Starting phenix.real_space_refine on Thu Jul 2 18:34:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kc9_37097/07_2026/8kc9_37097.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kc9_37097/07_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_37097/07_2026/8kc9_37097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kc9_37097/07_2026/8kc9_37097.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kc9_37097/07_2026/8kc9_37097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kc9_37097/07_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-dev-6108/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 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, 28 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 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: 1.74, per 1000 atoms: 0.18 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: 0.79 Conformation dependent library (CDL) restraints added in 331.0 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: 0.27 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: 1.22 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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=" N SAR E 7 " pdb=" CN SAR E 7 " ideal model delta sigma weight residual 1.443 1.502 -0.059 2.00e-02 2.50e+03 8.78e+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 ... (remaining 9942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 13101 2.25 - 4.49: 289 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: 561 45.94 - 68.91: 92 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 3.080 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: 0.420 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.810 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.280 ------------------------------------------------------------------------------- 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= 0.215 Angle : 0.801 11.232 13475 Z= 0.445 Chirality : 0.047 0.309 1421 Planarity : 0.004 0.064 1765 Dihedral : 18.981 114.850 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 0.00387 / 0.22 ( 9947) covalent geometry : angle 0.79472 / 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 : 0.362 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: 0.1072 time to fit residues: 36.0249 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 : 0.369 ------------------------------------------------------------------------------- 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... A 659 HIS B 266 HIS ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.096913 restraints weight = 17223.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.102037 restraints weight = 9853.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103161 restraints weight = 6005.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105849 restraints weight = 5553.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105855 restraints weight = 4905.663| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9956 Z= 0.210 Angle : 0.716 9.576 13475 Z= 0.366 Chirality : 0.046 0.340 1421 Planarity : 0.005 0.052 1765 Dihedral : 8.582 93.225 1431 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.21 % Favored : 93.54 % Rotamer: Outliers : 4.72 % Allowed : 22.15 % Favored : 73.13 % 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: 0.52 (0.25), residues: 1176 helix: 2.10 (0.21), residues: 620 sheet: 0.26 (0.64), residues: 60 loop : -2.09 (0.27), residues: 496 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 0.00489 / 0.21 ( 9947) covalent geometry : angle 0.70965 / 0.36 (13452) SS BOND : bond 0.00302 / 0.16 ( 4) SS BOND : angle 2.81989 / 1.50 ( 8) hydrogen bonds : bond 0.06130 / 4.20 ( 495) hydrogen bonds : angle 4.34516 / 3.23 ( 1497) link_NAG-ASN : bond 0.00353 / 0.19 ( 4) link_NAG-ASN : angle 2.39820 / 1.25 ( 12) link_TRANS : bond 0.00059 / 0.04 ( 1) link_TRANS : angle 0.17111 / 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 : 0.335 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7558 (t0) cc_final: 0.7239 (t0) REVERT: A 139 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: A 156 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7641 (tt) REVERT: A 202 THR cc_start: 0.7208 (m) cc_final: 0.6628 (p) REVERT: A 322 GLU cc_start: 0.8302 (tt0) cc_final: 0.7400 (tm-30) REVERT: A 323 CYS cc_start: 0.8273 (t) cc_final: 0.7503 (t) REVERT: A 423 ASN cc_start: 0.7900 (m-40) cc_final: 0.7279 (p0) REVERT: A 488 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.7757 (ptp90) REVERT: A 600 CYS cc_start: 0.7717 (m) cc_final: 0.6581 (t) REVERT: A 668 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7316 (mm-40) REVERT: B 113 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6519 (tp) REVERT: B 146 GLU cc_start: 0.8789 (pt0) cc_final: 0.7576 (pt0) REVERT: B 198 ILE cc_start: 0.8029 (mm) cc_final: 0.7624 (mp) REVERT: B 199 LYS cc_start: 0.8252 (mttt) cc_final: 0.7912 (mmtt) REVERT: B 202 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7417 (mm-30) REVERT: B 252 GLU cc_start: 0.7986 (pm20) cc_final: 0.7778 (pm20) REVERT: B 344 THR cc_start: 0.8155 (m) cc_final: 0.7942 (p) REVERT: B 382 ASP cc_start: 0.7704 (m-30) cc_final: 0.6801 (p0) REVERT: C 171 LYS cc_start: 0.8649 (tttm) cc_final: 0.8426 (tttp) REVERT: C 208 GLU cc_start: 0.8698 (pm20) cc_final: 0.8471 (pm20) outliers start: 48 outliers final: 22 residues processed: 181 average time/residue: 0.0938 time to fit residues: 24.2477 Evaluate side-chains 142 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 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 113 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 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: 2.9990 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3834 r_free = 0.3834 target = 0.141544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.100756 restraints weight = 16428.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.105361 restraints weight = 8820.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.108455 restraints weight = 5950.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.110679 restraints weight = 4603.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111878 restraints weight = 3844.314| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9956 Z= 0.121 Angle : 0.601 8.243 13475 Z= 0.304 Chirality : 0.041 0.216 1421 Planarity : 0.004 0.065 1765 Dihedral : 6.794 76.773 1423 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.25 % Favored : 95.49 % Rotamer: Outliers : 3.15 % Allowed : 25.39 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.25), residues: 1176 helix: 2.18 (0.20), residues: 617 sheet: 0.21 (0.64), residues: 60 loop : -1.91 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 471 TYR 0.021 0.001 TYR A 628 PHE 0.016 0.001 PHE C 153 TRP 0.012 0.001 TRP C 161 HIS 0.002 0.001 HIS A 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 9947) covalent geometry : angle 0.59440 / 0.30 (13452) SS BOND : bond 0.00338 / 0.18 ( 4) SS BOND : angle 2.73839 / 1.48 ( 8) hydrogen bonds : bond 0.04587 / 3.15 ( 495) hydrogen bonds : angle 3.90593 / 2.92 ( 1497) link_NAG-ASN : bond 0.00424 / 0.24 ( 4) link_NAG-ASN : angle 2.26919 / 1.28 ( 12) link_TRANS : bond 0.00057 / 0.04 ( 1) link_TRANS : angle 0.08215 / 0.04 ( 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 184 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.7715 (tt) cc_final: 0.7477 (tp) REVERT: A 139 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: A 156 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7339 (tt) REVERT: A 322 GLU cc_start: 0.8307 (tt0) cc_final: 0.7396 (tm-30) REVERT: A 374 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8016 (tm-30) REVERT: A 423 ASN cc_start: 0.8034 (m-40) cc_final: 0.7059 (t0) REVERT: A 488 ARG cc_start: 0.8034 (mtp-110) cc_final: 0.7802 (ptp90) REVERT: A 693 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7367 (mm) REVERT: B 113 LEU cc_start: 0.6418 (OUTLIER) cc_final: 0.6216 (tp) REVERT: B 146 GLU cc_start: 0.8481 (pt0) cc_final: 0.8103 (pt0) REVERT: B 198 ILE cc_start: 0.7972 (mm) cc_final: 0.7575 (mp) REVERT: B 243 CYS cc_start: 0.8946 (t) cc_final: 0.8569 (t) REVERT: B 252 GLU cc_start: 0.8037 (pm20) cc_final: 0.7770 (pm20) REVERT: B 282 THR cc_start: 0.9450 (m) cc_final: 0.8958 (p) REVERT: B 288 TYR cc_start: 0.6679 (m-80) cc_final: 0.6423 (m-80) REVERT: B 382 ASP cc_start: 0.7699 (m-30) cc_final: 0.6694 (t0) REVERT: C 59 ARG cc_start: 0.7681 (ttm110) cc_final: 0.6938 (ptm160) REVERT: C 171 LYS cc_start: 0.8544 (tttm) cc_final: 0.8317 (tttp) REVERT: C 208 GLU cc_start: 0.8807 (pm20) cc_final: 0.8587 (pm20) outliers start: 32 outliers final: 17 residues processed: 176 average time/residue: 0.0936 time to fit residues: 23.6939 Evaluate side-chains 149 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 466 LEU 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 113 LEU 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 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: 1.9990 chunk 34 optimal weight: 0.0470 chunk 66 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.138979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.098888 restraints weight = 16694.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.103249 restraints weight = 9120.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.106285 restraints weight = 6224.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108374 restraints weight = 4814.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.109633 restraints weight = 4052.737| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9956 Z= 0.136 Angle : 0.607 8.115 13475 Z= 0.304 Chirality : 0.042 0.187 1421 Planarity : 0.004 0.065 1765 Dihedral : 6.441 68.664 1423 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.10 % Favored : 94.64 % Rotamer: Outliers : 4.23 % Allowed : 25.30 % Favored : 70.47 % 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: 0.70 (0.25), residues: 1176 helix: 2.22 (0.20), residues: 615 sheet: 0.05 (0.64), residues: 63 loop : -1.88 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 354 TYR 0.020 0.001 TYR A 628 PHE 0.020 0.001 PHE C 153 TRP 0.011 0.001 TRP C 161 HIS 0.004 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 9947) covalent geometry : angle 0.59312 / 0.30 (13452) SS BOND : bond 0.00297 / 0.16 ( 4) SS BOND : angle 2.63613 / 1.43 ( 8) hydrogen bonds : bond 0.04692 / 3.24 ( 495) hydrogen bonds : angle 3.81423 / 2.85 ( 1497) link_NAG-ASN : bond 0.00385 / 0.22 ( 4) link_NAG-ASN : angle 3.80218 / 2.06 ( 12) link_TRANS : bond 0.00046 / 0.03 ( 1) link_TRANS : angle 0.05987 / 0.04 ( 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: 43 poor density : 131 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 139 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: A 156 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7439 (tt) REVERT: A 202 THR cc_start: 0.7230 (m) cc_final: 0.6702 (p) REVERT: A 206 MET cc_start: 0.7803 (tpp) cc_final: 0.7588 (mmm) REVERT: A 322 GLU cc_start: 0.8375 (tt0) cc_final: 0.7666 (tm-30) REVERT: A 323 CYS cc_start: 0.8929 (m) cc_final: 0.7927 (t) REVERT: A 374 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8071 (tm-30) REVERT: A 423 ASN cc_start: 0.7954 (m-40) cc_final: 0.6954 (t0) REVERT: A 479 SER cc_start: 0.6123 (OUTLIER) cc_final: 0.5562 (t) REVERT: A 488 ARG cc_start: 0.8064 (mtp-110) cc_final: 0.7849 (ptp90) REVERT: A 693 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7393 (mm) REVERT: B 113 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6296 (tp) REVERT: B 146 GLU cc_start: 0.8370 (pt0) cc_final: 0.8003 (pt0) REVERT: B 243 CYS cc_start: 0.8960 (t) cc_final: 0.8522 (t) REVERT: B 252 GLU cc_start: 0.8221 (pm20) cc_final: 0.7932 (pm20) REVERT: B 288 TYR cc_start: 0.6831 (m-80) cc_final: 0.6555 (m-80) REVERT: B 382 ASP cc_start: 0.7738 (m-30) cc_final: 0.6789 (t70) REVERT: C 59 ARG cc_start: 0.7697 (ttm110) cc_final: 0.6965 (ptm160) REVERT: C 171 LYS cc_start: 0.8653 (tttm) cc_final: 0.8424 (tttp) REVERT: C 190 ARG cc_start: 0.8107 (mtp180) cc_final: 0.7648 (mmm-85) REVERT: C 208 GLU cc_start: 0.8720 (pm20) cc_final: 0.8491 (pm20) outliers start: 43 outliers final: 30 residues processed: 165 average time/residue: 0.0867 time to fit residues: 20.9725 Evaluate side-chains 160 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 125 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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 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 113 LEU Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 380 MET 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: 2.9990 chunk 57 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 53 optimal weight: 0.0040 chunk 35 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.139564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098491 restraints weight = 16524.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.102862 restraints weight = 9183.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.105926 restraints weight = 6292.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.107987 restraints weight = 4877.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.109397 restraints weight = 4118.094| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9956 Z= 0.122 Angle : 0.585 9.082 13475 Z= 0.291 Chirality : 0.041 0.165 1421 Planarity : 0.004 0.066 1765 Dihedral : 5.829 59.041 1423 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.42 % Favored : 95.32 % Rotamer: Outliers : 4.63 % Allowed : 25.30 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.25), residues: 1176 helix: 2.29 (0.20), residues: 614 sheet: -0.43 (0.62), residues: 71 loop : -1.75 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 471 TYR 0.020 0.001 TYR A 628 PHE 0.017 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 0.00273 / 0.12 ( 9947) covalent geometry : angle 0.57346 / 0.29 (13452) SS BOND : bond 0.00309 / 0.16 ( 4) SS BOND : angle 2.54015 / 1.39 ( 8) hydrogen bonds : bond 0.04346 / 3.00 ( 495) hydrogen bonds : angle 3.71857 / 2.77 ( 1497) link_NAG-ASN : bond 0.00498 / 0.30 ( 4) link_NAG-ASN : angle 3.40796 / 1.94 ( 12) link_TRANS : bond 0.00025 / 0.02 ( 1) link_TRANS : angle 0.08193 / 0.05 ( 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 181 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 134 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9030 (mmm) cc_final: 0.8710 (mpp) REVERT: A 139 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: A 156 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7428 (tt) REVERT: A 322 GLU cc_start: 0.8378 (tt0) cc_final: 0.7780 (tm-30) REVERT: A 323 CYS cc_start: 0.8892 (m) cc_final: 0.7843 (t) REVERT: A 423 ASN cc_start: 0.8086 (m-40) cc_final: 0.7749 (m110) REVERT: A 488 ARG cc_start: 0.8047 (mtp-110) cc_final: 0.7744 (ptp90) REVERT: A 600 CYS cc_start: 0.7965 (m) cc_final: 0.7724 (m) REVERT: A 693 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7369 (mm) REVERT: B 146 GLU cc_start: 0.8385 (pt0) cc_final: 0.8027 (pt0) REVERT: B 243 CYS cc_start: 0.8930 (t) cc_final: 0.8424 (t) REVERT: B 252 GLU cc_start: 0.8281 (pm20) cc_final: 0.7986 (pm20) REVERT: B 382 ASP cc_start: 0.7771 (m-30) cc_final: 0.6821 (t70) REVERT: C 171 LYS cc_start: 0.8633 (tttm) cc_final: 0.8400 (tttp) REVERT: C 190 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7351 (mmm160) REVERT: C 208 GLU cc_start: 0.8750 (pm20) cc_final: 0.8547 (pm20) outliers start: 47 outliers final: 31 residues processed: 170 average time/residue: 0.0876 time to fit residues: 21.9341 Evaluate side-chains 158 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 124 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 120 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 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 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 253 ILE Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 277 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 347 LEU 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 113 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 213 ILE 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: 10.0000 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.140427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.104671 restraints weight = 17260.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108248 restraints weight = 10450.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109257 restraints weight = 7296.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110045 restraints weight = 6445.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110518 restraints weight = 6018.276| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9956 Z= 0.123 Angle : 0.589 9.683 13475 Z= 0.293 Chirality : 0.041 0.159 1421 Planarity : 0.004 0.067 1765 Dihedral : 5.298 48.152 1423 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.68 % Favored : 95.07 % Rotamer: Outliers : 5.22 % Allowed : 25.39 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.25), residues: 1176 helix: 2.29 (0.20), residues: 615 sheet: -0.40 (0.62), residues: 71 loop : -1.77 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 666 TYR 0.020 0.001 TYR A 628 PHE 0.018 0.001 PHE C 153 TRP 0.012 0.001 TRP C 161 HIS 0.003 0.001 HIS C 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 9947) covalent geometry : angle 0.57671 / 0.29 (13452) SS BOND : bond 0.00442 / 0.25 ( 4) SS BOND : angle 3.01525 / 1.62 ( 8) hydrogen bonds : bond 0.04312 / 2.99 ( 495) hydrogen bonds : angle 3.71268 / 2.77 ( 1497) link_NAG-ASN : bond 0.00372 / 0.21 ( 4) link_NAG-ASN : angle 3.30460 / 1.92 ( 12) link_TRANS : bond 0.00020 / 0.01 ( 1) link_TRANS : angle 0.04504 / 0.02 ( 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 180 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 0.382 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8848 (mmm) cc_final: 0.8498 (mpp) REVERT: A 139 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: A 156 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7237 (tt) REVERT: A 322 GLU cc_start: 0.8443 (tt0) cc_final: 0.7797 (tm-30) REVERT: A 323 CYS cc_start: 0.9012 (m) cc_final: 0.7885 (t) REVERT: A 423 ASN cc_start: 0.8234 (m-40) cc_final: 0.7820 (m110) REVERT: A 488 ARG cc_start: 0.8035 (mtp-110) cc_final: 0.7650 (ptp90) REVERT: A 693 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6999 (mm) REVERT: B 146 GLU cc_start: 0.8406 (pt0) cc_final: 0.7990 (pt0) REVERT: B 180 MET cc_start: 0.6613 (ttt) cc_final: 0.5497 (tpt) REVERT: B 243 CYS cc_start: 0.8893 (t) cc_final: 0.8309 (t) REVERT: B 252 GLU cc_start: 0.8307 (pm20) cc_final: 0.7936 (pm20) REVERT: B 382 ASP cc_start: 0.8013 (m-30) cc_final: 0.6986 (t70) REVERT: C 48 PHE cc_start: 0.7923 (m-80) cc_final: 0.7530 (m-10) REVERT: C 59 ARG cc_start: 0.8201 (ptp-110) cc_final: 0.7790 (ptp-110) REVERT: C 171 LYS cc_start: 0.8078 (tttm) cc_final: 0.7869 (tttp) REVERT: C 190 ARG cc_start: 0.8151 (mtp180) cc_final: 0.7300 (mmm160) REVERT: C 208 GLU cc_start: 0.8795 (pm20) cc_final: 0.8564 (pm20) outliers start: 53 outliers final: 38 residues processed: 168 average time/residue: 0.0806 time to fit residues: 20.2379 Evaluate side-chains 163 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 107 LEU Chi-restraints excluded: chain A residue 120 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 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 52 LEU Chi-restraints excluded: chain B residue 253 ILE 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 294 VAL Chi-restraints excluded: chain B residue 347 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 113 THR 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 182 VAL Chi-restraints excluded: chain C residue 187 THR 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: 1.9990 chunk 59 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 14 optimal weight: 8.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.139163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102807 restraints weight = 17178.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108545 restraints weight = 10380.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108598 restraints weight = 7114.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.109082 restraints weight = 5952.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109573 restraints weight = 5555.871| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9956 Z= 0.140 Angle : 0.612 10.243 13475 Z= 0.305 Chirality : 0.041 0.175 1421 Planarity : 0.004 0.069 1765 Dihedral : 5.044 46.278 1423 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.93 % Favored : 94.81 % Rotamer: Outliers : 4.82 % Allowed : 25.98 % Favored : 69.19 % 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: 0.74 (0.25), residues: 1176 helix: 2.24 (0.20), residues: 616 sheet: -0.25 (0.61), residues: 73 loop : -1.82 (0.27), residues: 487 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 0.020 0.001 PHE C 153 TRP 0.011 0.001 TRP C 161 HIS 0.003 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 9947) covalent geometry : angle 0.60182 / 0.30 (13452) SS BOND : bond 0.00317 / 0.17 ( 4) SS BOND : angle 2.81955 / 1.51 ( 8) hydrogen bonds : bond 0.04600 / 3.18 ( 495) hydrogen bonds : angle 3.81572 / 2.84 ( 1497) link_NAG-ASN : bond 0.00312 / 0.18 ( 4) link_NAG-ASN : angle 3.08568 / 1.76 ( 12) link_TRANS : bond 0.00013 / 0.01 ( 1) link_TRANS : angle 0.06476 / 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 175 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 139 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: A 156 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7239 (tt) REVERT: A 286 LEU cc_start: 0.8171 (mt) cc_final: 0.7863 (mp) REVERT: A 322 GLU cc_start: 0.8450 (tt0) cc_final: 0.7799 (tm-30) REVERT: A 323 CYS cc_start: 0.9051 (m) cc_final: 0.7891 (t) REVERT: A 471 ARG cc_start: 0.5912 (mtm-85) cc_final: 0.5270 (mtm-85) REVERT: A 488 ARG cc_start: 0.8039 (mtp-110) cc_final: 0.7643 (ptp90) REVERT: A 630 THR cc_start: 0.7734 (OUTLIER) cc_final: 0.7524 (m) REVERT: B 146 GLU cc_start: 0.8434 (pt0) cc_final: 0.8012 (pt0) REVERT: B 243 CYS cc_start: 0.8907 (t) cc_final: 0.8280 (t) REVERT: B 252 GLU cc_start: 0.8303 (pm20) cc_final: 0.7940 (pm20) REVERT: B 382 ASP cc_start: 0.8007 (m-30) cc_final: 0.7008 (t70) REVERT: C 59 ARG cc_start: 0.8174 (ptp-110) cc_final: 0.7819 (ptp-110) REVERT: C 171 LYS cc_start: 0.8117 (tttm) cc_final: 0.7871 (tttp) REVERT: C 190 ARG cc_start: 0.8055 (mtp180) cc_final: 0.7218 (mmm160) outliers start: 49 outliers final: 37 residues processed: 162 average time/residue: 0.0858 time to fit residues: 20.3783 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 : 0.366 ------------------------------------------------------------------------------- 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 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 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 630 THR Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 253 ILE 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 294 VAL Chi-restraints excluded: chain B residue 347 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 176 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 2 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 114 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 36 optimal weight: 0.0970 chunk 60 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.140655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.099635 restraints weight = 16674.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104172 restraints weight = 8914.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.107290 restraints weight = 6005.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109379 restraints weight = 4633.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.110646 restraints weight = 3900.069| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9956 Z= 0.108 Angle : 0.601 10.872 13475 Z= 0.293 Chirality : 0.040 0.172 1421 Planarity : 0.004 0.068 1765 Dihedral : 4.832 46.606 1423 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.42 % Favored : 95.32 % Rotamer: Outliers : 3.94 % Allowed : 27.26 % 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: 0.77 (0.25), residues: 1176 helix: 2.23 (0.20), residues: 623 sheet: -0.20 (0.60), residues: 73 loop : -1.83 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 666 TYR 0.018 0.001 TYR A 628 PHE 0.018 0.001 PHE C 100 TRP 0.010 0.001 TRP C 161 HIS 0.003 0.000 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 9947) covalent geometry : angle 0.59088 / 0.29 (13452) SS BOND : bond 0.00316 / 0.17 ( 4) SS BOND : angle 2.57537 / 1.40 ( 8) hydrogen bonds : bond 0.03844 / 2.66 ( 495) hydrogen bonds : angle 3.66821 / 2.74 ( 1497) link_NAG-ASN : bond 0.00379 / 0.21 ( 4) link_NAG-ASN : angle 3.05620 / 1.70 ( 12) link_TRANS : bond 0.00004 / 0.00 ( 1) link_TRANS : angle 0.04434 / 0.03 ( 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 169 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.6407 (OUTLIER) cc_final: 0.5772 (mmm) REVERT: A 88 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7478 (p0) REVERT: A 139 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: A 156 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7379 (tt) REVERT: A 218 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: A 286 LEU cc_start: 0.8484 (mt) cc_final: 0.8201 (mp) REVERT: A 322 GLU cc_start: 0.8377 (tt0) cc_final: 0.7820 (tm-30) REVERT: A 323 CYS cc_start: 0.8917 (m) cc_final: 0.7805 (t) REVERT: A 471 ARG cc_start: 0.6086 (mtm-85) cc_final: 0.5414 (mtm-85) REVERT: A 488 ARG cc_start: 0.8041 (mtp-110) cc_final: 0.7701 (ptp90) REVERT: B 146 GLU cc_start: 0.8402 (pt0) cc_final: 0.8021 (pt0) REVERT: B 180 MET cc_start: 0.6577 (ttt) cc_final: 0.5515 (tpt) REVERT: B 243 CYS cc_start: 0.8855 (t) cc_final: 0.8220 (t) REVERT: B 252 GLU cc_start: 0.8315 (pm20) cc_final: 0.7980 (pm20) REVERT: B 382 ASP cc_start: 0.7752 (m-30) cc_final: 0.6914 (t70) REVERT: C 48 PHE cc_start: 0.7875 (m-10) cc_final: 0.7576 (m-10) REVERT: C 59 ARG cc_start: 0.8038 (ptp-110) cc_final: 0.7812 (ptp-110) REVERT: C 171 LYS cc_start: 0.8580 (tttm) cc_final: 0.8365 (tttm) REVERT: C 190 ARG cc_start: 0.7927 (mtp180) cc_final: 0.7218 (mmm160) outliers start: 40 outliers final: 27 residues processed: 159 average time/residue: 0.0839 time to fit residues: 19.7875 Evaluate side-chains 152 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 88 ASP Chi-restraints excluded: chain A residue 120 LEU 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 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 B residue 253 ILE Chi-restraints excluded: chain B residue 284 VAL 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 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 187 THR 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: 3.9990 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.2980 chunk 80 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 30 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.142528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.102576 restraints weight = 17089.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106821 restraints weight = 9454.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.108290 restraints weight = 6044.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.111353 restraints weight = 5385.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.111435 restraints weight = 4690.897| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4075 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= 0.110 Angle : 0.614 11.158 13475 Z= 0.299 Chirality : 0.040 0.168 1421 Planarity : 0.004 0.068 1765 Dihedral : 4.629 45.705 1423 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.25 % Favored : 95.49 % Rotamer: Outliers : 3.54 % Allowed : 27.85 % 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: 0.80 (0.25), residues: 1176 helix: 2.22 (0.20), residues: 628 sheet: 0.05 (0.58), residues: 73 loop : -1.86 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 666 TYR 0.020 0.001 TYR A 628 PHE 0.012 0.001 PHE C 100 TRP 0.008 0.001 TRP C 161 HIS 0.004 0.001 HIS A 565 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9947) covalent geometry : angle 0.60503 / 0.30 (13452) SS BOND : bond 0.00312 / 0.17 ( 4) SS BOND : angle 2.56031 / 1.40 ( 8) hydrogen bonds : bond 0.03808 / 2.65 ( 495) hydrogen bonds : angle 3.64051 / 2.72 ( 1497) link_NAG-ASN : bond 0.00389 / 0.22 ( 4) link_NAG-ASN : angle 2.90210 / 1.60 ( 12) link_TRANS : bond 0.00004 / 0.00 ( 1) link_TRANS : angle 0.04536 / 0.02 ( 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 164 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 128 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LEU cc_start: 0.7806 (tt) cc_final: 0.7527 (tp) REVERT: A 139 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: A 156 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7341 (tt) REVERT: A 218 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: A 286 LEU cc_start: 0.8502 (mt) cc_final: 0.8220 (mp) REVERT: A 322 GLU cc_start: 0.8389 (tt0) cc_final: 0.7835 (tm-30) REVERT: A 471 ARG cc_start: 0.5974 (mtm-85) cc_final: 0.5513 (mtm-85) REVERT: A 482 GLU cc_start: 0.8642 (pm20) cc_final: 0.8427 (pm20) REVERT: A 488 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.7689 (ptp90) REVERT: A 600 CYS cc_start: 0.7456 (m) cc_final: 0.6828 (t) REVERT: B 146 GLU cc_start: 0.8264 (pt0) cc_final: 0.7876 (pt0) REVERT: B 180 MET cc_start: 0.6586 (ttt) cc_final: 0.5526 (tpt) REVERT: B 243 CYS cc_start: 0.8822 (t) cc_final: 0.8195 (t) REVERT: B 252 GLU cc_start: 0.8313 (pm20) cc_final: 0.7973 (pm20) REVERT: B 382 ASP cc_start: 0.7761 (m-30) cc_final: 0.6919 (t70) REVERT: C 59 ARG cc_start: 0.8045 (ptp-110) cc_final: 0.7725 (ptp-110) REVERT: C 190 ARG cc_start: 0.7970 (mtp180) cc_final: 0.7583 (mmm-85) outliers start: 36 outliers final: 26 residues processed: 152 average time/residue: 0.0895 time to fit residues: 19.8438 Evaluate side-chains 151 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 122 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 597 THR Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 284 VAL 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 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 187 THR 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: 2.9990 chunk 101 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 39 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.0000 chunk 55 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.5364 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.142183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.102566 restraints weight = 16657.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106976 restraints weight = 9056.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.109966 restraints weight = 6152.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112111 restraints weight = 4787.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113394 restraints weight = 4024.063| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4159 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= 0.109 Angle : 0.624 11.947 13475 Z= 0.302 Chirality : 0.040 0.193 1421 Planarity : 0.004 0.069 1765 Dihedral : 4.468 45.474 1423 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.42 % Favored : 95.32 % Rotamer: Outliers : 3.15 % Allowed : 28.35 % Favored : 68.50 % 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: 2.25 (0.20), residues: 628 sheet: 0.12 (0.57), residues: 71 loop : -1.84 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 666 TYR 0.015 0.001 TYR A 628 PHE 0.028 0.001 PHE C 100 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 0.00238 / 0.11 ( 9947) covalent geometry : angle 0.61600 / 0.30 (13452) SS BOND : bond 0.00303 / 0.17 ( 4) SS BOND : angle 2.50072 / 1.37 ( 8) hydrogen bonds : bond 0.03648 / 2.54 ( 495) hydrogen bonds : angle 3.60632 / 2.70 ( 1497) link_NAG-ASN : bond 0.00385 / 0.22 ( 4) link_NAG-ASN : angle 2.78097 / 1.52 ( 12) link_TRANS : bond 0.00007 / 0.00 ( 1) link_TRANS : angle 0.02242 / 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 162 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 MET cc_start: 0.8976 (mmm) cc_final: 0.8565 (mpp) REVERT: A 73 LEU cc_start: 0.7727 (tt) cc_final: 0.7458 (tp) REVERT: A 139 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: A 156 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7311 (tt) REVERT: A 198 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8616 (mmtt) REVERT: A 202 THR cc_start: 0.7083 (m) cc_final: 0.6555 (p) REVERT: A 218 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: A 256 ASN cc_start: 0.9384 (OUTLIER) cc_final: 0.9007 (m-40) REVERT: A 286 LEU cc_start: 0.8408 (mt) cc_final: 0.8110 (mp) REVERT: A 322 GLU cc_start: 0.8387 (tt0) cc_final: 0.7825 (tm-30) REVERT: A 471 ARG cc_start: 0.6067 (mtm-85) cc_final: 0.5578 (mtm-85) REVERT: A 488 ARG cc_start: 0.8028 (mtp-110) cc_final: 0.7712 (ptp90) REVERT: A 600 CYS cc_start: 0.7450 (m) cc_final: 0.6824 (t) REVERT: A 689 GLN cc_start: 0.7532 (mm-40) cc_final: 0.7270 (mm-40) REVERT: B 146 GLU cc_start: 0.8236 (pt0) cc_final: 0.7832 (pt0) REVERT: B 180 MET cc_start: 0.6560 (ttt) cc_final: 0.5519 (tpt) REVERT: B 191 LEU cc_start: 0.9019 (mp) cc_final: 0.8548 (tt) REVERT: B 207 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8819 (tm-30) REVERT: B 243 CYS cc_start: 0.8723 (t) cc_final: 0.8087 (t) REVERT: B 252 GLU cc_start: 0.8239 (pm20) cc_final: 0.7902 (pm20) REVERT: B 382 ASP cc_start: 0.7718 (m-30) cc_final: 0.6915 (t70) REVERT: C 59 ARG cc_start: 0.8033 (ptp-110) cc_final: 0.7727 (ptp-110) REVERT: C 190 ARG cc_start: 0.7902 (mtp180) cc_final: 0.7551 (mmm-85) outliers start: 32 outliers final: 24 residues processed: 153 average time/residue: 0.0928 time to fit residues: 20.3922 Evaluate side-chains 154 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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 256 ASN 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 696 MET 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 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 187 THR 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: 0.7980 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 0.0030 chunk 47 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.141747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.100633 restraints weight = 16766.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105157 restraints weight = 8999.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108287 restraints weight = 6091.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.110419 restraints weight = 4707.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.111716 restraints weight = 3961.184| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9956 Z= 0.115 Angle : 0.638 11.692 13475 Z= 0.309 Chirality : 0.041 0.186 1421 Planarity : 0.004 0.069 1765 Dihedral : 4.429 44.944 1423 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.25 % Favored : 95.49 % Rotamer: Outliers : 3.15 % Allowed : 27.95 % Favored : 68.90 % 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: 0.89 (0.25), residues: 1176 helix: 2.34 (0.20), residues: 620 sheet: 0.11 (0.57), residues: 71 loop : -1.80 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 666 TYR 0.015 0.001 TYR A 628 PHE 0.028 0.001 PHE C 100 TRP 0.007 0.001 TRP C 161 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 9947) covalent geometry : angle 0.63111 / 0.31 (13452) SS BOND : bond 0.00304 / 0.17 ( 4) SS BOND : angle 2.49330 / 1.37 ( 8) hydrogen bonds : bond 0.03770 / 2.62 ( 495) hydrogen bonds : angle 3.63156 / 2.72 ( 1497) link_NAG-ASN : bond 0.00361 / 0.21 ( 4) link_NAG-ASN : angle 2.64643 / 1.45 ( 12) link_TRANS : bond 0.00026 / 0.02 ( 1) link_TRANS : angle 0.03490 / 0.02 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1670.81 seconds wall clock time: 29 minutes 43.12 seconds (1783.12 seconds total)