Starting phenix.real_space_refine on Sat Sep 12 17:07:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7obq_12799/09_2026/7obq_12799_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7obq_12799/09_2026/7obq_12799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7obq_12799/09_2026/7obq_12799_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7obq_12799/09_2026/7obq_12799_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7obq_12799/09_2026/7obq_12799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7obq_12799/09_2026/7obq_12799.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 174 5.49 5 Mg 3 5.21 5 S 67 5.16 5 C 9823 2.51 5 N 2979 2.21 5 O 3622 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16668 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 3542 Classifications: {'RNA': 165} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 11, 'rna3p_pur': 79, 'rna3p_pyr': 61} Link IDs: {'rna2p': 24, 'rna3p': 140} Chain: "q" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 842 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "s" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "u" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3431 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 420} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'TYR:plan': 2, 'ASP:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 45 Chain: "u" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Chain: "v" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1563 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 194} Chain breaks: 1 Chain: "x" Number of atoms: 3049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3049 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 10, 'TRANS': 382} Chain breaks: 2 Chain: "y" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3483 Classifications: {'peptide': 454} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 443} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "z" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 5, 'TRANS': 56} Chain: "v" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "y" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.12, per 1000 atoms: 0.25 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: 1.91 Conformation dependent library (CDL) restraints added in 762.8 milliseconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3156 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 5 sheets defined 61.5% alpha, 7.9% beta 39 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 2.35 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: 3.55 Time building geometry restraints manager: 2.42 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: 23539 2.02 - 4.03: 522 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 119.70 125.60 -5.90 1.20e+00 6.94e-01 2.42e+01 angle pdb=" C3' U 1 236 " pdb=" O3' U 1 236 " pdb=" P G 1 237 " ideal model delta sigma weight residual 119.70 124.96 -5.26 1.20e+00 6.94e-01 1.92e+01 angle pdb=" O5' G 1 237 " pdb=" C5' G 1 237 " pdb=" C4' G 1 237 " ideal model delta sigma weight residual 109.40 112.67 -3.27 8.00e-01 1.56e+00 1.67e+01 angle pdb=" O5' C 1 242 " pdb=" C5' C 1 242 " pdb=" C4' C 1 242 " ideal model delta sigma weight residual 109.40 112.57 -3.17 8.00e-01 1.56e+00 1.57e+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: 2410 0.052 - 0.103: 284 0.103 - 0.155: 169 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: 8.100 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.440 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 17274 Z= 0.152 Angle : 0.583 10.077 24117 Z= 0.362 Chirality : 0.044 0.258 2866 Planarity : 0.003 0.030 2459 Dihedral : 17.779 178.468 7661 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.63 % Allowed : 6.29 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.21), residues: 1620 helix: 2.22 (0.18), residues: 905 sheet: 0.41 (0.39), residues: 166 loop : -0.83 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG q 74 TYR 0.006 0.001 TYR u 379 PHE 0.012 0.001 PHE y 8 TRP 0.005 0.001 TRP y 440 HIS 0.004 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (17274) covalent geometry : angle 0.58284 / 0.36 (24117) hydrogen bonds : bond 0.15862 / 15.72 ( 842) hydrogen bonds : angle 6.03003 / 8.00 ( 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 : 0.543 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: 0.5371 (t80) REVERT: q 75 ASP cc_start: 0.6167 (m-30) cc_final: 0.4864 (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: 0.8559 (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: 0.8130 (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: 0.1341 time to fit residues: 84.4145 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 : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 397 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 556 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0000 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 247 ASN u 346 GLN ** u 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 431 ASN u 468 GLN v 161 GLN v 182 GLN ** x 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 60 ASN y 61 GLN y 71 GLN y 444 ASN y 541 ASN y 617 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.089075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.068946 restraints weight = 69029.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070859 restraints weight = 39052.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.072157 restraints weight = 26761.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.072966 restraints weight = 20656.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.073469 restraints weight = 17361.576| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 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 = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1748 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= 0.153 Angle : 0.620 8.662 24117 Z= 0.319 Chirality : 0.040 0.392 2866 Planarity : 0.004 0.048 2459 Dihedral : 20.276 177.673 4505 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.85 % Allowed : 14.91 % Favored : 82.24 % 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: 1.42 (0.21), residues: 1620 helix: 2.09 (0.17), residues: 915 sheet: 0.45 (0.40), residues: 159 loop : -0.92 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG x 330 TYR 0.017 0.002 TYR u 186 PHE 0.021 0.002 PHE y 70 TRP 0.008 0.001 TRP x 94 HIS 0.005 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (17274) covalent geometry : angle 0.62009 / 0.32 (24117) hydrogen bonds : bond 0.06436 / 6.59 ( 842) hydrogen bonds : angle 4.36958 / 5.69 ( 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 323 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 284 time to evaluate : 0.458 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: 0.6122 (t80) cc_final: 0.5506 (t80) REVERT: q 75 ASP cc_start: 0.6690 (m-30) cc_final: 0.6042 (m-30) REVERT: q 77 GLN cc_start: 0.8244 (pm20) cc_final: 0.8004 (pm20) REVERT: q 102 LYS cc_start: 0.9430 (tptt) cc_final: 0.9145 (tppt) REVERT: u 141 GLU cc_start: 0.8802 (tp30) cc_final: 0.8558 (tp30) REVERT: u 260 MET cc_start: -0.0436 (tpt) cc_final: -0.0682 (mtm) REVERT: u 330 LYS cc_start: 0.8886 (tmtt) cc_final: 0.8370 (tptt) REVERT: u 431 ASN cc_start: 0.8839 (m110) cc_final: 0.8602 (m-40) REVERT: u 449 LYS cc_start: 0.7018 (mppt) cc_final: 0.6325 (tmmt) REVERT: v 90 ARG cc_start: 0.8696 (tpp80) cc_final: 0.8490 (tpp80) REVERT: v 98 ASP cc_start: 0.8861 (p0) cc_final: 0.8620 (p0) REVERT: v 130 GLU cc_start: 0.8443 (pp20) cc_final: 0.8220 (pp20) REVERT: v 152 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8236 (p) REVERT: x 33 LYS cc_start: 0.9138 (tppt) cc_final: 0.8609 (mmtm) REVERT: x 106 PHE cc_start: 0.8969 (m-80) cc_final: 0.8734 (m-10) REVERT: x 204 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7969 (mp0) REVERT: y 40 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.5489 (mp0) REVERT: y 128 SER cc_start: 0.7616 (m) cc_final: 0.7406 (p) REVERT: y 397 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6195 (tm-30) REVERT: y 405 LEU cc_start: 0.9097 (tp) cc_final: 0.8619 (tt) REVERT: y 409 MET cc_start: 0.8699 (mpp) cc_final: 0.8333 (mpp) REVERT: y 524 MET cc_start: 0.8679 (mmm) cc_final: 0.8195 (mpp) REVERT: y 560 ASP cc_start: 0.8705 (t70) cc_final: 0.8445 (t0) REVERT: y 612 PHE cc_start: 0.8589 (m-80) cc_final: 0.8313 (m-80) outliers start: 39 outliers final: 14 residues processed: 312 average time/residue: 0.1252 time to fit residues: 59.5316 Evaluate side-chains 257 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain v residue 152 VAL Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain y residue 14 VAL Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 397 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 605 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 52 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 18 optimal weight: 20.0000 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 0.6980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... u 247 ASN x 195 HIS y 412 GLN y 541 ASN y 556 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.088589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.068514 restraints weight = 69501.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.070422 restraints weight = 39471.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.071699 restraints weight = 27057.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072526 restraints weight = 20892.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072928 restraints weight = 17529.704| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3406 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3406 r_free = 0.3406 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.37 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3406 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17274 Z= 0.141 Angle : 0.622 12.754 24117 Z= 0.315 Chirality : 0.039 0.405 2866 Planarity : 0.004 0.051 2459 Dihedral : 20.249 179.244 4502 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.85 % Allowed : 15.42 % 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: 1.24 (0.21), residues: 1620 helix: 1.96 (0.17), residues: 922 sheet: 0.38 (0.41), residues: 159 loop : -1.07 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG u 342 TYR 0.016 0.002 TYR y 78 PHE 0.020 0.002 PHE v 148 TRP 0.013 0.001 TRP v 266 HIS 0.004 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (17274) covalent geometry : angle 0.62151 / 0.32 (24117) hydrogen bonds : bond 0.05516 / 5.75 ( 842) hydrogen bonds : angle 4.19908 / 5.47 ( 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 301 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 262 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 48 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8462 (pp20) REVERT: q 68 TYR cc_start: 0.6170 (t80) cc_final: 0.5548 (t80) REVERT: q 75 ASP cc_start: 0.6643 (m-30) cc_final: 0.6090 (m-30) REVERT: q 102 LYS cc_start: 0.9434 (tptt) cc_final: 0.9130 (tppt) REVERT: u 260 MET cc_start: -0.0597 (tpt) cc_final: -0.0852 (mtm) REVERT: u 312 LEU cc_start: 0.8156 (pp) cc_final: 0.7537 (mp) REVERT: u 342 ARG cc_start: 0.6608 (ttp-170) cc_final: 0.6388 (ttp-170) REVERT: u 449 LYS cc_start: 0.6912 (mppt) cc_final: 0.6361 (tmmt) REVERT: v 90 ARG cc_start: 0.8713 (tpp80) cc_final: 0.8504 (tpp80) REVERT: v 98 ASP cc_start: 0.8856 (p0) cc_final: 0.8605 (p0) REVERT: v 117 ASP cc_start: 0.8308 (t70) cc_final: 0.8100 (t0) REVERT: v 130 GLU cc_start: 0.8442 (pp20) cc_final: 0.8225 (pp20) REVERT: x 204 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7942 (mp0) REVERT: y 40 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.5440 (mp0) REVERT: y 116 ASP cc_start: 0.7659 (p0) cc_final: 0.7420 (p0) REVERT: y 130 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8681 (pt) REVERT: y 397 GLN cc_start: 0.7340 (OUTLIER) cc_final: 0.6265 (tm-30) REVERT: y 405 LEU cc_start: 0.9054 (tp) cc_final: 0.8665 (tp) REVERT: y 409 MET cc_start: 0.8714 (mpp) cc_final: 0.8351 (mpp) REVERT: y 491 LYS cc_start: 0.7353 (mmtp) cc_final: 0.6988 (mmtm) REVERT: y 503 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7705 (mt-10) REVERT: y 524 MET cc_start: 0.8617 (mmm) cc_final: 0.8227 (mmt) REVERT: y 560 ASP cc_start: 0.8648 (t70) cc_final: 0.8378 (t0) REVERT: y 612 PHE cc_start: 0.8600 (m-80) cc_final: 0.8322 (m-80) outliers start: 39 outliers final: 19 residues processed: 291 average time/residue: 0.1289 time to fit residues: 57.0707 Evaluate side-chains 265 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 77 HIS Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain y residue 17 CYS Chi-restraints excluded: chain y residue 40 GLU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 130 ILE Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 397 GLN Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 516 VAL Chi-restraints excluded: chain y residue 541 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 1 optimal weight: 40.0000 chunk 115 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 152 optimal weight: 0.1980 chunk 130 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 59 optimal weight: 0.0060 chunk 105 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 50.0000 overall best weight: 1.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... y 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.088783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.068450 restraints weight = 69224.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.070326 restraints weight = 39395.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.071582 restraints weight = 27130.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072412 restraints weight = 21100.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.072859 restraints weight = 17793.628| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17274 Z= 0.127 Angle : 0.605 12.332 24117 Z= 0.307 Chirality : 0.039 0.402 2866 Planarity : 0.003 0.042 2459 Dihedral : 20.238 179.179 4501 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.92 % Allowed : 16.23 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.21), residues: 1620 helix: 1.93 (0.17), residues: 921 sheet: 0.36 (0.41), residues: 159 loop : -1.17 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG x 408 TYR 0.015 0.002 TYR y 78 PHE 0.015 0.001 PHE q 61 TRP 0.009 0.001 TRP v 266 HIS 0.004 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (17274) covalent geometry : angle 0.60491 / 0.31 (24117) hydrogen bonds : bond 0.05081 / 5.31 ( 842) hydrogen bonds : angle 4.12563 / 5.28 ( 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 303 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 263 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 48 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8241 (pp20) REVERT: q 68 TYR cc_start: 0.6088 (t80) cc_final: 0.5491 (t80) REVERT: q 75 ASP cc_start: 0.6887 (m-30) cc_final: 0.6589 (m-30) REVERT: q 102 LYS cc_start: 0.9444 (tptt) cc_final: 0.9134 (tppt) REVERT: u 260 MET cc_start: -0.0624 (tpt) cc_final: -0.0875 (mtm) REVERT: u 342 ARG cc_start: 0.6670 (ttp-170) cc_final: 0.6053 (ttt180) REVERT: u 429 LEU cc_start: 0.9122 (pp) cc_final: 0.8700 (mm) REVERT: u 449 LYS cc_start: 0.6925 (mppt) cc_final: 0.6299 (tmmt) REVERT: u 453 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7596 (pp) REVERT: v 98 ASP cc_start: 0.8839 (p0) cc_final: 0.8612 (p0) REVERT: v 117 ASP cc_start: 0.8303 (t70) cc_final: 0.8102 (t0) REVERT: v 130 GLU cc_start: 0.8456 (pp20) cc_final: 0.8214 (pp20) REVERT: x 221 MET cc_start: 0.7970 (ppp) cc_final: 0.7484 (ppp) REVERT: x 277 GLU cc_start: 0.7737 (tt0) cc_final: 0.7312 (tt0) REVERT: x 379 MET cc_start: 0.8730 (ptm) cc_final: 0.8135 (ppp) REVERT: x 408 ARG cc_start: 0.8424 (mmp80) cc_final: 0.7875 (mmm-85) REVERT: x 424 TYR cc_start: 0.8082 (t80) cc_final: 0.7481 (t80) REVERT: y 40 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5400 (mp0) REVERT: y 116 ASP cc_start: 0.7717 (p0) cc_final: 0.7447 (p0) REVERT: y 130 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8673 (pt) REVERT: y 397 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.6359 (tm-30) REVERT: y 399 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6451 (pp30) REVERT: y 405 LEU cc_start: 0.9074 (tp) cc_final: 0.8667 (tp) REVERT: y 409 MET cc_start: 0.8742 (mpp) cc_final: 0.8363 (mpp) REVERT: y 503 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7810 (mt-10) REVERT: y 524 MET cc_start: 0.8620 (mmm) cc_final: 0.8356 (mmt) outliers start: 40 outliers final: 24 residues processed: 290 average time/residue: 0.1243 time to fit residues: 55.2404 Evaluate side-chains 267 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 197 LEU Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 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 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 128 SER Chi-restraints excluded: chain y residue 130 ILE Chi-restraints excluded: chain y residue 380 VAL Chi-restraints excluded: chain y residue 397 GLN Chi-restraints excluded: chain y residue 399 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 516 VAL Chi-restraints excluded: chain y residue 605 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 13 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 30.0000 chunk 132 optimal weight: 6.9990 chunk 168 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... u 431 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.086794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.066579 restraints weight = 69868.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.068390 restraints weight = 39822.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.069618 restraints weight = 27608.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.070413 restraints weight = 21467.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.070931 restraints weight = 18152.266| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3366 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3366 r_free = 0.3366 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3366 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17274 Z= 0.204 Angle : 0.654 9.616 24117 Z= 0.336 Chirality : 0.041 0.403 2866 Planarity : 0.004 0.036 2459 Dihedral : 20.294 179.336 4501 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.44 % Allowed : 16.81 % Favored : 79.75 % 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: 1.85 (0.17), residues: 922 sheet: 0.27 (0.42), residues: 159 loop : -1.19 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG q 83 TYR 0.018 0.002 TYR y 418 PHE 0.017 0.002 PHE v 243 TRP 0.009 0.002 TRP x 130 HIS 0.005 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (17274) covalent geometry : angle 0.65396 / 0.34 (24117) hydrogen bonds : bond 0.05195 / 5.46 ( 842) hydrogen bonds : angle 4.29482 / 5.43 ( 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 295 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 248 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 68 TYR cc_start: 0.6319 (t80) cc_final: 0.5677 (t80) REVERT: q 102 LYS cc_start: 0.9480 (tptt) cc_final: 0.9193 (tppt) REVERT: u 260 MET cc_start: -0.0891 (tpt) cc_final: -0.1141 (mtm) REVERT: u 449 LYS cc_start: 0.7056 (mppt) cc_final: 0.6329 (tmmt) REVERT: u 453 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7615 (pp) REVERT: v 98 ASP cc_start: 0.8950 (p0) cc_final: 0.8637 (p0) REVERT: v 122 GLU cc_start: 0.8012 (pm20) cc_final: 0.7777 (pm20) REVERT: v 130 GLU cc_start: 0.8555 (pp20) cc_final: 0.8332 (pp20) REVERT: x 204 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: x 221 MET cc_start: 0.7958 (ppp) cc_final: 0.7471 (ppp) REVERT: x 332 MET cc_start: 0.8459 (mtt) cc_final: 0.7980 (mtt) REVERT: x 376 MET cc_start: 0.8662 (mmt) cc_final: 0.8223 (mmm) REVERT: x 379 MET cc_start: 0.8832 (ptm) cc_final: 0.8586 (ppp) REVERT: x 408 ARG cc_start: 0.8416 (mmp80) cc_final: 0.7949 (mmm-85) REVERT: x 424 TYR cc_start: 0.8165 (t80) cc_final: 0.7605 (t80) REVERT: y 40 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.5435 (mp0) REVERT: y 397 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6472 (tm-30) REVERT: y 405 LEU cc_start: 0.9194 (tp) cc_final: 0.8785 (tp) REVERT: y 409 MET cc_start: 0.8756 (mpp) cc_final: 0.8358 (mpp) REVERT: y 485 MET cc_start: 0.8235 (mmm) cc_final: 0.7963 (mmm) REVERT: y 503 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7766 (mt-10) REVERT: y 524 MET cc_start: 0.8761 (mmm) cc_final: 0.8303 (mmt) REVERT: z 597 GLN cc_start: 0.7542 (mt0) cc_final: 0.7318 (mt0) outliers start: 47 outliers final: 33 residues processed: 279 average time/residue: 0.1190 time to fit residues: 51.3534 Evaluate side-chains 271 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 115 LEU Chi-restraints excluded: chain u residue 153 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 193 MET Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 437 GLN Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 197 LEU Chi-restraints excluded: chain x residue 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 y residue 2 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 128 SER 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 407 ASP Chi-restraints excluded: chain y residue 448 VAL Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 516 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 177 optimal weight: 0.9990 chunk 79 optimal weight: 0.0020 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 11 optimal weight: 30.0000 chunk 114 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 20.0000 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... u 78 GLN x 151 ASN y 45 ASN y 433 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.087767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067505 restraints weight = 69718.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.069362 restraints weight = 39407.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.070617 restraints weight = 27190.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071278 restraints weight = 21060.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.071888 restraints weight = 18025.177| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2835 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= 0.124 Angle : 0.611 11.783 24117 Z= 0.311 Chirality : 0.038 0.400 2866 Planarity : 0.003 0.034 2459 Dihedral : 20.330 179.781 4501 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.85 % Allowed : 18.64 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.21), residues: 1620 helix: 1.88 (0.17), residues: 921 sheet: 0.12 (0.42), residues: 163 loop : -1.22 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG u 296 TYR 0.016 0.002 TYR y 78 PHE 0.023 0.001 PHE y 70 TRP 0.047 0.002 TRP u 295 HIS 0.005 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (17274) covalent geometry : angle 0.61051 / 0.31 (24117) hydrogen bonds : bond 0.04797 / 5.04 ( 842) hydrogen bonds : angle 4.10546 / 5.23 ( 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 289 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 250 time to evaluate : 0.554 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 68 TYR cc_start: 0.6165 (t80) cc_final: 0.5553 (t80) REVERT: q 102 LYS cc_start: 0.9450 (tptt) cc_final: 0.9152 (tppt) REVERT: u 260 MET cc_start: -0.0969 (tpt) cc_final: -0.1211 (mtm) REVERT: u 429 LEU cc_start: 0.9136 (pp) cc_final: 0.8726 (mm) REVERT: u 449 LYS cc_start: 0.7088 (mppt) cc_final: 0.6484 (tmmt) REVERT: u 453 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7625 (pp) REVERT: v 98 ASP cc_start: 0.8902 (p0) cc_final: 0.8579 (p0) REVERT: v 130 GLU cc_start: 0.8509 (pp20) cc_final: 0.8284 (pp20) REVERT: v 244 LEU cc_start: 0.8703 (pp) cc_final: 0.8502 (pp) REVERT: x 221 MET cc_start: 0.8006 (ppp) cc_final: 0.7616 (ppp) REVERT: x 332 MET cc_start: 0.8329 (mtt) cc_final: 0.8039 (mtt) REVERT: x 342 MET cc_start: 0.8281 (tmm) cc_final: 0.7988 (ppp) REVERT: x 376 MET cc_start: 0.8624 (mmt) cc_final: 0.8095 (mmm) REVERT: x 408 ARG cc_start: 0.8337 (mmp80) cc_final: 0.8077 (mmm-85) REVERT: x 424 TYR cc_start: 0.8050 (t80) cc_final: 0.7316 (t80) REVERT: y 40 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.5407 (mp0) REVERT: y 116 ASP cc_start: 0.7718 (p0) cc_final: 0.7458 (p0) REVERT: y 344 MET cc_start: 0.9062 (mmm) cc_final: 0.8553 (mmm) REVERT: y 396 LEU cc_start: 0.8393 (tt) cc_final: 0.8117 (tt) REVERT: y 397 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.6006 (tm-30) REVERT: y 405 LEU cc_start: 0.9177 (tp) cc_final: 0.8769 (tp) REVERT: y 409 MET cc_start: 0.8719 (mpp) cc_final: 0.8349 (mpp) REVERT: y 454 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7301 (t0) REVERT: y 503 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7844 (mt-10) outliers start: 39 outliers final: 27 residues processed: 275 average time/residue: 0.1192 time to fit residues: 50.5533 Evaluate side-chains 268 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 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 437 GLN Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 264 GLU Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain y residue 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 454 ASP Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 516 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 101 optimal weight: 0.9990 chunk 145 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 100 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... y 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.087680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.067401 restraints weight = 69716.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.069283 restraints weight = 39407.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070551 restraints weight = 27088.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.071339 restraints weight = 20924.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.071868 restraints weight = 17726.488| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17274 Z= 0.132 Angle : 0.621 10.960 24117 Z= 0.317 Chirality : 0.039 0.399 2866 Planarity : 0.003 0.031 2459 Dihedral : 20.320 179.714 4501 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.22 % Allowed : 18.93 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.21), residues: 1620 helix: 1.90 (0.17), residues: 922 sheet: 0.13 (0.42), residues: 163 loop : -1.24 (0.24), residues: 535 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 0.030 0.002 PHE y 70 TRP 0.058 0.002 TRP u 295 HIS 0.008 0.001 HIS v 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (17274) covalent geometry : angle 0.62116 / 0.32 (24117) hydrogen bonds : bond 0.04705 / 4.94 ( 842) hydrogen bonds : angle 4.07525 / 5.20 ( 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 293 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 68 TYR cc_start: 0.6200 (t80) cc_final: 0.5581 (t80) REVERT: q 83 ARG cc_start: 0.8365 (mmp80) cc_final: 0.8143 (mmp80) REVERT: u 260 MET cc_start: -0.0941 (tpt) cc_final: -0.1186 (mtm) REVERT: u 289 THR cc_start: 0.8757 (t) cc_final: 0.8296 (m) REVERT: u 295 TRP cc_start: 0.7169 (p-90) cc_final: 0.6436 (p-90) REVERT: u 353 LYS cc_start: 0.7845 (ptpt) cc_final: 0.7073 (tppt) REVERT: u 449 LYS cc_start: 0.7065 (mppt) cc_final: 0.6504 (tmmt) REVERT: u 453 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7619 (pp) REVERT: v 98 ASP cc_start: 0.8903 (p0) cc_final: 0.8583 (p0) REVERT: v 130 GLU cc_start: 0.8546 (pp20) cc_final: 0.8326 (pp20) REVERT: v 244 LEU cc_start: 0.8662 (pp) cc_final: 0.8435 (pp) REVERT: x 125 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.8825 (m-10) REVERT: x 221 MET cc_start: 0.7985 (ppp) cc_final: 0.7579 (ppp) REVERT: x 376 MET cc_start: 0.8642 (mmt) cc_final: 0.8418 (mmm) REVERT: x 408 ARG cc_start: 0.8326 (mmp80) cc_final: 0.8109 (mmm-85) REVERT: x 424 TYR cc_start: 0.8102 (t80) cc_final: 0.7683 (t80) REVERT: y 40 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.5397 (mp0) REVERT: y 397 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6226 (tm-30) REVERT: y 405 LEU cc_start: 0.9189 (tp) cc_final: 0.8712 (tp) REVERT: y 409 MET cc_start: 0.8736 (mpp) cc_final: 0.8338 (mpp) REVERT: y 454 ASP cc_start: 0.8335 (OUTLIER) cc_final: 0.7619 (t0) REVERT: y 518 VAL cc_start: 0.9523 (t) cc_final: 0.9255 (m) outliers start: 44 outliers final: 30 residues processed: 276 average time/residue: 0.1206 time to fit residues: 51.3388 Evaluate side-chains 272 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain u residue 60 LEU Chi-restraints excluded: chain u residue 72 LEU Chi-restraints excluded: chain u residue 181 LEU Chi-restraints excluded: chain u residue 190 LEU Chi-restraints excluded: chain u residue 198 HIS Chi-restraints excluded: chain u residue 241 ILE Chi-restraints excluded: chain u residue 437 GLN Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 126 LEU Chi-restraints excluded: chain v residue 264 GLU Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 125 TYR Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain 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 128 SER 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 516 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 119 optimal weight: 0.0470 chunk 48 optimal weight: 7.9990 chunk 13 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 overall best weight: 0.9680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... q 43 ASN v 93 GLN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.088510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.068049 restraints weight = 68918.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.069928 restraints weight = 39016.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.071183 restraints weight = 26888.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.072006 restraints weight = 20925.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072435 restraints weight = 17690.732| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17274 Z= 0.121 Angle : 0.640 13.497 24117 Z= 0.323 Chirality : 0.039 0.396 2866 Planarity : 0.003 0.032 2459 Dihedral : 20.319 179.851 4501 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.14 % Allowed : 19.08 % Favored : 77.78 % 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: 1.92 (0.17), residues: 921 sheet: 0.13 (0.42), residues: 163 loop : -1.28 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG q 83 TYR 0.020 0.002 TYR y 78 PHE 0.040 0.001 PHE y 70 TRP 0.031 0.001 TRP u 295 HIS 0.004 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (17274) covalent geometry : angle 0.63971 / 0.32 (24117) hydrogen bonds : bond 0.04526 / 4.78 ( 842) hydrogen bonds : angle 4.02202 / 5.14 ( 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 295 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 252 time to evaluate : 0.536 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: 0.9012 (mp0) cc_final: 0.8353 (pp20) REVERT: q 68 TYR cc_start: 0.6106 (t80) cc_final: 0.5475 (t80) REVERT: q 83 ARG cc_start: 0.8247 (mmp80) cc_final: 0.8016 (mmp80) REVERT: q 102 LYS cc_start: 0.9307 (tppt) cc_final: 0.9033 (tppt) REVERT: q 112 ILE cc_start: 0.7637 (mt) cc_final: 0.7176 (mt) REVERT: u 260 MET cc_start: -0.1076 (tpt) cc_final: -0.1293 (mtm) REVERT: u 429 LEU cc_start: 0.9247 (pp) cc_final: 0.8855 (mm) REVERT: u 449 LYS cc_start: 0.7117 (mppt) cc_final: 0.6494 (tmmt) REVERT: u 453 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7620 (pp) REVERT: v 98 ASP cc_start: 0.8861 (p0) cc_final: 0.8612 (p0) REVERT: v 130 GLU cc_start: 0.8510 (pp20) cc_final: 0.8290 (pp20) REVERT: v 179 CYS cc_start: 0.7081 (p) cc_final: 0.6875 (p) REVERT: x 125 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8793 (m-10) REVERT: x 221 MET cc_start: 0.8008 (ppp) cc_final: 0.7626 (ppp) REVERT: x 408 ARG cc_start: 0.8288 (mmp80) cc_final: 0.7958 (mmm-85) REVERT: y 40 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.5384 (mp0) REVERT: y 344 MET cc_start: 0.9060 (mmm) cc_final: 0.8544 (mmm) REVERT: y 397 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6633 (tm-30) REVERT: y 405 LEU cc_start: 0.9178 (tp) cc_final: 0.8690 (tp) REVERT: y 409 MET cc_start: 0.8706 (mpp) cc_final: 0.8302 (mpp) REVERT: y 454 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7628 (t0) REVERT: y 485 MET cc_start: 0.8207 (mmm) cc_final: 0.7886 (mmm) REVERT: y 518 VAL cc_start: 0.9524 (t) cc_final: 0.9259 (m) outliers start: 43 outliers final: 28 residues processed: 279 average time/residue: 0.1220 time to fit residues: 52.5754 Evaluate side-chains 273 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 240 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 437 GLN Chi-restraints excluded: chain u residue 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 264 GLU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 83 LEU Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 125 TYR Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain 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 128 SER 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 516 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 75 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 137 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 15 optimal weight: 30.0000 chunk 173 optimal weight: 5.9990 chunk 130 optimal weight: 0.0020 chunk 5 optimal weight: 20.0000 chunk 172 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 overall best weight: 3.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 399 GLN y 556 ASN y 617 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.086263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.066031 restraints weight = 69398.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.067865 restraints weight = 39498.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.069087 restraints weight = 27213.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069896 restraints weight = 21160.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.070296 restraints weight = 17848.102| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 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 = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 17274 Z= 0.204 Angle : 0.696 12.151 24117 Z= 0.352 Chirality : 0.041 0.399 2866 Planarity : 0.004 0.034 2459 Dihedral : 20.361 179.606 4501 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.14 % Allowed : 19.23 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.21), residues: 1620 helix: 1.79 (0.17), residues: 924 sheet: 0.12 (0.43), residues: 159 loop : -1.30 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG x 330 TYR 0.019 0.002 TYR u 375 PHE 0.032 0.002 PHE y 70 TRP 0.044 0.003 TRP u 295 HIS 0.005 0.001 HIS u 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (17274) covalent geometry : angle 0.69582 / 0.35 (24117) hydrogen bonds : bond 0.04864 / 5.16 ( 842) hydrogen bonds : angle 4.20726 / 5.35 ( 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 280 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 0.553 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: 0.9054 (mp0) cc_final: 0.8371 (pp20) REVERT: q 68 TYR cc_start: 0.6439 (t80) cc_final: 0.5859 (t80) REVERT: q 102 LYS cc_start: 0.9332 (tppt) cc_final: 0.9058 (tppt) REVERT: q 112 ILE cc_start: 0.7603 (mt) cc_final: 0.7133 (mt) REVERT: u 260 MET cc_start: -0.1072 (tpt) cc_final: -0.1352 (mtm) REVERT: u 353 LYS cc_start: 0.7884 (ptpt) cc_final: 0.7069 (tppt) REVERT: u 449 LYS cc_start: 0.7202 (mppt) cc_final: 0.6603 (tmmt) REVERT: u 453 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7578 (pp) REVERT: v 98 ASP cc_start: 0.9033 (p0) cc_final: 0.8743 (p0) REVERT: x 125 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.8893 (m-10) REVERT: x 221 MET cc_start: 0.8007 (ppp) cc_final: 0.7518 (ppp) REVERT: x 424 TYR cc_start: 0.7977 (t80) cc_final: 0.7713 (t80) REVERT: y 40 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.5657 (mp0) REVERT: y 397 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6229 (tm-30) REVERT: y 405 LEU cc_start: 0.9216 (tp) cc_final: 0.8766 (tp) REVERT: y 409 MET cc_start: 0.8731 (mpp) cc_final: 0.8348 (mpp) REVERT: y 454 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.7803 (t0) REVERT: y 485 MET cc_start: 0.8196 (mmm) cc_final: 0.7933 (mmm) REVERT: y 602 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8480 (mtm) outliers start: 43 outliers final: 31 residues processed: 264 average time/residue: 0.1154 time to fit residues: 47.2228 Evaluate side-chains 263 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 125 TYR Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain 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 448 VAL Chi-restraints excluded: chain y residue 454 ASP Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 514 ASP Chi-restraints excluded: chain y residue 516 VAL Chi-restraints excluded: chain y residue 602 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 99 optimal weight: 0.9990 chunk 117 optimal weight: 0.0770 chunk 109 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... v 236 GLN ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 399 GLN y 617 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.088202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.068065 restraints weight = 68307.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.069949 restraints weight = 38804.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071160 restraints weight = 26674.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.071968 restraints weight = 20845.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.072551 restraints weight = 17546.027| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17274 Z= 0.128 Angle : 0.703 13.948 24117 Z= 0.351 Chirality : 0.040 0.394 2866 Planarity : 0.003 0.031 2459 Dihedral : 20.399 179.563 4501 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.63 % Allowed : 20.10 % Favored : 77.27 % 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: 0.87 (0.21), residues: 1620 helix: 1.74 (0.17), residues: 921 sheet: -0.17 (0.41), residues: 170 loop : -1.25 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG u 102 TYR 0.020 0.002 TYR y 78 PHE 0.030 0.002 PHE y 70 TRP 0.053 0.003 TRP u 295 HIS 0.007 0.001 HIS u 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (17274) covalent geometry : angle 0.70297 / 0.35 (24117) hydrogen bonds : bond 0.04532 / 4.82 ( 842) hydrogen bonds : angle 4.10076 / 5.20 ( 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 287 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 251 time to evaluate : 0.504 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 48 GLU cc_start: 0.9066 (mp0) cc_final: 0.8418 (pp20) REVERT: q 68 TYR cc_start: 0.6242 (t80) cc_final: 0.5639 (t80) REVERT: q 112 ILE cc_start: 0.7606 (mt) cc_final: 0.7148 (mt) REVERT: u 260 MET cc_start: -0.1065 (tpt) cc_final: -0.1361 (mtt) REVERT: u 289 THR cc_start: 0.8813 (t) cc_final: 0.8510 (m) REVERT: u 353 LYS cc_start: 0.7899 (ptpt) cc_final: 0.7110 (tppt) REVERT: u 429 LEU cc_start: 0.9230 (pp) cc_final: 0.8908 (mp) REVERT: u 449 LYS cc_start: 0.7108 (mppt) cc_final: 0.6482 (tmmt) REVERT: u 453 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7570 (pp) REVERT: v 98 ASP cc_start: 0.8953 (p0) cc_final: 0.8649 (p0) REVERT: x 103 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7617 (m) REVERT: x 106 PHE cc_start: 0.8916 (m-80) cc_final: 0.8706 (m-80) REVERT: x 125 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.8840 (m-10) REVERT: x 221 MET cc_start: 0.8014 (ppp) cc_final: 0.7580 (ppp) REVERT: x 374 LYS cc_start: 0.9160 (pttm) cc_final: 0.8952 (ptpp) REVERT: x 424 TYR cc_start: 0.7597 (t80) cc_final: 0.7310 (t80) REVERT: y 40 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.5414 (mp0) REVERT: y 344 MET cc_start: 0.8895 (mmm) cc_final: 0.8461 (mmt) REVERT: y 397 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6564 (tm-30) REVERT: y 399 GLN cc_start: 0.7082 (OUTLIER) cc_final: 0.6597 (pp30) REVERT: y 405 LEU cc_start: 0.9174 (tp) cc_final: 0.8650 (mt) REVERT: y 409 MET cc_start: 0.8694 (mpp) cc_final: 0.8304 (mpp) REVERT: y 454 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7853 (t0) REVERT: y 485 MET cc_start: 0.8174 (mmm) cc_final: 0.7901 (mmm) REVERT: y 518 VAL cc_start: 0.9499 (t) cc_final: 0.9273 (m) REVERT: y 602 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8451 (mtm) outliers start: 36 outliers final: 24 residues processed: 274 average time/residue: 0.1169 time to fit residues: 49.4294 Evaluate side-chains 264 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 453 LEU Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 92 THR Chi-restraints excluded: chain v residue 264 GLU Chi-restraints excluded: chain x residue 40 LEU Chi-restraints excluded: chain x residue 52 LEU Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 125 TYR Chi-restraints excluded: chain x residue 204 GLU Chi-restraints excluded: chain x residue 205 MET Chi-restraints excluded: chain x residue 242 VAL Chi-restraints excluded: chain x residue 271 ILE Chi-restraints excluded: chain 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 399 GLN Chi-restraints excluded: chain y residue 402 VAL Chi-restraints excluded: chain y residue 448 VAL Chi-restraints excluded: chain y residue 454 ASP Chi-restraints excluded: chain y residue 486 VAL Chi-restraints excluded: chain y residue 516 VAL Chi-restraints excluded: chain y residue 602 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 172 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 171 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** x 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 399 GLN y 444 ASN y 617 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.087787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.067790 restraints weight = 68210.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.069650 restraints weight = 38694.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.070871 restraints weight = 26585.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.071702 restraints weight = 20678.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.072174 restraints weight = 17422.359| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.155 17274 Z= 0.229 Angle : 0.884 59.199 24117 Z= 0.485 Chirality : 0.043 0.660 2866 Planarity : 0.004 0.031 2459 Dihedral : 20.395 179.639 4501 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.52 % Favored : 96.42 % Rotamer: Outliers : 2.49 % Allowed : 20.83 % Favored : 76.68 % Cbeta Deviations : 0.06 % 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: 0.86 (0.21), residues: 1620 helix: 1.72 (0.17), residues: 921 sheet: -0.16 (0.41), residues: 170 loop : -1.26 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG x 415 TYR 0.034 0.002 TYR x 424 PHE 0.036 0.002 PHE q 98 TRP 0.045 0.003 TRP u 295 HIS 0.005 0.001 HIS u 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.23 (17274) covalent geometry : angle 0.88441 / 0.49 (24117) hydrogen bonds : bond 0.04573 / 4.86 ( 842) hydrogen bonds : angle 4.11312 / 5.22 ( 2339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3266.75 seconds wall clock time: 57 minutes 19.18 seconds (3439.18 seconds total)