Starting phenix.real_space_refine on Wed Mar 4 23:17:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7obq_12799/03_2026/7obq_12799_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7obq_12799/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7obq_12799/03_2026/7obq_12799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7obq_12799/03_2026/7obq_12799.map" model { file = "/net/cci-nas-00/data/ceres_data/7obq_12799/03_2026/7obq_12799_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7obq_12799/03_2026/7obq_12799_neut.cif" } 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-5986/lib/python3.9/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: 3.52, 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: 1.48 Conformation dependent library (CDL) restraints added in 523.0 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: 1.92 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: 2.81 Time building geometry restraints manager: 1.96 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: 5.750 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: 0.050 Set scattering table: 0.060 Process input model: 16.550 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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= 0.135 Angle : 0.483 10.077 24117 Z= 0.253 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 covalent geometry : bond 0.00257 (17274) covalent geometry : angle 0.48344 (24117) hydrogen bonds : bond 0.15862 ( 842) hydrogen bonds : angle 6.03003 ( 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 : 0.561 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: 0.1399 time to fit residues: 87.5323 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 : 0.565 ------------------------------------------------------------------------------- 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: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 5.9990 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... Flipped N/Q/H residues before XYZ refinement: ** q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 = 0.3739 r_free = 0.3739 target = 0.088670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.068535 restraints weight = 68841.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070445 restraints weight = 39084.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.071674 restraints weight = 26759.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.072540 restraints weight = 20731.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.072993 restraints weight = 17402.727| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 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 = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17274 Z= 0.158 Angle : 0.632 8.192 24117 Z= 0.314 Chirality : 0.038 0.217 2866 Planarity : 0.004 0.049 2459 Dihedral : 20.380 179.716 4505 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.78 % Allowed : 15.35 % Favored : 81.87 % 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: 1.55 (0.21), residues: 1620 helix: 2.21 (0.17), residues: 924 sheet: 0.44 (0.40), residues: 159 loop : -0.94 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG y 401 TYR 0.017 0.002 TYR x 123 PHE 0.022 0.002 PHE x 80 TRP 0.005 0.001 TRP x 130 HIS 0.005 0.001 HIS u 70 Details of bonding type rmsd covalent geometry : bond 0.00342 (17274) covalent geometry : angle 0.63199 (24117) hydrogen bonds : bond 0.05507 ( 842) hydrogen bonds : angle 4.19165 ( 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 319 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 281 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 68 TYR cc_start: 0.6151 (t80) cc_final: 0.5706 (t80) REVERT: q 75 ASP cc_start: 0.6595 (m-30) cc_final: 0.5750 (m-30) REVERT: q 77 GLN cc_start: 0.8263 (pm20) cc_final: 0.7869 (pm20) REVERT: q 102 LYS cc_start: 0.9432 (tptt) cc_final: 0.9135 (tppt) REVERT: u 260 MET cc_start: -0.0612 (tpt) cc_final: -0.0864 (mtm) REVERT: u 274 LYS cc_start: 0.9193 (ptpt) cc_final: 0.8956 (ptpt) REVERT: u 342 ARG cc_start: 0.6685 (ttp-170) cc_final: 0.6006 (ttt180) REVERT: u 449 LYS cc_start: 0.6906 (mppt) cc_final: 0.6295 (tmmt) REVERT: v 90 ARG cc_start: 0.8684 (tpp80) cc_final: 0.8466 (tpp80) REVERT: v 98 ASP cc_start: 0.8868 (p0) cc_final: 0.8642 (p0) REVERT: v 117 ASP cc_start: 0.8313 (t70) cc_final: 0.8088 (t0) REVERT: v 152 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8219 (p) REVERT: x 33 LYS cc_start: 0.9140 (tppt) cc_final: 0.8623 (mmtm) REVERT: x 204 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7990 (mp0) REVERT: x 424 TYR cc_start: 0.7929 (t80) cc_final: 0.7426 (t80) REVERT: y 40 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5427 (mp0) REVERT: y 128 SER cc_start: 0.7399 (m) cc_final: 0.7195 (p) REVERT: y 397 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.6187 (tm-30) REVERT: y 405 LEU cc_start: 0.9088 (tp) cc_final: 0.8712 (tp) REVERT: y 409 MET cc_start: 0.8703 (mpp) cc_final: 0.8357 (mpp) REVERT: y 524 MET cc_start: 0.8680 (mmm) cc_final: 0.8255 (mpp) REVERT: y 560 ASP cc_start: 0.8715 (t70) cc_final: 0.8470 (t0) outliers start: 38 outliers final: 14 residues processed: 307 average time/residue: 0.1255 time to fit residues: 58.7052 Evaluate side-chains 267 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 333 LEU Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 152 VAL 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 242 VAL Chi-restraints excluded: chain x residue 372 LEU 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 486 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 247 ASN y 412 GLN y 541 ASN y 556 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.086542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.066467 restraints weight = 70654.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068283 restraints weight = 40014.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.069475 restraints weight = 27562.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.070299 restraints weight = 21447.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.070831 restraints weight = 18091.865| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17274 Z= 0.193 Angle : 0.636 10.994 24117 Z= 0.323 Chirality : 0.039 0.220 2866 Planarity : 0.004 0.045 2459 Dihedral : 20.448 179.753 4501 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.73 % Allowed : 14.55 % Favored : 81.73 % 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: 1.25 (0.21), residues: 1620 helix: 1.99 (0.17), residues: 922 sheet: 0.29 (0.41), residues: 159 loop : -1.07 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG y 401 TYR 0.015 0.002 TYR y 78 PHE 0.018 0.002 PHE v 148 TRP 0.007 0.001 TRP x 130 HIS 0.005 0.001 HIS u 70 Details of bonding type rmsd covalent geometry : bond 0.00410 (17274) covalent geometry : angle 0.63561 (24117) hydrogen bonds : bond 0.04950 ( 842) hydrogen bonds : angle 4.20122 ( 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 298 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 247 time to evaluate : 0.405 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: 0.6794 (t80) cc_final: 0.6065 (t80) REVERT: q 75 ASP cc_start: 0.7129 (m-30) cc_final: 0.6482 (m-30) REVERT: q 77 GLN cc_start: 0.8472 (pm20) cc_final: 0.8249 (pm20) REVERT: q 102 LYS cc_start: 0.9482 (tptt) cc_final: 0.9170 (tppt) REVERT: u 102 ARG cc_start: 0.7711 (mpp80) cc_final: 0.7100 (mpp80) REVERT: u 260 MET cc_start: -0.0763 (tpt) cc_final: -0.1010 (mtm) REVERT: u 274 LYS cc_start: 0.9224 (ptpt) cc_final: 0.8985 (ptpt) REVERT: u 342 ARG cc_start: 0.6831 (ttp-170) cc_final: 0.6110 (ttt180) REVERT: u 449 LYS cc_start: 0.7053 (mppt) cc_final: 0.6405 (tmmt) REVERT: v 98 ASP cc_start: 0.8933 (p0) cc_final: 0.8633 (p0) REVERT: v 130 GLU cc_start: 0.8507 (pp20) cc_final: 0.8285 (pp20) REVERT: v 198 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7705 (mm-30) REVERT: x 204 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8035 (mp0) REVERT: x 424 TYR cc_start: 0.7916 (t80) cc_final: 0.7702 (t80) REVERT: y 40 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.5485 (mp0) REVERT: y 116 ASP cc_start: 0.8123 (p0) cc_final: 0.7721 (p0) REVERT: y 397 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.6170 (tm-30) REVERT: y 405 LEU cc_start: 0.9133 (tp) cc_final: 0.8761 (tp) REVERT: y 409 MET cc_start: 0.8721 (mpp) cc_final: 0.8356 (mpp) REVERT: y 418 TYR cc_start: 0.9105 (t80) cc_final: 0.8782 (t80) REVERT: y 560 ASP cc_start: 0.8652 (t70) cc_final: 0.8389 (t0) outliers start: 51 outliers final: 24 residues processed: 282 average time/residue: 0.1200 time to fit residues: 51.6998 Evaluate side-chains 252 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 333 LEU 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 115 LEU 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 77 HIS Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 372 LEU 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 397 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 486 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 1 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 152 optimal weight: 0.2980 chunk 130 optimal weight: 1.9990 chunk 175 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 105 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 247 ASN u 431 ASN y 399 GLN z 597 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.086640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.066401 restraints weight = 70405.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.068247 restraints weight = 39856.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.069456 restraints weight = 27531.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070262 restraints weight = 21487.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070802 restraints weight = 18179.208| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17274 Z= 0.171 Angle : 0.646 11.320 24117 Z= 0.323 Chirality : 0.039 0.420 2866 Planarity : 0.004 0.042 2459 Dihedral : 20.494 179.931 4501 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.22 % Allowed : 16.08 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.21), residues: 1620 helix: 1.92 (0.17), residues: 921 sheet: 0.29 (0.42), residues: 159 loop : -1.20 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG x 408 TYR 0.016 0.002 TYR y 78 PHE 0.023 0.002 PHE x 80 TRP 0.034 0.002 TRP u 295 HIS 0.006 0.001 HIS u 70 Details of bonding type rmsd covalent geometry : bond 0.00366 (17274) covalent geometry : angle 0.64639 (24117) hydrogen bonds : bond 0.04625 ( 842) hydrogen bonds : angle 4.15066 ( 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 295 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 251 time to evaluate : 0.479 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: 0.6802 (t80) cc_final: 0.6085 (t80) REVERT: q 75 ASP cc_start: 0.7463 (m-30) cc_final: 0.6781 (m-30) REVERT: q 102 LYS cc_start: 0.9487 (tptt) cc_final: 0.9166 (tppt) REVERT: u 260 MET cc_start: -0.0875 (tpt) cc_final: -0.1152 (mtm) REVERT: u 274 LYS cc_start: 0.9234 (ptpt) cc_final: 0.9002 (ptpt) REVERT: u 342 ARG cc_start: 0.6807 (ttp-170) cc_final: 0.6081 (ttt180) REVERT: u 429 LEU cc_start: 0.9168 (pp) cc_final: 0.8772 (mm) REVERT: u 449 LYS cc_start: 0.7269 (mppt) cc_final: 0.6582 (tmmt) REVERT: u 453 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7556 (pp) REVERT: v 98 ASP cc_start: 0.8983 (p0) cc_final: 0.8728 (p0) REVERT: v 130 GLU cc_start: 0.8555 (pp20) cc_final: 0.8319 (pp20) REVERT: v 202 ASN cc_start: 0.8695 (t0) cc_final: 0.8481 (t0) REVERT: x 125 TYR cc_start: 0.9071 (OUTLIER) cc_final: 0.8868 (m-10) REVERT: x 204 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7962 (mp0) REVERT: x 221 MET cc_start: 0.8033 (ppp) cc_final: 0.7606 (ppp) REVERT: x 379 MET cc_start: 0.9345 (ptm) cc_final: 0.8975 (ppp) REVERT: y 40 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.5484 (mp0) REVERT: y 116 ASP cc_start: 0.7954 (p0) cc_final: 0.7580 (p0) REVERT: y 397 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.6151 (tm-30) REVERT: y 405 LEU cc_start: 0.9170 (tp) cc_final: 0.8718 (tp) REVERT: y 409 MET cc_start: 0.8724 (mpp) cc_final: 0.8355 (mpp) REVERT: y 485 MET cc_start: 0.8228 (mmm) cc_final: 0.8023 (mmm) REVERT: y 560 ASP cc_start: 0.8594 (t70) cc_final: 0.8343 (t0) REVERT: z 597 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7336 (mt0) outliers start: 44 outliers final: 31 residues processed: 280 average time/residue: 0.1288 time to fit residues: 54.7128 Evaluate side-chains 259 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 223 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 125 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 333 LEU 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 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 125 TYR Chi-restraints excluded: chain x residue 217 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 372 LEU 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 397 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 404 MET Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain z residue 597 GLN 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: 0.5980 chunk 165 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 78 GLN x 151 ASN y 87 HIS y 399 GLN y 433 ASN y 617 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.085013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064661 restraints weight = 70370.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066475 restraints weight = 40069.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067665 restraints weight = 27736.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.068469 restraints weight = 21666.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.068927 restraints weight = 18380.235| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17274 Z= 0.214 Angle : 0.672 9.353 24117 Z= 0.340 Chirality : 0.040 0.312 2866 Planarity : 0.004 0.056 2459 Dihedral : 20.578 179.934 4501 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.17 % Allowed : 16.15 % Favored : 79.68 % 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: 0.91 (0.21), residues: 1620 helix: 1.74 (0.17), residues: 922 sheet: 0.12 (0.42), residues: 161 loop : -1.26 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG x 415 TYR 0.015 0.002 TYR y 418 PHE 0.018 0.002 PHE q 15 TRP 0.014 0.002 TRP v 266 HIS 0.006 0.001 HIS u 70 Details of bonding type rmsd covalent geometry : bond 0.00455 (17274) covalent geometry : angle 0.67236 (24117) hydrogen bonds : bond 0.04743 ( 842) hydrogen bonds : angle 4.30344 ( 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 299 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 242 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: q 17 CYS cc_start: 0.8748 (m) cc_final: 0.8148 (t) REVERT: q 68 TYR cc_start: 0.6906 (t80) cc_final: 0.6012 (t80) REVERT: q 72 TRP cc_start: 0.8550 (p-90) cc_final: 0.7861 (p-90) REVERT: q 75 ASP cc_start: 0.7796 (m-30) cc_final: 0.7513 (m-30) REVERT: q 102 LYS cc_start: 0.9530 (tptt) cc_final: 0.9199 (tppt) REVERT: u 260 MET cc_start: -0.0866 (tpt) cc_final: -0.1171 (mtm) REVERT: u 274 LYS cc_start: 0.9243 (ptpt) cc_final: 0.9027 (ptpt) REVERT: u 449 LYS cc_start: 0.7363 (mppt) cc_final: 0.6737 (tmmt) REVERT: v 98 ASP cc_start: 0.9044 (p0) cc_final: 0.8731 (p0) REVERT: x 106 PHE cc_start: 0.8944 (m-80) cc_final: 0.8405 (m-10) REVERT: x 376 MET cc_start: 0.8790 (mmt) cc_final: 0.8335 (mmm) REVERT: x 379 MET cc_start: 0.9289 (ptm) cc_final: 0.8946 (ppp) REVERT: x 424 TYR cc_start: 0.7772 (t80) cc_final: 0.7402 (t80) REVERT: y 40 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.5637 (mp0) REVERT: y 397 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.6173 (tm-30) REVERT: y 405 LEU cc_start: 0.9209 (tp) cc_final: 0.8716 (tp) REVERT: y 409 MET cc_start: 0.8723 (mpp) cc_final: 0.8357 (mpp) REVERT: y 560 ASP cc_start: 0.8543 (t70) cc_final: 0.8328 (t0) REVERT: y 602 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8490 (mtm) outliers start: 57 outliers final: 39 residues processed: 279 average time/residue: 0.1225 time to fit residues: 52.6536 Evaluate side-chains 270 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 125 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 333 LEU Chi-restraints excluded: chain u residue 338 LEU Chi-restraints excluded: chain u residue 394 ASN 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 126 LEU Chi-restraints excluded: chain v residue 197 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 77 HIS Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 119 SER Chi-restraints excluded: chain x residue 136 CYS Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 217 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 372 LEU 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 397 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 404 MET Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 514 ASP 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: 0.0170 chunk 79 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 chunk 94 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: q 85 GLN v 93 GLN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 399 GLN y 617 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.086926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.066781 restraints weight = 68800.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.068639 restraints weight = 38844.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.069913 restraints weight = 26664.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.070731 restraints weight = 20594.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.071175 restraints weight = 17310.270| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17274 Z= 0.126 Angle : 0.637 13.875 24117 Z= 0.316 Chirality : 0.038 0.269 2866 Planarity : 0.003 0.028 2459 Dihedral : 20.535 179.178 4501 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.44 % Allowed : 17.91 % Favored : 78.65 % 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: 1.07 (0.21), residues: 1620 helix: 1.87 (0.17), residues: 922 sheet: 0.18 (0.42), residues: 162 loop : -1.22 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG x 415 TYR 0.017 0.002 TYR y 78 PHE 0.025 0.002 PHE x 80 TRP 0.014 0.001 TRP v 266 HIS 0.004 0.001 HIS u 70 Details of bonding type rmsd covalent geometry : bond 0.00272 (17274) covalent geometry : angle 0.63700 (24117) hydrogen bonds : bond 0.04250 ( 842) hydrogen bonds : angle 4.08048 ( 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 307 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 0.535 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 17 CYS cc_start: 0.8634 (m) cc_final: 0.8112 (t) REVERT: q 48 GLU cc_start: 0.9094 (mp0) cc_final: 0.8496 (pp20) REVERT: q 68 TYR cc_start: 0.6798 (t80) cc_final: 0.6071 (t80) REVERT: q 102 LYS cc_start: 0.9470 (tptt) cc_final: 0.9126 (tppt) REVERT: u 169 LEU cc_start: 0.9407 (mt) cc_final: 0.9047 (tt) REVERT: u 260 MET cc_start: -0.1067 (tpt) cc_final: -0.1382 (mtm) REVERT: u 274 LYS cc_start: 0.9222 (ptpt) cc_final: 0.9016 (ptpt) REVERT: u 353 LYS cc_start: 0.8000 (ptpt) cc_final: 0.7277 (tppt) REVERT: u 429 LEU cc_start: 0.9210 (pp) cc_final: 0.8822 (mm) REVERT: u 449 LYS cc_start: 0.7214 (mppt) cc_final: 0.6746 (tmmt) REVERT: v 98 ASP cc_start: 0.9000 (p0) cc_final: 0.8710 (p0) REVERT: x 106 PHE cc_start: 0.8972 (m-80) cc_final: 0.8420 (m-10) REVERT: x 221 MET cc_start: 0.7991 (ppp) cc_final: 0.7572 (ppp) REVERT: x 222 ASP cc_start: 0.7946 (t0) cc_final: 0.7723 (t0) REVERT: x 332 MET cc_start: 0.8171 (mtt) cc_final: 0.7916 (mtt) REVERT: x 376 MET cc_start: 0.8728 (mmt) cc_final: 0.8154 (mmm) REVERT: x 379 MET cc_start: 0.9182 (ptm) cc_final: 0.8743 (ppp) REVERT: x 424 TYR cc_start: 0.7919 (t80) cc_final: 0.7667 (t80) REVERT: y 40 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.5468 (mp0) REVERT: y 397 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.6403 (tm-30) REVERT: y 405 LEU cc_start: 0.9177 (tp) cc_final: 0.8683 (mt) REVERT: y 409 MET cc_start: 0.8702 (mpp) cc_final: 0.8313 (mpp) REVERT: y 602 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8461 (mtm) REVERT: y 612 PHE cc_start: 0.8816 (m-80) cc_final: 0.8529 (m-80) outliers start: 47 outliers final: 32 residues processed: 288 average time/residue: 0.1285 time to fit residues: 56.7282 Evaluate side-chains 268 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 333 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 77 HIS Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 217 ILE Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 372 LEU 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 342 ASP 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 404 MET Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 602 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 101 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 617 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.086235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066190 restraints weight = 68827.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.068028 restraints weight = 38880.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.069257 restraints weight = 26741.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.070070 restraints weight = 20734.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070517 restraints weight = 17473.992| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3460 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= 0.149 Angle : 0.666 14.242 24117 Z= 0.332 Chirality : 0.039 0.434 2866 Planarity : 0.003 0.037 2459 Dihedral : 20.529 179.399 4501 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.73 % Allowed : 19.81 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.03 (0.21), residues: 1620 helix: 1.87 (0.17), residues: 922 sheet: 0.12 (0.42), residues: 164 loop : -1.28 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG u 102 TYR 0.017 0.002 TYR y 78 PHE 0.029 0.002 PHE y 70 TRP 0.049 0.003 TRP u 295 HIS 0.004 0.001 HIS u 70 Details of bonding type rmsd covalent geometry : bond 0.00325 (17274) covalent geometry : angle 0.66615 (24117) hydrogen bonds : bond 0.04276 ( 842) hydrogen bonds : angle 4.11483 ( 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 289 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 0.437 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 17 CYS cc_start: 0.8596 (m) cc_final: 0.7511 (t) REVERT: q 68 TYR cc_start: 0.6812 (t80) cc_final: 0.6056 (t80) REVERT: u 260 MET cc_start: -0.1048 (tpt) cc_final: -0.1371 (mtm) REVERT: u 274 LYS cc_start: 0.9218 (ptpt) cc_final: 0.9000 (ptpt) REVERT: u 449 LYS cc_start: 0.7189 (mppt) cc_final: 0.6680 (tmmt) REVERT: u 453 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7511 (pp) REVERT: v 98 ASP cc_start: 0.8990 (p0) cc_final: 0.8693 (p0) REVERT: x 106 PHE cc_start: 0.8959 (m-80) cc_final: 0.8427 (m-10) REVERT: x 342 MET cc_start: 0.8052 (tmm) cc_final: 0.7532 (ppp) REVERT: x 376 MET cc_start: 0.8709 (mmt) cc_final: 0.8195 (mmm) REVERT: x 379 MET cc_start: 0.9264 (ptm) cc_final: 0.8724 (ppp) REVERT: x 424 TYR cc_start: 0.7970 (t80) cc_final: 0.7698 (t80) REVERT: y 40 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.5588 (mp0) REVERT: y 344 MET cc_start: 0.8941 (mmm) cc_final: 0.8462 (mmt) REVERT: y 397 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: y 405 LEU cc_start: 0.9198 (tp) cc_final: 0.8674 (mt) REVERT: y 409 MET cc_start: 0.8719 (mpp) cc_final: 0.8431 (mpp) REVERT: y 485 MET cc_start: 0.8220 (mmm) cc_final: 0.7935 (mmm) REVERT: y 602 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8564 (mtm) REVERT: y 612 PHE cc_start: 0.8848 (m-80) cc_final: 0.8577 (m-80) outliers start: 51 outliers final: 36 residues processed: 270 average time/residue: 0.1160 time to fit residues: 49.4248 Evaluate side-chains 265 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 333 LEU 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 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 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 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain x residue 295 LEU Chi-restraints excluded: chain x residue 372 LEU 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 342 ASP Chi-restraints excluded: chain y residue 376 THR 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 404 MET Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 514 ASP Chi-restraints excluded: chain y residue 602 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 119 optimal weight: 0.0970 chunk 48 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 138 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 556 ASN ** y 617 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.086800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.066876 restraints weight = 69867.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.068817 restraints weight = 38139.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.070072 restraints weight = 25648.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.070920 restraints weight = 19718.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.071483 restraints weight = 16496.550| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3573 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= 0.141 Angle : 0.675 14.408 24117 Z= 0.336 Chirality : 0.039 0.398 2866 Planarity : 0.003 0.037 2459 Dihedral : 20.530 179.182 4501 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.65 % Allowed : 19.96 % Favored : 76.39 % 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: 1.84 (0.17), residues: 922 sheet: 0.19 (0.42), residues: 164 loop : -1.31 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG q 83 TYR 0.017 0.002 TYR y 78 PHE 0.027 0.002 PHE x 80 TRP 0.044 0.002 TRP u 295 HIS 0.004 0.001 HIS u 70 Details of bonding type rmsd covalent geometry : bond 0.00309 (17274) covalent geometry : angle 0.67497 (24117) hydrogen bonds : bond 0.04170 ( 842) hydrogen bonds : angle 4.13942 ( 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 285 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 235 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 68 TYR cc_start: 0.6663 (t80) cc_final: 0.5876 (t80) REVERT: q 83 ARG cc_start: 0.8562 (mmp80) cc_final: 0.8208 (mmp80) REVERT: q 102 LYS cc_start: 0.9489 (tptt) cc_final: 0.9178 (tppt) REVERT: u 260 MET cc_start: -0.1029 (tpt) cc_final: -0.1354 (mtm) REVERT: u 274 LYS cc_start: 0.9223 (ptpt) cc_final: 0.9019 (ptpt) REVERT: u 290 MET cc_start: 0.8117 (pmm) cc_final: 0.7834 (pmm) REVERT: u 353 LYS cc_start: 0.7931 (ptpt) cc_final: 0.7199 (tppt) REVERT: u 429 LEU cc_start: 0.9263 (pp) cc_final: 0.8965 (mp) REVERT: u 449 LYS cc_start: 0.7135 (mppt) cc_final: 0.6643 (tmmt) REVERT: u 453 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7506 (pp) REVERT: v 98 ASP cc_start: 0.9030 (p0) cc_final: 0.8710 (p0) REVERT: v 269 LYS cc_start: 0.8952 (ptpt) cc_final: 0.8732 (pttm) REVERT: x 106 PHE cc_start: 0.9074 (m-80) cc_final: 0.8590 (m-10) REVERT: x 166 MET cc_start: 0.7350 (tpt) cc_final: 0.7090 (tpp) REVERT: x 204 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.8847 (pm20) REVERT: x 333 TYR cc_start: 0.8798 (t80) cc_final: 0.8465 (t80) REVERT: x 376 MET cc_start: 0.8739 (mmt) cc_final: 0.8432 (mmm) REVERT: x 379 MET cc_start: 0.9318 (ptm) cc_final: 0.8912 (ptm) REVERT: y 40 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.5697 (mp0) REVERT: y 344 MET cc_start: 0.9035 (mmm) cc_final: 0.8599 (mmt) REVERT: y 397 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.5996 (tm-30) REVERT: y 405 LEU cc_start: 0.9174 (tp) cc_final: 0.8636 (mt) REVERT: y 409 MET cc_start: 0.8734 (mpp) cc_final: 0.8431 (mpp) REVERT: y 485 MET cc_start: 0.8333 (mmm) cc_final: 0.8082 (mmm) REVERT: y 602 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8617 (mtm) REVERT: y 612 PHE cc_start: 0.8875 (m-80) cc_final: 0.8572 (m-80) outliers start: 50 outliers final: 37 residues processed: 265 average time/residue: 0.1133 time to fit residues: 47.3295 Evaluate side-chains 272 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 125 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 333 LEU 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 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 295 LEU Chi-restraints excluded: chain x residue 372 LEU 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 342 ASP Chi-restraints excluded: chain y residue 376 THR 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 404 MET Chi-restraints excluded: chain y residue 448 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 514 ASP Chi-restraints excluded: chain y residue 602 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 75 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 172 optimal weight: 0.9980 chunk 6 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: v 236 GLN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 45 ASN y 60 ASN y 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.083078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.063155 restraints weight = 69852.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.064912 restraints weight = 40075.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.066045 restraints weight = 27744.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.066837 restraints weight = 21776.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.067229 restraints weight = 18346.057| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17274 Z= 0.272 Angle : 0.770 12.401 24117 Z= 0.390 Chirality : 0.042 0.420 2866 Planarity : 0.005 0.042 2459 Dihedral : 20.730 179.990 4501 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.65 % Allowed : 20.03 % Favored : 76.32 % 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: 0.55 (0.20), residues: 1620 helix: 1.46 (0.17), residues: 923 sheet: -0.05 (0.41), residues: 167 loop : -1.46 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG z 576 TYR 0.064 0.003 TYR x 424 PHE 0.029 0.003 PHE y 70 TRP 0.038 0.003 TRP u 295 HIS 0.006 0.001 HIS u 70 Details of bonding type rmsd covalent geometry : bond 0.00577 (17274) covalent geometry : angle 0.76969 (24117) hydrogen bonds : bond 0.05071 ( 842) hydrogen bonds : angle 4.61291 ( 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 273 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 48 GLU cc_start: 0.9068 (mp0) cc_final: 0.8471 (pp20) REVERT: q 68 TYR cc_start: 0.7078 (t80) cc_final: 0.6350 (t80) REVERT: q 102 LYS cc_start: 0.9504 (tptt) cc_final: 0.9234 (tppt) REVERT: u 260 MET cc_start: -0.0750 (tpt) cc_final: -0.1089 (mtm) REVERT: u 274 LYS cc_start: 0.9254 (ptpt) cc_final: 0.9045 (ptpt) REVERT: u 449 LYS cc_start: 0.7268 (mppt) cc_final: 0.6909 (tmmt) REVERT: v 98 ASP cc_start: 0.9038 (p0) cc_final: 0.8820 (p0) REVERT: x 41 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8682 (mm-30) REVERT: x 106 PHE cc_start: 0.8976 (m-80) cc_final: 0.8449 (m-10) REVERT: x 229 CYS cc_start: 0.8630 (p) cc_final: 0.8165 (p) REVERT: x 332 MET cc_start: 0.8713 (mmm) cc_final: 0.8478 (mmt) REVERT: x 374 LYS cc_start: 0.9294 (pttm) cc_final: 0.9029 (ptpp) REVERT: x 376 MET cc_start: 0.8665 (mmt) cc_final: 0.8276 (mmm) REVERT: x 379 MET cc_start: 0.9395 (ptm) cc_final: 0.8922 (ppp) REVERT: y 40 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.5979 (mp0) REVERT: y 344 MET cc_start: 0.9005 (mmm) cc_final: 0.8597 (mmt) REVERT: y 397 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6218 (tm-30) REVERT: y 405 LEU cc_start: 0.9227 (tp) cc_final: 0.8744 (mt) REVERT: y 409 MET cc_start: 0.8653 (mpp) cc_final: 0.8328 (mpp) REVERT: y 454 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8110 (t0) REVERT: y 485 MET cc_start: 0.8281 (mmm) cc_final: 0.8056 (mmm) REVERT: y 602 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8629 (mtm) outliers start: 50 outliers final: 36 residues processed: 256 average time/residue: 0.1212 time to fit residues: 48.2498 Evaluate side-chains 251 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 211 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 18 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 333 LEU Chi-restraints excluded: chain u residue 394 ASN 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 77 HIS Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 117 THR 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 372 LEU 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 342 ASP Chi-restraints excluded: chain y residue 376 THR 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 404 MET 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 602 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 99 optimal weight: 0.2980 chunk 117 optimal weight: 0.0980 chunk 109 optimal weight: 1.9990 chunk 145 optimal weight: 8.9990 chunk 130 optimal weight: 0.7980 chunk 138 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 431 ASN v 236 GLN x 77 HIS ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 181 ASN y 60 ASN y 433 ASN y 541 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.087011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.066938 restraints weight = 68019.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.068795 restraints weight = 38759.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.070033 restraints weight = 26758.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070864 restraints weight = 20784.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.071322 restraints weight = 17523.042| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17274 Z= 0.132 Angle : 0.742 15.550 24117 Z= 0.366 Chirality : 0.040 0.459 2866 Planarity : 0.003 0.030 2459 Dihedral : 20.633 177.622 4501 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.07 % Allowed : 21.49 % Favored : 75.44 % 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: 0.67 (0.21), residues: 1620 helix: 1.56 (0.17), residues: 923 sheet: -0.08 (0.41), residues: 168 loop : -1.40 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG y 414 TYR 0.024 0.002 TYR x 424 PHE 0.029 0.002 PHE y 70 TRP 0.040 0.002 TRP u 295 HIS 0.005 0.001 HIS x 77 Details of bonding type rmsd covalent geometry : bond 0.00285 (17274) covalent geometry : angle 0.74209 (24117) hydrogen bonds : bond 0.04265 ( 842) hydrogen bonds : angle 4.25039 ( 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 286 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 244 time to evaluate : 0.341 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: 0.9074 (mp0) cc_final: 0.8441 (pp20) REVERT: q 68 TYR cc_start: 0.6588 (t80) cc_final: 0.5983 (t80) REVERT: q 102 LYS cc_start: 0.9471 (tptt) cc_final: 0.9168 (tppt) REVERT: u 260 MET cc_start: -0.1058 (tpt) cc_final: -0.1367 (mtm) REVERT: u 353 LYS cc_start: 0.7969 (ptpt) cc_final: 0.7217 (tppt) REVERT: u 429 LEU cc_start: 0.9245 (pp) cc_final: 0.8941 (mp) REVERT: u 449 LYS cc_start: 0.7246 (mppt) cc_final: 0.6843 (tmmt) REVERT: u 453 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7465 (pp) REVERT: v 232 PHE cc_start: 0.8625 (t80) cc_final: 0.8406 (t80) REVERT: x 106 PHE cc_start: 0.9009 (m-80) cc_final: 0.8631 (m-10) REVERT: x 221 MET cc_start: 0.8019 (ppp) cc_final: 0.7660 (ppp) REVERT: x 333 TYR cc_start: 0.8679 (t80) cc_final: 0.8215 (t80) REVERT: x 374 LYS cc_start: 0.9241 (pttm) cc_final: 0.8960 (ptpp) REVERT: x 376 MET cc_start: 0.8633 (mmt) cc_final: 0.8195 (mmm) REVERT: x 379 MET cc_start: 0.9354 (ptm) cc_final: 0.8925 (ptm) REVERT: x 396 PHE cc_start: 0.8557 (m-80) cc_final: 0.7953 (m-80) REVERT: y 40 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.5377 (mp0) REVERT: y 344 MET cc_start: 0.8977 (mmm) cc_final: 0.8583 (mmt) REVERT: y 405 LEU cc_start: 0.9184 (tp) cc_final: 0.8615 (mt) REVERT: y 409 MET cc_start: 0.8677 (mpp) cc_final: 0.8359 (mpp) REVERT: y 485 MET cc_start: 0.8274 (mmm) cc_final: 0.8050 (mmm) outliers start: 42 outliers final: 27 residues processed: 271 average time/residue: 0.1242 time to fit residues: 51.9427 Evaluate side-chains 261 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 232 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 84 CYS Chi-restraints excluded: chain u residue 110 VAL 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 333 LEU Chi-restraints excluded: chain u residue 453 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 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 295 LEU Chi-restraints excluded: chain x residue 372 LEU 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 376 THR Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 404 MET Chi-restraints excluded: chain y residue 448 VAL Chi-restraints excluded: chain y residue 486 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 172 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 159 optimal weight: 0.0970 chunk 26 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 108 optimal weight: 0.2980 chunk 171 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: u 431 ASN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.086262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.066357 restraints weight = 68336.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.068174 restraints weight = 39045.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.069398 restraints weight = 26884.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.070214 restraints weight = 20844.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.070663 restraints weight = 17599.912| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4022 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= 0.145 Angle : 0.733 13.964 24117 Z= 0.365 Chirality : 0.040 0.474 2866 Planarity : 0.003 0.034 2459 Dihedral : 20.531 178.582 4498 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.49 % Allowed : 22.44 % Favored : 75.07 % 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: 0.61 (0.21), residues: 1620 helix: 1.54 (0.17), residues: 923 sheet: -0.13 (0.41), residues: 170 loop : -1.45 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG q 74 TYR 0.027 0.002 TYR x 424 PHE 0.027 0.002 PHE x 179 TRP 0.035 0.002 TRP u 295 HIS 0.006 0.001 HIS x 77 Details of bonding type rmsd covalent geometry : bond 0.00319 (17274) covalent geometry : angle 0.73287 (24117) hydrogen bonds : bond 0.04306 ( 842) hydrogen bonds : angle 4.34289 ( 2339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3250.38 seconds wall clock time: 56 minutes 59.85 seconds (3419.85 seconds total)