Starting phenix.real_space_refine on Wed Aug 5 11:48:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kc9_37097/08_2026/8kc9_37097.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kc9_37097/08_2026/8kc9_37097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kc9_37097/08_2026/8kc9_37097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kc9_37097/08_2026/8kc9_37097.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kc9_37097/08_2026/8kc9_37097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kc9_37097/08_2026/8kc9_37097.map" } resolution = 3.75 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= 0.006 sd= 0.088 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: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 51 5.16 5 C 6193 2.51 5 N 1648 2.21 5 O 1821 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9714 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5162 Classifications: {'peptide': 642} Link IDs: {'PTRANS': 33, 'TRANS': 608} Chain breaks: 2 Chain: "B" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2994 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "C" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1416 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 6, 'TRANS': 175} Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Classifications: {'peptide': 11} Modifications used: {'PEPT-D': 1} Link IDs: {'NMTRANS': 7, 'TRANS': 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'MLE:plan-1': 4, 'MVA:plan-1': 1, 'BMT:plan-1': 1, 'ABA:plan-1': 1, 'SAR:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' FE': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.60, per 1000 atoms: 0.16 Number of scatterers: 9714 At special positions: 0 Unit cell: (94.6, 113.3, 126.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 51 16.00 O 1821 8.00 N 1648 7.00 C 6193 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 119 " distance=2.03 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 282 " distance=2.03 Simple disulfide: pdb=" SG CYS A 246 " - pdb=" SG CYS A 278 " distance=2.03 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 540 " " NAG A 802 " - " ASN A 316 " " NAG B 501 " - " ASN B 87 " " NAG B 502 " - " ASN B 363 " TRANS " DAL E 1 " - " ALA E 11 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 312.5 milliseconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL E 1 " Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 57.4% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.894A pdb=" N LEU A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 82 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.620A pdb=" N ALA A 98 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.826A pdb=" N GLY A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 131 removed outlier: 3.511A pdb=" N ALA A 129 " --> pdb=" O PRO A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 143 removed outlier: 3.630A pdb=" N GLU A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 203 through 218 removed outlier: 3.590A pdb=" N GLN A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE A 209 " --> pdb=" O HIS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 244 removed outlier: 3.549A pdb=" N VAL A 225 " --> pdb=" O PRO A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix removed outlier: 3.599A pdb=" N ALA A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 286 removed outlier: 3.553A pdb=" N CYS A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 removed outlier: 3.567A pdb=" N TYR A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.724A pdb=" N PHE A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 359 through 384 Processing helix chain 'A' and resid 395 through 399 removed outlier: 3.684A pdb=" N VAL A 398 " --> pdb=" O PRO A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 428 removed outlier: 3.705A pdb=" N LYS A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.534A pdb=" N LEU A 466 " --> pdb=" O ASN A 462 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 467' Processing helix chain 'A' and resid 479 through 493 removed outlier: 3.999A pdb=" N GLN A 484 " --> pdb=" O ASP A 480 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N GLU A 485 " --> pdb=" O HIS A 481 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 486 " --> pdb=" O GLU A 482 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 528 Processing helix chain 'A' and resid 531 through 553 removed outlier: 3.797A pdb=" N ALA A 535 " --> pdb=" O PRO A 531 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 698 Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.886A pdb=" N GLU B 40 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B 41 " --> pdb=" O ARG B 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 37 through 41' Processing helix chain 'B' and resid 43 through 57 Processing helix chain 'B' and resid 60 through 87 removed outlier: 3.946A pdb=" N ASN B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 102 removed outlier: 3.592A pdb=" N SER B 102 " --> pdb=" O GLY B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.808A pdb=" N GLN B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 131 removed outlier: 6.136A pdb=" N ALA B 128 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN B 131 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.606A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 191 Processing helix chain 'B' and resid 204 through 219 Processing helix chain 'B' and resid 222 through 246 Proline residue: B 234 - end of helix Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.669A pdb=" N ASP B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N HIS B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N TYR B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 removed outlier: 3.540A pdb=" N LEU B 281 " --> pdb=" O CYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 308 Processing helix chain 'B' and resid 310 through 325 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 348 through 353 removed outlier: 3.569A pdb=" N PHE B 352 " --> pdb=" O ASP B 349 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 353 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 379 removed outlier: 3.732A pdb=" N GLN B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASN B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 81 Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.809A pdb=" N VAL C 179 " --> pdb=" O GLY C 175 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 471 through 475 removed outlier: 4.380A pdb=" N ARG A 647 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR A 563 " --> pdb=" O TRP A 675 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N THR A 677 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N PHE A 561 " --> pdb=" O THR A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 475 removed outlier: 4.380A pdb=" N ARG A 647 " --> pdb=" O TYR A 617 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP A 623 " --> pdb=" O THR A 665 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 592 through 593 removed outlier: 3.661A pdb=" N ILE A 592 " --> pdb=" O VAL A 601 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL A 601 " --> pdb=" O ILE A 592 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 637 through 641 removed outlier: 6.588A pdb=" N PHE A 629 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU A 640 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 627 " --> pdb=" O GLU A 640 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AA6, first strand: chain 'B' and resid 384 through 386 removed outlier: 3.561A pdb=" N GLY C 39 " --> pdb=" O GLY B 385 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'C' and resid 55 through 56 removed outlier: 3.605A pdb=" N ASP C 201 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG C 51 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE C 199 " --> pdb=" O ARG C 51 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 152 through 154 removed outlier: 6.837A pdb=" N MET C 140 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL C 168 " --> pdb=" O MET C 140 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1497 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.40 Time building geometry restraints manager: 1.25 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: 3179 1.34 - 1.46: 2368 1.46 - 1.59: 4323 1.59 - 1.71: 0 1.71 - 1.83: 77 Bond restraints: 9947 Sorted by residual: bond pdb=" N MLE E 3 " pdb=" CN MLE E 3 " ideal model delta sigma weight residual 1.451 1.518 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" N MLE E 10 " pdb=" CN MLE E 10 " ideal model delta sigma weight residual 1.451 1.513 -0.062 2.00e-02 2.50e+03 9.67e+00 bond pdb=" CA SER A 699 " pdb=" CB SER A 699 " ideal model delta sigma weight residual 1.529 1.496 0.033 1.13e-02 7.83e+03 8.61e+00 bond pdb=" N MVA E 4 " pdb=" CN MVA E 4 " ideal model delta sigma weight residual 1.449 1.506 -0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" N MET A 703 " pdb=" CA MET A 703 " ideal model delta sigma weight residual 1.452 1.486 -0.034 1.22e-02 6.72e+03 7.57e+00 ... (remaining 9942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 13100 2.25 - 4.49: 290 4.49 - 6.74: 50 6.74 - 8.99: 9 8.99 - 11.23: 3 Bond angle restraints: 13452 Sorted by residual: angle pdb=" CA LYS C 98 " pdb=" C LYS C 98 " pdb=" N ASP C 99 " ideal model delta sigma weight residual 117.22 123.43 -6.21 1.17e+00 7.31e-01 2.81e+01 angle pdb=" N PHE C 107 " pdb=" CA PHE C 107 " pdb=" C PHE C 107 " ideal model delta sigma weight residual 113.41 107.65 5.76 1.22e+00 6.72e-01 2.23e+01 angle pdb=" N LYS C 165 " pdb=" CA LYS C 165 " pdb=" C LYS C 165 " ideal model delta sigma weight residual 113.72 108.33 5.39 1.30e+00 5.92e-01 1.72e+01 angle pdb=" N TRP C 161 " pdb=" CA TRP C 161 " pdb=" C TRP C 161 " ideal model delta sigma weight residual 111.11 106.60 4.51 1.20e+00 6.94e-01 1.41e+01 angle pdb=" CA LYS C 98 " pdb=" C LYS C 98 " pdb=" O LYS C 98 " ideal model delta sigma weight residual 120.63 116.57 4.06 1.08e+00 8.57e-01 1.41e+01 ... (remaining 13447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.97: 5338 22.97 - 45.94: 560 45.94 - 68.91: 93 68.91 - 91.88: 13 91.88 - 114.85: 17 Dihedral angle restraints: 6021 sinusoidal: 2514 harmonic: 3507 Sorted by residual: dihedral pdb=" CB CYS A 246 " pdb=" SG CYS A 246 " pdb=" SG CYS A 278 " pdb=" CB CYS A 278 " ideal model delta sinusoidal sigma weight residual 93.00 156.26 -63.26 1 1.00e+01 1.00e-02 5.28e+01 dihedral pdb=" CA CYS A 79 " pdb=" C CYS A 79 " pdb=" N ALA A 80 " pdb=" CA ALA A 80 " ideal model delta harmonic sigma weight residual 180.00 153.95 26.05 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CB CYS A 79 " pdb=" SG CYS A 79 " pdb=" SG CYS A 119 " pdb=" CB CYS A 119 " ideal model delta sinusoidal sigma weight residual -86.00 -125.87 39.87 1 1.00e+01 1.00e-02 2.23e+01 ... (remaining 6018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1226 0.062 - 0.124: 167 0.124 - 0.185: 20 0.185 - 0.247: 5 0.247 - 0.309: 3 Chirality restraints: 1421 Sorted by residual: chirality pdb=" CB BMT E 5 " pdb=" CA BMT E 5 " pdb=" OG1 BMT E 5 " pdb=" CG2 BMT E 5 " both_signs ideal model delta sigma weight residual False 2.37 2.68 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 363 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA MVA E 4 " pdb=" N MVA E 4 " pdb=" C MVA E 4 " pdb=" CB MVA E 4 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 1418 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 155 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C THR C 155 " 0.051 2.00e-02 2.50e+03 pdb=" O THR C 155 " -0.019 2.00e-02 2.50e+03 pdb=" N THR C 156 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 123 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO C 124 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 124 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 124 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 604 " 0.033 5.00e-02 4.00e+02 4.99e-02 3.99e+00 pdb=" N PRO A 605 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 605 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 605 " 0.028 5.00e-02 4.00e+02 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 325 2.71 - 3.26: 9807 3.26 - 3.81: 15727 3.81 - 4.35: 17583 4.35 - 4.90: 30112 Nonbonded interactions: 73554 Sorted by model distance: nonbonded pdb=" OD1 ASP B 258 " pdb=" N PHE B 259 " model vdw 2.168 3.120 nonbonded pdb=" NE2 HIS A 659 " pdb="FE FE A 803 " model vdw 2.178 2.340 nonbonded pdb=" O MET B 180 " pdb=" ND2 ASN B 184 " model vdw 2.198 3.120 nonbonded pdb=" O GLU A 351 " pdb=" OG SER A 355 " model vdw 2.220 3.040 nonbonded pdb=" O TYR B 187 " pdb=" OG SER B 190 " model vdw 2.244 3.040 ... (remaining 73549 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.680 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6364 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 : 0.004 0.067 9956 Z= 0.214 Angle : 0.802 11.232 13475 Z= 0.445 Chirality : 0.047 0.309 1421 Planarity : 0.004 0.064 1765 Dihedral : 18.993 114.850 3756 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.34 % Favored : 95.32 % Rotamer: Outliers : 1.18 % Allowed : 22.93 % Favored : 75.89 % 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: 0.48 (0.26), residues: 1176 helix: 2.13 (0.21), residues: 613 sheet: -0.27 (0.75), residues: 50 loop : -2.03 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.026 0.001 TYR B 267 PHE 0.017 0.001 PHE C 153 TRP 0.033 0.001 TRP A 91 HIS 0.003 0.000 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.21 ( 9947) covalent geometry : angle 0.79570 / 0.44 (13452) SS BOND : bond 0.00255 / 0.14 ( 4) SS BOND : angle 2.91884 / 1.59 ( 8) hydrogen bonds : bond 0.17221 / 11.48 ( 495) hydrogen bonds : angle 5.70491 / 4.18 ( 1497) link_NAG-ASN : bond 0.00457 / 0.25 ( 4) link_NAG-ASN : angle 2.30289 / 1.23 ( 12) link_TRANS : bond 0.00081 / 0.05 ( 1) link_TRANS : angle 1.67063 / 0.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7426 (t0) cc_final: 0.7063 (t0) REVERT: A 322 GLU cc_start: 0.7897 (tt0) cc_final: 0.7122 (tm-30) REVERT: A 323 CYS cc_start: 0.8139 (t) cc_final: 0.7590 (t) REVERT: A 334 ASP cc_start: 0.7394 (t0) cc_final: 0.7012 (t0) REVERT: A 423 ASN cc_start: 0.7424 (m-40) cc_final: 0.6579 (t0) REVERT: A 487 GLN cc_start: 0.8205 (mt0) cc_final: 0.7785 (mm110) REVERT: A 488 ARG cc_start: 0.7847 (mtp-110) cc_final: 0.7623 (ptp-110) REVERT: A 635 LYS cc_start: 0.8787 (tppt) cc_final: 0.8529 (mmtp) REVERT: A 668 GLN cc_start: 0.7486 (mm-40) cc_final: 0.7121 (mm-40) REVERT: A 702 GLU cc_start: 0.5134 (OUTLIER) cc_final: 0.4880 (pm20) REVERT: A 703 MET cc_start: 0.6026 (OUTLIER) cc_final: 0.5806 (mtt) REVERT: B 88 CYS cc_start: 0.8789 (m) cc_final: 0.7314 (m) REVERT: B 184 ASN cc_start: 0.8962 (m-40) cc_final: 0.8596 (m110) REVERT: B 199 LYS cc_start: 0.7445 (mttt) cc_final: 0.7232 (mmtm) REVERT: B 202 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7109 (mm-30) REVERT: B 215 ARG cc_start: 0.8835 (tpt-90) cc_final: 0.8629 (mmm-85) REVERT: B 228 ASP cc_start: 0.9052 (m-30) cc_final: 0.8822 (m-30) REVERT: B 278 GLU cc_start: 0.8337 (tm-30) cc_final: 0.7845 (tm-30) REVERT: B 329 LYS cc_start: 0.9398 (mppt) cc_final: 0.9086 (mmtm) REVERT: B 351 HIS cc_start: 0.6434 (m-70) cc_final: 0.6226 (m90) REVERT: B 381 ASP cc_start: 0.8689 (m-30) cc_final: 0.8109 (p0) REVERT: B 382 ASP cc_start: 0.7827 (m-30) cc_final: 0.6811 (p0) REVERT: C 97 ILE cc_start: 0.7293 (tt) cc_final: 0.7049 (mt) REVERT: C 159 THR cc_start: 0.7893 (p) cc_final: 0.7345 (p) REVERT: C 171 LYS cc_start: 0.7028 (tttm) cc_final: 0.6718 (tttp) REVERT: C 174 GLU cc_start: 0.7999 (tp30) cc_final: 0.7602 (tp30) REVERT: C 176 MET cc_start: 0.7185 (mmp) cc_final: 0.6961 (mmt) outliers start: 12 outliers final: 3 residues processed: 248 average time/residue: 0.1020 time to fit residues: 34.3545 Evaluate side-chains 149 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 703 MET Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 162 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 266 HIS ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.096496 restraints weight = 17215.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101458 restraints weight = 9525.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102579 restraints weight = 5919.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.105571 restraints weight = 5421.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.105475 restraints weight = 4736.109| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9956 Z= 0.210 Angle : 0.721 9.416 13475 Z= 0.369 Chirality : 0.046 0.340 1421 Planarity : 0.005 0.052 1765 Dihedral : 8.378 90.503 1431 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.21 % Favored : 93.54 % Rotamer: Outliers : 4.72 % Allowed : 22.74 % Favored : 72.54 % 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: 0.49 (0.25), residues: 1176 helix: 2.07 (0.21), residues: 621 sheet: 0.11 (0.70), residues: 48 loop : -2.03 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 214 TYR 0.031 0.002 TYR B 267 PHE 0.027 0.002 PHE C 153 TRP 0.024 0.002 TRP B 345 HIS 0.006 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 ( 9947) covalent geometry : angle 0.71473 / 0.37 (13452) SS BOND : bond 0.00289 / 0.15 ( 4) SS BOND : angle 2.82171 / 1.50 ( 8) hydrogen bonds : bond 0.06156 / 4.22 ( 495) hydrogen bonds : angle 4.32003 / 3.21 ( 1497) link_NAG-ASN : bond 0.00380 / 0.20 ( 4) link_NAG-ASN : angle 2.35969 / 1.24 ( 12) link_TRANS : bond 0.00071 / 0.04 ( 1) link_TRANS : angle 0.18294 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7579 (t0) cc_final: 0.7266 (t0) REVERT: A 139 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: A 156 ILE cc_start: 0.8223 (tp) cc_final: 0.7676 (tt) REVERT: A 202 THR cc_start: 0.7224 (m) cc_final: 0.6655 (p) REVERT: A 322 GLU cc_start: 0.8336 (tt0) cc_final: 0.7402 (tm-30) REVERT: A 323 CYS cc_start: 0.8273 (t) cc_final: 0.7505 (t) REVERT: A 423 ASN cc_start: 0.7906 (m-40) cc_final: 0.7299 (p0) REVERT: A 488 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7752 (ptp90) REVERT: A 600 CYS cc_start: 0.7725 (m) cc_final: 0.6601 (t) REVERT: A 668 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7258 (mm-40) REVERT: B 146 GLU cc_start: 0.8779 (pt0) cc_final: 0.7548 (pt0) REVERT: B 198 ILE cc_start: 0.8026 (mm) cc_final: 0.7626 (mp) REVERT: B 199 LYS cc_start: 0.8228 (mttt) cc_final: 0.7885 (mmtt) REVERT: B 252 GLU cc_start: 0.8025 (pm20) cc_final: 0.7815 (pm20) REVERT: B 344 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7956 (p) REVERT: B 382 ASP cc_start: 0.7700 (m-30) cc_final: 0.6792 (p0) REVERT: C 59 ARG cc_start: 0.7641 (ttm110) cc_final: 0.7309 (ttm170) REVERT: C 208 GLU cc_start: 0.8724 (pm20) cc_final: 0.8503 (pm20) outliers start: 48 outliers final: 22 residues processed: 181 average time/residue: 0.0831 time to fit residues: 21.7357 Evaluate side-chains 138 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain E residue 9 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 GLN B 339 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.140915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098532 restraints weight = 17047.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.103104 restraints weight = 9468.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.106287 restraints weight = 6518.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.108452 restraints weight = 5090.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109971 restraints weight = 4308.048| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9956 Z= 0.126 Angle : 0.602 8.139 13475 Z= 0.306 Chirality : 0.041 0.222 1421 Planarity : 0.004 0.065 1765 Dihedral : 6.904 76.338 1423 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.68 % Favored : 95.07 % Rotamer: Outliers : 3.35 % Allowed : 25.30 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1176 helix: 2.21 (0.20), residues: 614 sheet: -0.12 (0.64), residues: 62 loop : -1.92 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 471 TYR 0.020 0.001 TYR A 628 PHE 0.016 0.001 PHE C 153 TRP 0.012 0.001 TRP C 161 HIS 0.003 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 9947) covalent geometry : angle 0.59478 / 0.30 (13452) SS BOND : bond 0.00626 / 0.36 ( 4) SS BOND : angle 2.79061 / 1.50 ( 8) hydrogen bonds : bond 0.04701 / 3.23 ( 495) hydrogen bonds : angle 3.93274 / 2.93 ( 1497) link_NAG-ASN : bond 0.00437 / 0.25 ( 4) link_NAG-ASN : angle 2.30631 / 1.31 ( 12) link_TRANS : bond 0.00033 / 0.02 ( 1) link_TRANS : angle 0.06493 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.7670 (tt) cc_final: 0.7427 (tp) REVERT: A 139 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.6762 (mp0) REVERT: A 156 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7315 (tt) REVERT: A 322 GLU cc_start: 0.8306 (tt0) cc_final: 0.7333 (tm-30) REVERT: A 323 CYS cc_start: 0.8248 (t) cc_final: 0.7506 (t) REVERT: A 374 GLU cc_start: 0.8349 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 423 ASN cc_start: 0.8003 (m-40) cc_final: 0.7031 (t0) REVERT: A 482 GLU cc_start: 0.8503 (mp0) cc_final: 0.8275 (mp0) REVERT: A 488 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7816 (ptp90) REVERT: A 693 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7303 (mm) REVERT: B 146 GLU cc_start: 0.8407 (pt0) cc_final: 0.8011 (pt0) REVERT: B 198 ILE cc_start: 0.7966 (mm) cc_final: 0.7580 (mp) REVERT: B 252 GLU cc_start: 0.8081 (pm20) cc_final: 0.7810 (pm20) REVERT: B 288 TYR cc_start: 0.6720 (m-80) cc_final: 0.6456 (m-80) REVERT: B 382 ASP cc_start: 0.7744 (m-30) cc_final: 0.6735 (t0) REVERT: C 59 ARG cc_start: 0.7723 (ttm110) cc_final: 0.6973 (ptm160) REVERT: C 208 GLU cc_start: 0.8785 (pm20) cc_final: 0.8570 (pm20) REVERT: C 213 ILE cc_start: 0.8940 (tp) cc_final: 0.8718 (tt) outliers start: 34 outliers final: 19 residues processed: 174 average time/residue: 0.0751 time to fit residues: 18.9059 Evaluate side-chains 147 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain E residue 9 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 0.0060 chunk 66 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 368 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.136790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.095261 restraints weight = 16688.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.099583 restraints weight = 9142.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102572 restraints weight = 6246.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104608 restraints weight = 4863.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.105981 restraints weight = 4108.972| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9956 Z= 0.172 Angle : 0.638 8.019 13475 Z= 0.323 Chirality : 0.043 0.187 1421 Planarity : 0.004 0.065 1765 Dihedral : 6.574 66.831 1423 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.70 % Favored : 94.05 % Rotamer: Outliers : 4.63 % Allowed : 26.28 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.25), residues: 1176 helix: 2.14 (0.20), residues: 615 sheet: 0.22 (0.72), residues: 49 loop : -1.90 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.022 0.001 TYR A 628 PHE 0.022 0.002 PHE C 153 TRP 0.012 0.001 TRP C 161 HIS 0.005 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 9947) covalent geometry : angle 0.62389 / 0.32 (13452) SS BOND : bond 0.00317 / 0.17 ( 4) SS BOND : angle 2.77333 / 1.49 ( 8) hydrogen bonds : bond 0.05242 / 3.62 ( 495) hydrogen bonds : angle 3.99184 / 2.97 ( 1497) link_NAG-ASN : bond 0.00236 / 0.12 ( 4) link_NAG-ASN : angle 3.87404 / 2.10 ( 12) link_TRANS : bond 0.00061 / 0.04 ( 1) link_TRANS : angle 0.18836 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9123 (mmm) cc_final: 0.8751 (mpp) REVERT: A 139 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: A 156 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7496 (tt) REVERT: A 322 GLU cc_start: 0.8322 (tt0) cc_final: 0.7803 (tm-30) REVERT: A 323 CYS cc_start: 0.8287 (t) cc_final: 0.7568 (t) REVERT: A 423 ASN cc_start: 0.7995 (m-40) cc_final: 0.7566 (m110) REVERT: A 479 SER cc_start: 0.5819 (OUTLIER) cc_final: 0.4696 (t) REVERT: A 488 ARG cc_start: 0.8062 (mtp-110) cc_final: 0.7752 (ptp90) REVERT: A 600 CYS cc_start: 0.7834 (m) cc_final: 0.7616 (m) REVERT: A 689 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7148 (mm-40) REVERT: A 693 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7418 (mm) REVERT: B 146 GLU cc_start: 0.8524 (pt0) cc_final: 0.8173 (pt0) REVERT: B 243 CYS cc_start: 0.8906 (t) cc_final: 0.8481 (t) REVERT: B 252 GLU cc_start: 0.8233 (pm20) cc_final: 0.7952 (pm20) REVERT: B 382 ASP cc_start: 0.7792 (m-30) cc_final: 0.6873 (t70) REVERT: C 59 ARG cc_start: 0.7697 (ttm110) cc_final: 0.6979 (ptm160) REVERT: C 113 THR cc_start: 0.8578 (m) cc_final: 0.8339 (p) REVERT: C 190 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7638 (mmm-85) REVERT: C 195 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8520 (mtmt) REVERT: C 208 GLU cc_start: 0.8717 (pm20) cc_final: 0.8484 (pm20) outliers start: 47 outliers final: 35 residues processed: 164 average time/residue: 0.0786 time to fit residues: 18.9727 Evaluate side-chains 160 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain E residue 9 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.2980 chunk 57 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 90 optimal weight: 0.0970 chunk 93 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 35 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 339 GLN B 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.141977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.106750 restraints weight = 17150.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.110891 restraints weight = 10532.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111354 restraints weight = 8366.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111885 restraints weight = 6653.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.113038 restraints weight = 6088.531| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9956 Z= 0.108 Angle : 0.575 9.201 13475 Z= 0.285 Chirality : 0.040 0.168 1421 Planarity : 0.004 0.067 1765 Dihedral : 5.897 59.944 1423 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.91 % Favored : 95.83 % Rotamer: Outliers : 3.44 % Allowed : 27.07 % Favored : 69.49 % 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: 0.81 (0.25), residues: 1176 helix: 2.26 (0.20), residues: 617 sheet: -0.39 (0.62), residues: 71 loop : -1.71 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 666 TYR 0.021 0.001 TYR A 628 PHE 0.014 0.001 PHE C 153 TRP 0.008 0.001 TRP C 161 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 9947) covalent geometry : angle 0.56197 / 0.28 (13452) SS BOND : bond 0.00308 / 0.16 ( 4) SS BOND : angle 2.51256 / 1.37 ( 8) hydrogen bonds : bond 0.04024 / 2.77 ( 495) hydrogen bonds : angle 3.68957 / 2.75 ( 1497) link_NAG-ASN : bond 0.00513 / 0.30 ( 4) link_NAG-ASN : angle 3.58213 / 2.02 ( 12) link_TRANS : bond 0.00000 / 0.00 ( 1) link_TRANS : angle 0.10791 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 139 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5657 (mmm) REVERT: A 58 MET cc_start: 0.8908 (mmm) cc_final: 0.8551 (mpp) REVERT: A 73 LEU cc_start: 0.7341 (tt) cc_final: 0.7118 (tp) REVERT: A 139 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: A 156 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7148 (tt) REVERT: A 322 GLU cc_start: 0.8383 (tt0) cc_final: 0.7822 (tm-30) REVERT: A 423 ASN cc_start: 0.8178 (m-40) cc_final: 0.7865 (m110) REVERT: A 482 GLU cc_start: 0.8495 (pm20) cc_final: 0.8237 (pm20) REVERT: A 488 ARG cc_start: 0.8014 (mtp-110) cc_final: 0.7628 (ptp90) REVERT: A 600 CYS cc_start: 0.7881 (m) cc_final: 0.7654 (m) REVERT: A 693 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.7029 (mm) REVERT: B 146 GLU cc_start: 0.8419 (pt0) cc_final: 0.7973 (pt0) REVERT: B 243 CYS cc_start: 0.8893 (t) cc_final: 0.8383 (t) REVERT: B 252 GLU cc_start: 0.8259 (pm20) cc_final: 0.7875 (pm20) REVERT: B 297 MET cc_start: 0.8234 (ttm) cc_final: 0.7955 (mtp) REVERT: B 382 ASP cc_start: 0.7939 (m-30) cc_final: 0.6912 (t70) REVERT: C 59 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7165 (ptp-110) REVERT: C 190 ARG cc_start: 0.8140 (mtp180) cc_final: 0.7304 (mmm160) REVERT: C 195 LYS cc_start: 0.8743 (mmmm) cc_final: 0.8414 (mtmt) REVERT: C 208 GLU cc_start: 0.8811 (pm20) cc_final: 0.8585 (pm20) outliers start: 35 outliers final: 21 residues processed: 167 average time/residue: 0.0656 time to fit residues: 16.2245 Evaluate side-chains 145 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain E residue 9 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 66 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 34 optimal weight: 0.0050 chunk 102 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 35 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 52 optimal weight: 0.0670 chunk 37 optimal weight: 0.9980 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.140876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103910 restraints weight = 16808.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109754 restraints weight = 10194.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110087 restraints weight = 6126.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110799 restraints weight = 5499.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111158 restraints weight = 5155.149| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9956 Z= 0.104 Angle : 0.571 9.785 13475 Z= 0.280 Chirality : 0.040 0.151 1421 Planarity : 0.004 0.067 1765 Dihedral : 5.310 59.687 1423 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.25 % Favored : 95.49 % Rotamer: Outliers : 3.35 % Allowed : 27.56 % Favored : 69.09 % 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: 0.83 (0.25), residues: 1176 helix: 2.29 (0.20), residues: 621 sheet: -0.36 (0.60), residues: 71 loop : -1.76 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 669 TYR 0.024 0.001 TYR C 133 PHE 0.014 0.001 PHE C 153 TRP 0.011 0.001 TRP C 161 HIS 0.003 0.000 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 9947) covalent geometry : angle 0.55785 / 0.28 (13452) SS BOND : bond 0.00310 / 0.17 ( 4) SS BOND : angle 2.93225 / 1.57 ( 8) hydrogen bonds : bond 0.03559 / 2.47 ( 495) hydrogen bonds : angle 3.56843 / 2.66 ( 1497) link_NAG-ASN : bond 0.00434 / 0.25 ( 4) link_NAG-ASN : angle 3.39412 / 1.93 ( 12) link_TRANS : bond 0.00004 / 0.00 ( 1) link_TRANS : angle 0.07196 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.6157 (OUTLIER) cc_final: 0.5556 (mmm) REVERT: A 139 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: A 156 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.6978 (tt) REVERT: A 286 LEU cc_start: 0.8123 (mt) cc_final: 0.7811 (mp) REVERT: A 322 GLU cc_start: 0.8408 (tt0) cc_final: 0.7649 (tm-30) REVERT: A 423 ASN cc_start: 0.8224 (m-40) cc_final: 0.7809 (m110) REVERT: A 471 ARG cc_start: 0.5510 (mtm-85) cc_final: 0.5005 (mtm-85) REVERT: A 482 GLU cc_start: 0.8559 (pm20) cc_final: 0.8270 (pm20) REVERT: A 488 ARG cc_start: 0.7993 (mtp-110) cc_final: 0.7680 (ptp90) REVERT: A 693 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6948 (mm) REVERT: B 146 GLU cc_start: 0.8274 (pt0) cc_final: 0.7730 (pt0) REVERT: B 180 MET cc_start: 0.6578 (ttt) cc_final: 0.5486 (tpt) REVERT: B 242 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7545 (tm-30) REVERT: B 243 CYS cc_start: 0.8844 (t) cc_final: 0.8238 (t) REVERT: B 252 GLU cc_start: 0.8200 (pm20) cc_final: 0.7792 (pm20) REVERT: B 297 MET cc_start: 0.8150 (ttm) cc_final: 0.7929 (mtp) REVERT: B 382 ASP cc_start: 0.7942 (m-30) cc_final: 0.6892 (t70) REVERT: C 59 ARG cc_start: 0.7548 (ttm110) cc_final: 0.7157 (ptp-110) REVERT: C 89 LYS cc_start: 0.8087 (tppp) cc_final: 0.7884 (tptt) REVERT: C 159 THR cc_start: 0.9346 (p) cc_final: 0.9126 (p) REVERT: C 190 ARG cc_start: 0.8056 (mtp180) cc_final: 0.7239 (mmm160) REVERT: C 195 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8390 (mtmt) outliers start: 34 outliers final: 23 residues processed: 162 average time/residue: 0.0701 time to fit residues: 16.6491 Evaluate side-chains 152 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain E residue 9 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 94 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 368 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097402 restraints weight = 16749.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.101013 restraints weight = 9245.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102712 restraints weight = 5898.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.104680 restraints weight = 4962.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105226 restraints weight = 4339.102| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9956 Z= 0.167 Angle : 0.637 10.631 13475 Z= 0.318 Chirality : 0.042 0.173 1421 Planarity : 0.004 0.069 1765 Dihedral : 5.253 57.773 1423 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.53 % Favored : 94.22 % Rotamer: Outliers : 4.92 % Allowed : 26.48 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.25), residues: 1176 helix: 2.28 (0.21), residues: 617 sheet: 0.58 (0.75), residues: 49 loop : -1.84 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 212 TYR 0.019 0.001 TYR A 628 PHE 0.023 0.001 PHE C 153 TRP 0.010 0.001 TRP C 161 HIS 0.004 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 9947) covalent geometry : angle 0.62754 / 0.32 (13452) SS BOND : bond 0.00319 / 0.17 ( 4) SS BOND : angle 2.92193 / 1.56 ( 8) hydrogen bonds : bond 0.05019 / 3.48 ( 495) hydrogen bonds : angle 3.90321 / 2.92 ( 1497) link_NAG-ASN : bond 0.00341 / 0.20 ( 4) link_NAG-ASN : angle 2.95746 / 1.67 ( 12) link_TRANS : bond 0.00015 / 0.01 ( 1) link_TRANS : angle 0.06437 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9097 (mmm) cc_final: 0.8783 (mpp) REVERT: A 88 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7547 (p0) REVERT: A 139 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: A 156 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7484 (tt) REVERT: A 218 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 286 LEU cc_start: 0.8464 (mt) cc_final: 0.8183 (mp) REVERT: A 322 GLU cc_start: 0.8372 (tt0) cc_final: 0.7863 (tm-30) REVERT: A 423 ASN cc_start: 0.8352 (m-40) cc_final: 0.8116 (m-40) REVERT: A 471 ARG cc_start: 0.6398 (mtm-85) cc_final: 0.5885 (mtm-85) REVERT: A 482 GLU cc_start: 0.8542 (pm20) cc_final: 0.8245 (pm20) REVERT: A 488 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7730 (ptp90) REVERT: A 693 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7418 (mm) REVERT: B 146 GLU cc_start: 0.8452 (pt0) cc_final: 0.8044 (pt0) REVERT: B 252 GLU cc_start: 0.8334 (pm20) cc_final: 0.8008 (pm20) REVERT: B 382 ASP cc_start: 0.7819 (m-30) cc_final: 0.6952 (t70) REVERT: C 59 ARG cc_start: 0.7590 (ttm110) cc_final: 0.7247 (ptp-110) REVERT: C 190 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7571 (mmm-85) REVERT: C 195 LYS cc_start: 0.8817 (mmmm) cc_final: 0.8305 (mtmt) outliers start: 50 outliers final: 35 residues processed: 163 average time/residue: 0.0759 time to fit residues: 18.1511 Evaluate side-chains 160 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain E residue 9 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 115 optimal weight: 0.0670 chunk 30 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 60 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 368 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.140182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.098825 restraints weight = 16656.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103295 restraints weight = 9006.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.106420 restraints weight = 6120.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.108534 restraints weight = 4732.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.109806 restraints weight = 3987.966| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9956 Z= 0.107 Angle : 0.598 10.710 13475 Z= 0.291 Chirality : 0.040 0.169 1421 Planarity : 0.004 0.068 1765 Dihedral : 4.999 59.735 1423 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.51 % Favored : 95.24 % Rotamer: Outliers : 3.35 % Allowed : 27.85 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.82 (0.25), residues: 1176 helix: 2.25 (0.20), residues: 626 sheet: -0.05 (0.60), residues: 73 loop : -1.82 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 72 TYR 0.018 0.001 TYR A 628 PHE 0.014 0.001 PHE C 153 TRP 0.009 0.001 TRP C 161 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 9947) covalent geometry : angle 0.58877 / 0.29 (13452) SS BOND : bond 0.00346 / 0.19 ( 4) SS BOND : angle 2.56907 / 1.40 ( 8) hydrogen bonds : bond 0.03863 / 2.68 ( 495) hydrogen bonds : angle 3.66110 / 2.74 ( 1497) link_NAG-ASN : bond 0.00416 / 0.24 ( 4) link_NAG-ASN : angle 3.02985 / 1.67 ( 12) link_TRANS : bond 0.00010 / 0.01 ( 1) link_TRANS : angle 0.08107 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7516 (p0) REVERT: A 139 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6764 (mp0) REVERT: A 156 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7326 (tt) REVERT: A 286 LEU cc_start: 0.8494 (mt) cc_final: 0.8198 (mp) REVERT: A 322 GLU cc_start: 0.8345 (tt0) cc_final: 0.7871 (tm-30) REVERT: A 471 ARG cc_start: 0.6178 (mtm-85) cc_final: 0.5604 (mtm-85) REVERT: A 482 GLU cc_start: 0.8542 (pm20) cc_final: 0.8284 (pm20) REVERT: A 488 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7680 (ptp90) REVERT: A 693 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7464 (mm) REVERT: B 146 GLU cc_start: 0.8370 (pt0) cc_final: 0.7926 (pt0) REVERT: B 180 MET cc_start: 0.6566 (ttt) cc_final: 0.5520 (tpt) REVERT: B 243 CYS cc_start: 0.8899 (t) cc_final: 0.8296 (t) REVERT: B 252 GLU cc_start: 0.8321 (pm20) cc_final: 0.8009 (pm20) REVERT: B 297 MET cc_start: 0.8306 (ttm) cc_final: 0.7969 (mtp) REVERT: B 382 ASP cc_start: 0.7754 (m-30) cc_final: 0.6915 (t70) REVERT: C 59 ARG cc_start: 0.7613 (ttm110) cc_final: 0.7289 (ptp-110) REVERT: C 190 ARG cc_start: 0.7949 (mtp180) cc_final: 0.7236 (mmm160) REVERT: C 195 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8419 (mtmt) outliers start: 34 outliers final: 25 residues processed: 155 average time/residue: 0.0758 time to fit residues: 17.3531 Evaluate side-chains 150 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain E residue 9 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 73 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 0.0970 chunk 80 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 46 optimal weight: 7.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.140516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099204 restraints weight = 16469.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103605 restraints weight = 9007.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106669 restraints weight = 6155.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108761 restraints weight = 4780.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.110199 restraints weight = 4027.976| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9956 Z= 0.111 Angle : 0.611 11.767 13475 Z= 0.296 Chirality : 0.040 0.164 1421 Planarity : 0.004 0.068 1765 Dihedral : 4.915 58.688 1423 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.85 % Favored : 94.90 % Rotamer: Outliers : 3.64 % Allowed : 28.35 % Favored : 68.01 % 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: 0.83 (0.25), residues: 1176 helix: 2.27 (0.20), residues: 628 sheet: 0.06 (0.57), residues: 73 loop : -1.87 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 666 TYR 0.017 0.001 TYR A 628 PHE 0.013 0.001 PHE C 100 TRP 0.009 0.001 TRP C 161 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 9947) covalent geometry : angle 0.60291 / 0.29 (13452) SS BOND : bond 0.00308 / 0.17 ( 4) SS BOND : angle 2.58198 / 1.40 ( 8) hydrogen bonds : bond 0.03833 / 2.66 ( 495) hydrogen bonds : angle 3.64611 / 2.74 ( 1497) link_NAG-ASN : bond 0.00395 / 0.23 ( 4) link_NAG-ASN : angle 2.81022 / 1.54 ( 12) link_TRANS : bond 0.00007 / 0.00 ( 1) link_TRANS : angle 0.05135 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.7744 (tt) cc_final: 0.7448 (tp) REVERT: A 139 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: A 156 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7325 (tt) REVERT: A 202 THR cc_start: 0.7017 (m) cc_final: 0.6518 (p) REVERT: A 218 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: A 286 LEU cc_start: 0.8488 (mt) cc_final: 0.8204 (mp) REVERT: A 322 GLU cc_start: 0.8342 (tt0) cc_final: 0.7875 (tm-30) REVERT: A 423 ASN cc_start: 0.8203 (m110) cc_final: 0.7593 (p0) REVERT: A 471 ARG cc_start: 0.5953 (mtm-85) cc_final: 0.5405 (mtm-85) REVERT: A 488 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.7682 (ptp90) REVERT: A 689 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7219 (mm-40) REVERT: A 693 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7467 (mm) REVERT: B 146 GLU cc_start: 0.8288 (pt0) cc_final: 0.7876 (pt0) REVERT: B 180 MET cc_start: 0.6555 (ttt) cc_final: 0.5530 (tpt) REVERT: B 243 CYS cc_start: 0.8823 (t) cc_final: 0.8160 (t) REVERT: B 252 GLU cc_start: 0.8309 (pm20) cc_final: 0.8026 (pm20) REVERT: B 382 ASP cc_start: 0.7761 (m-30) cc_final: 0.6894 (t70) REVERT: C 190 ARG cc_start: 0.7934 (mtp180) cc_final: 0.7627 (mmm-85) REVERT: C 195 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8280 (mtmt) outliers start: 37 outliers final: 24 residues processed: 160 average time/residue: 0.0864 time to fit residues: 20.1337 Evaluate side-chains 150 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain E residue 9 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 111 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.139111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097962 restraints weight = 16735.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102300 restraints weight = 9231.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105255 restraints weight = 6343.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.107311 restraints weight = 4959.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.108653 restraints weight = 4197.902| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9956 Z= 0.127 Angle : 0.643 12.058 13475 Z= 0.312 Chirality : 0.041 0.169 1421 Planarity : 0.004 0.069 1765 Dihedral : 4.859 58.475 1423 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.10 % Favored : 94.64 % Rotamer: Outliers : 3.25 % Allowed : 28.84 % Favored : 67.91 % 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: 0.83 (0.25), residues: 1176 helix: 2.27 (0.20), residues: 631 sheet: -0.01 (0.57), residues: 73 loop : -1.89 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 666 TYR 0.016 0.001 TYR A 628 PHE 0.015 0.001 PHE C 100 TRP 0.010 0.001 TRP C 161 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9947) covalent geometry : angle 0.63539 / 0.31 (13452) SS BOND : bond 0.00306 / 0.17 ( 4) SS BOND : angle 2.58629 / 1.41 ( 8) hydrogen bonds : bond 0.04042 / 2.80 ( 495) hydrogen bonds : angle 3.68808 / 2.77 ( 1497) link_NAG-ASN : bond 0.00359 / 0.21 ( 4) link_NAG-ASN : angle 2.70630 / 1.49 ( 12) link_TRANS : bond 0.00010 / 0.01 ( 1) link_TRANS : angle 0.02655 / 0.01 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.7798 (tt) cc_final: 0.7497 (tp) REVERT: A 139 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: A 156 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7353 (tt) REVERT: A 198 LYS cc_start: 0.8915 (mmtm) cc_final: 0.8619 (mmtt) REVERT: A 202 THR cc_start: 0.7039 (m) cc_final: 0.6532 (p) REVERT: A 218 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 286 LEU cc_start: 0.8527 (mt) cc_final: 0.8240 (mp) REVERT: A 322 GLU cc_start: 0.8338 (tt0) cc_final: 0.7882 (tm-30) REVERT: A 328 LEU cc_start: 0.8862 (mt) cc_final: 0.8662 (mt) REVERT: A 423 ASN cc_start: 0.8165 (m110) cc_final: 0.7554 (p0) REVERT: A 471 ARG cc_start: 0.6187 (mtm-85) cc_final: 0.5523 (mtm-85) REVERT: A 488 ARG cc_start: 0.7982 (mtp-110) cc_final: 0.7702 (ptp90) REVERT: A 568 CYS cc_start: 0.7980 (m) cc_final: 0.7687 (p) REVERT: A 600 CYS cc_start: 0.7507 (m) cc_final: 0.6729 (t) REVERT: A 689 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7257 (mm-40) REVERT: A 693 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7463 (mm) REVERT: B 27 GLN cc_start: 0.7792 (pm20) cc_final: 0.7125 (pp30) REVERT: B 146 GLU cc_start: 0.8310 (pt0) cc_final: 0.7403 (pt0) REVERT: B 180 MET cc_start: 0.6560 (ttt) cc_final: 0.5542 (tpt) REVERT: B 221 ASN cc_start: 0.7282 (t0) cc_final: 0.5983 (m-40) REVERT: B 243 CYS cc_start: 0.8876 (t) cc_final: 0.8232 (t) REVERT: B 252 GLU cc_start: 0.8365 (pm20) cc_final: 0.8059 (pm20) REVERT: B 288 TYR cc_start: 0.6954 (m-80) cc_final: 0.6682 (m-80) REVERT: B 382 ASP cc_start: 0.7759 (m-30) cc_final: 0.6937 (t70) REVERT: C 59 ARG cc_start: 0.8017 (ptp-110) cc_final: 0.7794 (ttm170) REVERT: C 107 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7007 (p90) REVERT: C 163 ASP cc_start: 0.8499 (t0) cc_final: 0.8293 (m-30) REVERT: C 190 ARG cc_start: 0.7989 (mtp180) cc_final: 0.7627 (mmm-85) REVERT: C 195 LYS cc_start: 0.8806 (mmmm) cc_final: 0.8276 (mtmt) outliers start: 33 outliers final: 26 residues processed: 156 average time/residue: 0.0777 time to fit residues: 17.6023 Evaluate side-chains 157 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain E residue 9 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 49 optimal weight: 0.0370 chunk 97 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099581 restraints weight = 16910.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.104084 restraints weight = 9126.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107159 restraints weight = 6188.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109231 restraints weight = 4803.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110495 restraints weight = 4057.443| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9956 Z= 0.113 Angle : 0.628 12.099 13475 Z= 0.304 Chirality : 0.040 0.176 1421 Planarity : 0.004 0.068 1765 Dihedral : 4.742 57.979 1423 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.85 % Favored : 94.90 % Rotamer: Outliers : 3.44 % Allowed : 28.74 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.83 (0.25), residues: 1176 helix: 2.28 (0.20), residues: 630 sheet: -0.08 (0.55), residues: 73 loop : -1.89 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 666 TYR 0.017 0.001 TYR A 628 PHE 0.026 0.001 PHE C 100 TRP 0.009 0.001 TRP C 161 HIS 0.002 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 9947) covalent geometry : angle 0.62069 / 0.30 (13452) SS BOND : bond 0.00313 / 0.17 ( 4) SS BOND : angle 2.51190 / 1.37 ( 8) hydrogen bonds : bond 0.03759 / 2.61 ( 495) hydrogen bonds : angle 3.64713 / 2.73 ( 1497) link_NAG-ASN : bond 0.00396 / 0.23 ( 4) link_NAG-ASN : angle 2.63576 / 1.44 ( 12) link_TRANS : bond 0.00013 / 0.01 ( 1) link_TRANS : angle 0.02063 / 0.01 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1474.96 seconds wall clock time: 26 minutes 7.80 seconds (1567.80 seconds total)