) cc_final: 0.8419 (m-10) REVERT: x 204 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8031 (mp0) REVERT: x 221 MET cc_start: 0.7962 (ppp) cc_final: 0.7591 (ppp) REVERT: x 332 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7801 (mtt) REVERT: x 376 MET cc_start: 0.8562 (mmt) cc_final: 0.8100 (mmm) REVERT: x 424 TYR cc_start: 0.7987 (t80) cc_final: 0.7570 (t80) REVERT: y 40 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5344 (mp0) REVERT: y 397 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6636 (tm-30) REVERT: y 405 LEU cc_start: 0.9117 (tp) cc_final: 0.8729 (tp) REVERT: y 409 MET cc_start: 0.8713 (mpp) cc_final: 0.8347 (mpp) REVERT: y 418 TYR cc_start: 0.9010 (t80) cc_final: 0.8713 (t80) REVERT: y 485 MET cc_start: 0.8280 (mmm) cc_final: 0.8038 (mmm) REVERT: y 524 MET cc_start: 0.8705 (mmm) cc_final: 0.8352 (mmt) REVERT: y 560 ASP cc_start: 0.8596 (t70) cc_final: 0.8335 (t0) REVERT: y 602 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8581 (ttm) REVERT: y 612 PHE cc_start: 0.8609 (m-80) cc_final: 0.8324 (m-80) outliers start: 40 outliers final: 27 residues processed: 279 average time/residue: 0.1145 time to fit residues: 49.5152 Evaluate side-chains 271 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 193 MET Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 340 GLU Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 85 LEU Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 332 MET Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 130 ILE Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 397 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 516 VAL Chi-restraints excluded: chain y residue 602 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 177 optimal weight: 4.9990 chunk 79 optimal weight: 0.0570 chunk 59 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 58 optimal weight: 8.9990 overall best weight: 2.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... y 399 GLN y 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.087093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.066832 restraints weight = 69731.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.068656 restraints weight = 39813.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.069876 restraints weight = 27591.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.070668 restraints weight = 21533.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071197 restraints weight = 18213.472| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.52 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17274 Z= 0.186 Angle : 0.632 11.236 24117 Z= 0.329 Chirality : 0.039 0.253 2866 Planarity : 0.004 0.073 2459 Dihedral : 20.399 179.765 4501 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.58 % Allowed : 17.54 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.21), residues: 1620 helix: 1.82 (0.17), residues: 923 sheet: 0.14 (0.42), residues: 161 loop : -1.25 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG x 408 TYR 0.017 0.002 TYR y 78 PHE 0.023 0.002 PHE y 70 TRP 0.015 0.002 TRP q 72 HIS 0.005 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (17274) covalent geometry : angle 0.63217 / 0.33 (24117) hydrogen bonds : bond 0.04890 / 4.79 ( 842) hydrogen bonds : angle 4.17532 / 5.10 ( 2339) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 0.569 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: q 48 GLU cc_start: 0.9033 (mp0) cc_final: 0.8272 (pp20) REVERT: q 68 TYR cc_start: 0.6848 (t80) cc_final: 0.6279 (t80) REVERT: q 102 LYS cc_start: 0.9437 (tptt) cc_final: 0.9137 (tppt) REVERT: u 260 MET cc_start: -0.0910 (tpt) cc_final: -0.1157 (mtm) REVERT: u 429 LEU cc_start: 0.9168 (pp) cc_final: 0.8741 (mm) REVERT: u 449 LYS cc_start: 0.6950 (mppt) cc_final: 0.6319 (tmmt) REVERT: u 453 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7656 (pp) REVERT: v 98 ASP cc_start: 0.8895 (p0) cc_final: 0.8585 (p0) REVERT: v 130 GLU cc_start: 0.8567 (pp20) cc_final: 0.8355 (pp20) REVERT: x 106 PHE cc_start: 0.8906 (m-80) cc_final: 0.8382 (m-10) REVERT: x 221 MET cc_start: 0.7985 (ppp) cc_final: 0.7566 (ppp) REVERT: x 329 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8688 (mm) REVERT: x 332 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7684 (mtt) REVERT: x 376 MET cc_start: 0.8658 (mmt) cc_final: 0.8451 (mmm) REVERT: x 424 TYR cc_start: 0.8121 (t80) cc_final: 0.7558 (t80) REVERT: y 40 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.5495 (mp0) REVERT: y 397 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: y 399 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.7118 (pp30) REVERT: y 405 LEU cc_start: 0.9208 (tp) cc_final: 0.8787 (tp) REVERT: y 409 MET cc_start: 0.8725 (mpp) cc_final: 0.8367 (mpp) REVERT: y 418 TYR cc_start: 0.9099 (t80) cc_final: 0.8846 (t80) REVERT: y 454 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7612 (t0) REVERT: y 518 VAL cc_start: 0.9537 (t) cc_final: 0.9259 (m) REVERT: y 560 ASP cc_start: 0.8594 (t70) cc_final: 0.8361 (t0) outliers start: 49 outliers final: 33 residues processed: 280 average time/residue: 0.1161 time to fit residues: 50.1354 Evaluate side-chains 264 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 115 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 340 GLU Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 85 LEU Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 264 GLU Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 77 HIS Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 329 LEU Chi-restraints excluded: chain x residue 332 MET Chi-restraints excluded: chain y residue 14 VAL Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 130 ILE Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 397 GLN Chi-restraints excluded: chain y residue 399 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 404 MET Chi-restraints excluded: chain y residue 448 VAL Chi-restraints excluded: chain y residue 454 ASP Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 516 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 101 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... y 399 GLN y 444 ASN y 617 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.087796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.067582 restraints weight = 69263.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.069449 restraints weight = 39208.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.070679 restraints weight = 26981.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071463 restraints weight = 20996.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.072015 restraints weight = 17795.702| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17274 Z= 0.131 Angle : 0.625 12.139 24117 Z= 0.321 Chirality : 0.038 0.213 2866 Planarity : 0.004 0.045 2459 Dihedral : 20.431 179.834 4501 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.29 % Allowed : 18.71 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.21), residues: 1620 helix: 1.89 (0.17), residues: 923 sheet: 0.08 (0.42), residues: 165 loop : -1.23 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG x 415 TYR 0.018 0.002 TYR y 78 PHE 0.036 0.002 PHE y 70 TRP 0.011 0.001 TRP q 72 HIS 0.005 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (17274) covalent geometry : angle 0.62486 / 0.32 (24117) hydrogen bonds : bond 0.04584 / 4.49 ( 842) hydrogen bonds : angle 4.06958 / 4.99 ( 2339) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 68 TYR cc_start: 0.6748 (t80) cc_final: 0.6154 (t80) REVERT: u 260 MET cc_start: -0.0938 (tpt) cc_final: -0.1181 (mtm) REVERT: u 353 LYS cc_start: 0.7839 (ptpt) cc_final: 0.7066 (tppt) REVERT: u 449 LYS cc_start: 0.7058 (mppt) cc_final: 0.6441 (tmmt) REVERT: u 453 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7609 (pp) REVERT: v 98 ASP cc_start: 0.8872 (p0) cc_final: 0.8570 (p0) REVERT: x 106 PHE cc_start: 0.8893 (m-80) cc_final: 0.8395 (m-10) REVERT: x 221 MET cc_start: 0.7962 (ppp) cc_final: 0.7567 (ppp) REVERT: x 332 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7973 (mtt) REVERT: x 424 TYR cc_start: 0.8024 (t80) cc_final: 0.7720 (t80) REVERT: y 40 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5328 (mp0) REVERT: y 405 LEU cc_start: 0.9193 (tp) cc_final: 0.8766 (tp) REVERT: y 409 MET cc_start: 0.8705 (mpp) cc_final: 0.8340 (mpp) REVERT: y 418 TYR cc_start: 0.9084 (t80) cc_final: 0.8771 (t80) REVERT: y 454 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.7641 (t0) REVERT: y 518 VAL cc_start: 0.9527 (t) cc_final: 0.9260 (m) outliers start: 45 outliers final: 29 residues processed: 277 average time/residue: 0.1079 time to fit residues: 46.5526 Evaluate side-chains 266 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 340 GLU Chi-restraints excluded: chain u residue 437 GLN Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 85 LEU Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 264 GLU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 332 MET Chi-restraints excluded: chain y residue 14 VAL Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 404 MET Chi-restraints excluded: chain y residue 454 ASP Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 516 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 34 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 chunk 119 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... y 45 ASN y 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.088400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.068080 restraints weight = 68932.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069927 restraints weight = 39104.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.071179 restraints weight = 26947.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072007 restraints weight = 20856.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072419 restraints weight = 17567.218| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17274 Z= 0.128 Angle : 0.636 13.145 24117 Z= 0.325 Chirality : 0.038 0.215 2866 Planarity : 0.003 0.033 2459 Dihedral : 20.374 179.847 4498 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.14 % Allowed : 19.01 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.21), residues: 1620 helix: 1.86 (0.17), residues: 922 sheet: 0.09 (0.42), residues: 163 loop : -1.28 (0.25), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG x 415 TYR 0.018 0.002 TYR y 78 PHE 0.026 0.001 PHE y 70 TRP 0.018 0.001 TRP q 72 HIS 0.004 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (17274) covalent geometry : angle 0.63598 / 0.33 (24117) hydrogen bonds : bond 0.04489 / 4.40 ( 842) hydrogen bonds : angle 4.05448 / 4.98 ( 2339) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 48 GLU cc_start: 0.9104 (mp0) cc_final: 0.8382 (pp20) REVERT: q 68 TYR cc_start: 0.6769 (t80) cc_final: 0.6134 (t80) REVERT: q 102 LYS cc_start: 0.9315 (tppt) cc_final: 0.9010 (tppt) REVERT: q 112 ILE cc_start: 0.7621 (mt) cc_final: 0.7247 (mt) REVERT: u 260 MET cc_start: -0.1034 (tpt) cc_final: -0.1258 (mtm) REVERT: u 290 MET cc_start: 0.8079 (pmm) cc_final: 0.7834 (pmm) REVERT: u 429 LEU cc_start: 0.9268 (pp) cc_final: 0.8872 (mm) REVERT: u 449 LYS cc_start: 0.7064 (mppt) cc_final: 0.6451 (tmmt) REVERT: u 453 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7617 (pp) REVERT: v 98 ASP cc_start: 0.8858 (p0) cc_final: 0.8555 (p0) REVERT: x 106 PHE cc_start: 0.8911 (m-80) cc_final: 0.8382 (m-10) REVERT: x 125 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8775 (m-10) REVERT: x 221 MET cc_start: 0.7962 (ppp) cc_final: 0.7556 (ppp) REVERT: x 332 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8026 (mtt) REVERT: y 40 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.5400 (mp0) REVERT: y 396 LEU cc_start: 0.8444 (tt) cc_final: 0.8164 (tt) REVERT: y 405 LEU cc_start: 0.9186 (tp) cc_final: 0.8744 (mt) REVERT: y 409 MET cc_start: 0.8707 (mpp) cc_final: 0.8326 (mpp) REVERT: y 418 TYR cc_start: 0.9073 (t80) cc_final: 0.8784 (t80) REVERT: y 454 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.7679 (t0) REVERT: y 485 MET cc_start: 0.8239 (mmm) cc_final: 0.7925 (mmm) REVERT: y 518 VAL cc_start: 0.9517 (t) cc_final: 0.9236 (m) outliers start: 43 outliers final: 32 residues processed: 274 average time/residue: 0.1117 time to fit residues: 47.7397 Evaluate side-chains 271 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 18 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 84 CYS Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 340 GLU Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 85 LEU Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 130 GLU Chi-restraints excluded: chain v residue 264 GLU Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 125 TYR Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 332 MET Chi-restraints excluded: chain y residue 14 VAL Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 454 ASP Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 516 VAL Chi-restraints excluded: chain y residue 556 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 75 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 137 optimal weight: 0.1980 chunk 78 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 173 optimal weight: 6.9990 chunk 130 optimal weight: 0.0030 chunk 5 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 overall best weight: 3.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... v 236 GLN y 617 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.085512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.065383 restraints weight = 69591.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.067183 restraints weight = 39866.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.068384 restraints weight = 27514.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.069187 restraints weight = 21348.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.069690 restraints weight = 18009.835| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17274 Z= 0.236 Angle : 0.728 12.163 24117 Z= 0.373 Chirality : 0.040 0.218 2866 Planarity : 0.004 0.053 2459 Dihedral : 20.457 179.924 4498 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.29 % Allowed : 19.08 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.21), residues: 1620 helix: 1.66 (0.17), residues: 925 sheet: -0.07 (0.42), residues: 161 loop : -1.32 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG u 391 TYR 0.018 0.002 TYR x 424 PHE 0.025 0.002 PHE y 70 TRP 0.037 0.003 TRP q 72 HIS 0.006 0.001 HIS u 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.24 (17274) covalent geometry : angle 0.72848 / 0.37 (24117) hydrogen bonds : bond 0.04970 / 4.90 ( 842) hydrogen bonds : angle 4.35709 / 5.30 ( 2339) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 234 time to evaluate : 0.622 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: q 48 GLU cc_start: 0.9112 (mp0) cc_final: 0.8431 (pp20) REVERT: q 68 TYR cc_start: 0.6992 (t80) cc_final: 0.6219 (t80) REVERT: q 83 ARG cc_start: 0.8463 (mmp80) cc_final: 0.8247 (mmp80) REVERT: q 102 LYS cc_start: 0.9343 (tppt) cc_final: 0.9100 (tppt) REVERT: q 112 ILE cc_start: 0.7603 (mt) cc_final: 0.7259 (mt) REVERT: u 260 MET cc_start: -0.0971 (tpt) cc_final: -0.1268 (mtm) REVERT: u 353 LYS cc_start: 0.7933 (ptpt) cc_final: 0.7114 (tppt) REVERT: u 449 LYS cc_start: 0.7169 (mppt) cc_final: 0.6625 (tmmt) REVERT: u 453 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7607 (pp) REVERT: v 98 ASP cc_start: 0.9021 (p0) cc_final: 0.8719 (p0) REVERT: x 106 PHE cc_start: 0.8898 (m-80) cc_final: 0.8440 (m-10) REVERT: x 332 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8096 (mtt) REVERT: x 374 LYS cc_start: 0.9178 (pttm) cc_final: 0.8961 (pttm) REVERT: x 376 MET cc_start: 0.8821 (mmm) cc_final: 0.8599 (mmt) REVERT: y 40 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5604 (mp0) REVERT: y 405 LEU cc_start: 0.9229 (tp) cc_final: 0.8787 (tp) REVERT: y 409 MET cc_start: 0.8700 (mpp) cc_final: 0.8343 (mpp) REVERT: y 418 TYR cc_start: 0.9139 (t80) cc_final: 0.8847 (t80) REVERT: y 454 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.7863 (t0) REVERT: y 485 MET cc_start: 0.8180 (mmm) cc_final: 0.7918 (mmm) REVERT: y 602 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8485 (mtm) outliers start: 45 outliers final: 31 residues processed: 262 average time/residue: 0.1233 time to fit residues: 50.4411 Evaluate side-chains 258 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 84 CYS Chi-restraints excluded: chain u residue 115 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 340 GLU Chi-restraints excluded: chain u residue 437 GLN Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 126 LEU Chi-restraints excluded: chain v residue 264 GLU Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 332 MET Chi-restraints excluded: chain y residue 14 VAL Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 454 ASP Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 514 ASP Chi-restraints excluded: chain y residue 516 VAL Chi-restraints excluded: chain y residue 602 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 99 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 145 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 79 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... q 43 ASN u 431 ASN v 236 GLN y 556 ASN y 617 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.087182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.067165 restraints weight = 68572.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.069105 restraints weight = 38321.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.070349 restraints weight = 26107.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.071187 restraints weight = 20254.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.071737 restraints weight = 17018.137| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17274 Z= 0.130 Angle : 0.692 14.032 24117 Z= 0.348 Chirality : 0.039 0.332 2866 Planarity : 0.003 0.036 2459 Dihedral : 20.480 179.073 4498 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.70 % Allowed : 20.10 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.21), residues: 1620 helix: 1.67 (0.17), residues: 924 sheet: -0.11 (0.42), residues: 165 loop : -1.33 (0.25), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG x 415 TYR 0.020 0.002 TYR y 78 PHE 0.044 0.002 PHE q 98 TRP 0.033 0.002 TRP q 72 HIS 0.005 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (17274) covalent geometry : angle 0.69231 / 0.35 (24117) hydrogen bonds : bond 0.04505 / 4.45 ( 842) hydrogen bonds : angle 4.15888 / 5.07 ( 2339) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.518 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: q 48 GLU cc_start: 0.9102 (mp0) cc_final: 0.8419 (pp20) REVERT: q 68 TYR cc_start: 0.6751 (t80) cc_final: 0.6094 (t80) REVERT: q 102 LYS cc_start: 0.9295 (tppt) cc_final: 0.8974 (tppt) REVERT: q 112 ILE cc_start: 0.7609 (mt) cc_final: 0.7248 (mt) REVERT: u 260 MET cc_start: -0.1043 (tpt) cc_final: -0.1348 (mtt) REVERT: u 353 LYS cc_start: 0.7913 (ptpt) cc_final: 0.7124 (tppt) REVERT: u 429 LEU cc_start: 0.9242 (pp) cc_final: 0.8924 (mp) REVERT: u 449 LYS cc_start: 0.7193 (mppt) cc_final: 0.6636 (tmmt) REVERT: u 453 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7573 (pp) REVERT: v 98 ASP cc_start: 0.9004 (p0) cc_final: 0.8713 (p0) REVERT: x 221 MET cc_start: 0.8032 (ppp) cc_final: 0.7601 (ppp) REVERT: x 333 TYR cc_start: 0.8440 (t80) cc_final: 0.8004 (t80) REVERT: x 376 MET cc_start: 0.8799 (mmm) cc_final: 0.8408 (mmt) REVERT: x 379 MET cc_start: 0.8839 (ppp) cc_final: 0.8140 (ppp) REVERT: y 40 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.5462 (mp0) REVERT: y 344 MET cc_start: 0.9132 (mmm) cc_final: 0.8572 (mmm) REVERT: y 405 LEU cc_start: 0.9177 (tp) cc_final: 0.8642 (mt) REVERT: y 409 MET cc_start: 0.8696 (mpp) cc_final: 0.8304 (mpp) REVERT: y 418 TYR cc_start: 0.9119 (t80) cc_final: 0.8758 (t80) REVERT: y 454 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7893 (t0) REVERT: y 485 MET cc_start: 0.8216 (mmm) cc_final: 0.7921 (mmm) REVERT: y 518 VAL cc_start: 0.9481 (t) cc_final: 0.9268 (m) REVERT: y 602 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8533 (mtm) outliers start: 37 outliers final: 26 residues processed: 264 average time/residue: 0.1212 time to fit residues: 50.3869 Evaluate side-chains 256 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 84 CYS Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 290 MET Chi-restraints excluded: chain u residue 340 GLU Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 264 GLU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 448 VAL Chi-restraints excluded: chain y residue 454 ASP Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 516 VAL Chi-restraints excluded: chain y residue 602 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 172 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 109 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... v 236 GLN y 87 HIS y 444 ASN y 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.084617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.064753 restraints weight = 69675.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.066542 restraints weight = 39808.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.067756 restraints weight = 27390.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.068474 restraints weight = 21248.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069019 restraints weight = 18070.846| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17274 Z= 0.253 Angle : 0.765 12.913 24117 Z= 0.391 Chirality : 0.042 0.218 2866 Planarity : 0.005 0.051 2459 Dihedral : 20.523 179.833 4498 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.70 % Allowed : 20.39 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.21), residues: 1620 helix: 1.52 (0.17), residues: 921 sheet: -0.19 (0.42), residues: 161 loop : -1.40 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG u 298 TYR 0.034 0.002 TYR x 424 PHE 0.049 0.003 PHE q 98 TRP 0.050 0.005 TRP u 295 HIS 0.005 0.001 HIS x 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.25 (17274) covalent geometry : angle 0.76467 / 0.39 (24117) hydrogen bonds : bond 0.05087 / 5.02 ( 842) hydrogen bonds : angle 4.43808 / 5.34 ( 2339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3175.11 seconds wall clock time: 55 minutes 43.90 seconds (3343.90 seconds total)