Starting phenix.real_space_refine on Tue May 13 04:32:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kc9_37097/05_2025/8kc9_37097.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kc9_37097/05_2025/8kc9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kc9_37097/05_2025/8kc9_37097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kc9_37097/05_2025/8kc9_37097.map" model { file = "/net/cci-nas-00/data/ceres_data/8kc9_37097/05_2025/8kc9_37097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kc9_37097/05_2025/8kc9_37097.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'SAR:plan-1': 1, 'ABA:plan-1': 1, 'BMT:plan-1': 1, 'MVA:plan-1': 1, 'MLE:plan-1': 4} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' FE': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.55, per 1000 atoms: 0.57 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: 2.98 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.07 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: 2.59 Time building geometry restraints manager: 3.17 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 2.340 nonbonded pdb=" O MET B 180 " pdb=" ND2 ASN B 184 " model vdw 2.198 3.120 nonbonded pdb=" O GLU A 351 " pdb=" OG SER A 355 " model vdw 2.220 3.040 nonbonded pdb=" O TYR B 187 " pdb=" OG SER B 190 " model vdw 2.244 3.040 ... (remaining 73549 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.600 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6197 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.001 TRP A 91 HIS 0.003 0.000 HIS B 266 PHE 0.017 0.001 PHE C 153 TYR 0.026 0.001 TYR B 267 ARG 0.003 0.000 ARG C 190 Details of bonding type rmsd link_TRANS : bond 0.00081 ( 1) link_TRANS : angle 1.67063 ( 3) link_NAG-ASN : bond 0.00457 ( 4) link_NAG-ASN : angle 2.30289 ( 12) hydrogen bonds : bond 0.17221 ( 495) hydrogen bonds : angle 5.70491 ( 1497) SS BOND : bond 0.00255 ( 4) SS BOND : angle 2.91884 ( 8) covalent geometry : bond 0.00387 ( 9947) covalent geometry : angle 0.79472 (13452) *********************** 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 : 0.990 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: 0.5807 (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: 0.8598 (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: 0.7346 (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: 0.2391 time to fit residues: 79.8050 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 : 1.066 ------------------------------------------------------------------------------- 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 100 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS ** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.144054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.101990 restraints weight = 16890.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.106887 restraints weight = 9179.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.110319 restraints weight = 6229.714| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9956 Z= 0.128 Angle : 0.639 9.295 13475 Z= 0.321 Chirality : 0.042 0.315 1421 Planarity : 0.005 0.051 1765 Dihedral : 8.162 95.631 1431 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.27 % Favored : 94.47 % Rotamer: Outliers : 2.85 % Allowed : 23.13 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.25), residues: 1176 helix: 2.27 (0.21), residues: 623 sheet: -0.24 (0.63), residues: 70 loop : -1.99 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 345 HIS 0.005 0.001 HIS A 227 PHE 0.020 0.001 PHE C 153 TYR 0.027 0.001 TYR B 267 ARG 0.008 0.000 ARG A 214 Details of bonding type rmsd link_TRANS : bond 0.00030 ( 1) link_TRANS : angle 0.17203 ( 3) link_NAG-ASN : bond 0.00450 ( 4) link_NAG-ASN : angle 2.10746 ( 12) hydrogen bonds : bond 0.04794 ( 495) hydrogen bonds : angle 3.96602 ( 1497) SS BOND : bond 0.00262 ( 4) SS BOND : angle 2.38433 ( 8) covalent geometry : bond 0.00276 ( 9947) covalent geometry : angle 0.63350 (13452) *********************** 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 192 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7536 (t0) cc_final: 0.7132 (t0) REVERT: A 156 ILE cc_start: 0.7930 (tp) cc_final: 0.7387 (tt) REVERT: A 202 THR cc_start: 0.7260 (m) cc_final: 0.6743 (p) REVERT: A 208 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6998 (tp30) REVERT: A 322 GLU cc_start: 0.8281 (tt0) cc_final: 0.7349 (tm-30) REVERT: A 323 CYS cc_start: 0.8198 (t) cc_final: 0.7465 (t) REVERT: A 374 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8002 (tm-30) REVERT: A 423 ASN cc_start: 0.7871 (m-40) cc_final: 0.7251 (p0) REVERT: A 487 GLN cc_start: 0.8524 (mt0) cc_final: 0.8057 (tp-100) REVERT: A 488 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7735 (ptp90) REVERT: A 600 CYS cc_start: 0.7689 (m) cc_final: 0.6531 (t) REVERT: B 146 GLU cc_start: 0.8699 (pt0) cc_final: 0.7397 (pt0) REVERT: B 198 ILE cc_start: 0.7979 (mm) cc_final: 0.7545 (mp) REVERT: B 199 LYS cc_start: 0.8239 (mttt) cc_final: 0.7903 (mmtm) REVERT: B 202 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 242 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7280 (tm-30) REVERT: B 252 GLU cc_start: 0.7823 (pm20) cc_final: 0.7605 (pm20) REVERT: B 273 CYS cc_start: 0.7997 (t) cc_final: 0.7775 (m) REVERT: B 329 LYS cc_start: 0.9361 (mppt) cc_final: 0.9092 (mmtm) REVERT: B 382 ASP cc_start: 0.7732 (m-30) cc_final: 0.6725 (p0) REVERT: C 59 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7069 (ptm160) REVERT: C 174 GLU cc_start: 0.8023 (tp30) cc_final: 0.7798 (tp30) REVERT: C 208 GLU cc_start: 0.8642 (pm20) cc_final: 0.8441 (pm20) outliers start: 29 outliers final: 11 residues processed: 185 average time/residue: 0.2016 time to fit residues: 52.4737 Evaluate side-chains 138 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 225 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 277 CYS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 42 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.133928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096804 restraints weight = 16936.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102136 restraints weight = 9960.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102523 restraints weight = 5768.690| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9956 Z= 0.255 Angle : 0.746 12.099 13475 Z= 0.381 Chirality : 0.047 0.338 1421 Planarity : 0.005 0.067 1765 Dihedral : 6.974 75.990 1423 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.61 % Favored : 94.13 % Rotamer: Outliers : 5.91 % Allowed : 23.03 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1176 helix: 1.97 (0.20), residues: 619 sheet: -0.58 (0.69), residues: 58 loop : -1.98 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 161 HIS 0.007 0.001 HIS C 132 PHE 0.028 0.002 PHE C 153 TYR 0.024 0.002 TYR B 267 ARG 0.005 0.001 ARG A 554 Details of bonding type rmsd link_TRANS : bond 0.00006 ( 1) link_TRANS : angle 0.22715 ( 3) link_NAG-ASN : bond 0.00956 ( 4) link_NAG-ASN : angle 4.91979 ( 12) hydrogen bonds : bond 0.06595 ( 495) hydrogen bonds : angle 4.46772 ( 1497) SS BOND : bond 0.00538 ( 4) SS BOND : angle 3.19593 ( 8) covalent geometry : bond 0.00603 ( 9947) covalent geometry : angle 0.72742 (13452) *********************** 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 193 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 133 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.9195 (mmm) cc_final: 0.8877 (mmm) REVERT: A 156 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.7669 (tt) REVERT: A 202 THR cc_start: 0.7344 (m) cc_final: 0.6825 (p) REVERT: A 322 GLU cc_start: 0.8316 (tt0) cc_final: 0.7682 (tm-30) REVERT: A 323 CYS cc_start: 0.8313 (t) cc_final: 0.7527 (t) REVERT: A 347 MET cc_start: 0.8514 (tpp) cc_final: 0.8055 (mmp) REVERT: A 374 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8114 (tm-30) REVERT: A 423 ASN cc_start: 0.8052 (m-40) cc_final: 0.7697 (m-40) REVERT: A 488 ARG cc_start: 0.8249 (mtp-110) cc_final: 0.7992 (ptp90) REVERT: B 113 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6594 (tt) REVERT: B 146 GLU cc_start: 0.8556 (pt0) cc_final: 0.8260 (pt0) REVERT: B 198 ILE cc_start: 0.7960 (mm) cc_final: 0.7584 (mp) REVERT: B 252 GLU cc_start: 0.8236 (pm20) cc_final: 0.7969 (pm20) REVERT: B 288 TYR cc_start: 0.7069 (m-80) cc_final: 0.6824 (m-80) REVERT: B 382 ASP cc_start: 0.7905 (m-30) cc_final: 0.6975 (t0) REVERT: C 59 ARG cc_start: 0.7638 (ttm110) cc_final: 0.6743 (ptm160) REVERT: C 208 GLU cc_start: 0.8744 (pm20) cc_final: 0.8494 (pm20) outliers start: 60 outliers final: 37 residues processed: 177 average time/residue: 0.2133 time to fit residues: 54.1825 Evaluate side-chains 156 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 156 ILE Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 686 ASP Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 181 MET 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 284 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 46 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 176 MET Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 189 SER 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 89 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.139806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098284 restraints weight = 16283.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102711 restraints weight = 8921.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.105763 restraints weight = 6085.618| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9956 Z= 0.119 Angle : 0.613 11.527 13475 Z= 0.303 Chirality : 0.041 0.242 1421 Planarity : 0.004 0.065 1765 Dihedral : 6.167 66.965 1423 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.51 % Favored : 95.24 % Rotamer: Outliers : 3.64 % Allowed : 26.77 % Favored : 69.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1176 helix: 2.16 (0.20), residues: 612 sheet: -0.67 (0.66), residues: 62 loop : -1.81 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 161 HIS 0.003 0.001 HIS A 565 PHE 0.015 0.001 PHE C 153 TYR 0.029 0.001 TYR B 267 ARG 0.003 0.000 ARG A 354 Details of bonding type rmsd link_TRANS : bond 0.00021 ( 1) link_TRANS : angle 0.11794 ( 3) link_NAG-ASN : bond 0.00926 ( 4) link_NAG-ASN : angle 5.02372 ( 12) hydrogen bonds : bond 0.04615 ( 495) hydrogen bonds : angle 3.89208 ( 1497) SS BOND : bond 0.00347 ( 4) SS BOND : angle 2.60534 ( 8) covalent geometry : bond 0.00258 ( 9947) covalent geometry : angle 0.59130 (13452) *********************** 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 173 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.7790 (tt) cc_final: 0.7525 (tp) REVERT: A 156 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7390 (tt) REVERT: A 322 GLU cc_start: 0.8313 (tt0) cc_final: 0.7717 (tm-30) REVERT: A 323 CYS cc_start: 0.8331 (t) cc_final: 0.7547 (t) REVERT: A 334 ASP cc_start: 0.7847 (t0) cc_final: 0.7623 (t0) REVERT: A 374 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8082 (tm-30) REVERT: A 423 ASN cc_start: 0.7957 (m-40) cc_final: 0.7574 (m110) REVERT: A 479 SER cc_start: 0.5918 (OUTLIER) cc_final: 0.5409 (t) REVERT: A 488 ARG cc_start: 0.8039 (mtp-110) cc_final: 0.7720 (ptp90) REVERT: B 146 GLU cc_start: 0.8447 (pt0) cc_final: 0.8094 (pt0) REVERT: B 243 CYS cc_start: 0.8902 (t) cc_final: 0.8355 (t) REVERT: B 252 GLU cc_start: 0.8230 (pm20) cc_final: 0.7931 (pm20) REVERT: B 288 TYR cc_start: 0.7106 (m-80) cc_final: 0.6904 (m-80) REVERT: B 382 ASP cc_start: 0.7824 (m-30) cc_final: 0.6831 (t70) REVERT: C 190 ARG cc_start: 0.7945 (mtp180) cc_final: 0.7237 (mmm160) REVERT: C 208 GLU cc_start: 0.8768 (pm20) cc_final: 0.8502 (pm20) outliers start: 37 outliers final: 25 residues processed: 164 average time/residue: 0.1930 time to fit residues: 45.8003 Evaluate side-chains 149 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 120 LEU Chi-restraints excluded: chain A residue 123 CYS 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 246 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 84 CYS Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 347 LEU 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 176 MET 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 31 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.093164 restraints weight = 17626.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.096479 restraints weight = 10388.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097831 restraints weight = 6907.195| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9956 Z= 0.276 Angle : 0.745 11.199 13475 Z= 0.379 Chirality : 0.047 0.286 1421 Planarity : 0.005 0.068 1765 Dihedral : 6.129 57.886 1423 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.78 % Favored : 93.96 % Rotamer: Outliers : 5.41 % Allowed : 25.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1176 helix: 1.82 (0.20), residues: 619 sheet: -1.04 (0.64), residues: 66 loop : -1.90 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 161 HIS 0.008 0.001 HIS C 132 PHE 0.027 0.002 PHE C 153 TYR 0.028 0.002 TYR B 267 ARG 0.005 0.001 ARG A 76 Details of bonding type rmsd link_TRANS : bond 0.00083 ( 1) link_TRANS : angle 0.57971 ( 3) link_NAG-ASN : bond 0.00796 ( 4) link_NAG-ASN : angle 4.90509 ( 12) hydrogen bonds : bond 0.06454 ( 495) hydrogen bonds : angle 4.43911 ( 1497) SS BOND : bond 0.00340 ( 4) SS BOND : angle 3.12257 ( 8) covalent geometry : bond 0.00650 ( 9947) covalent geometry : angle 0.72656 (13452) *********************** 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 176 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 121 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 156 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7608 (tt) REVERT: A 286 LEU cc_start: 0.8537 (mt) cc_final: 0.8264 (mp) REVERT: A 322 GLU cc_start: 0.8421 (tt0) cc_final: 0.7735 (tm-30) REVERT: A 323 CYS cc_start: 0.8485 (t) cc_final: 0.7714 (t) REVERT: A 423 ASN cc_start: 0.7923 (m-40) cc_final: 0.7675 (m110) REVERT: A 488 ARG cc_start: 0.8155 (mtp-110) cc_final: 0.7834 (ptp90) REVERT: A 560 TYR cc_start: 0.8609 (m-80) cc_final: 0.8387 (m-80) REVERT: B 27 GLN cc_start: 0.7918 (pm20) cc_final: 0.6846 (pp30) REVERT: B 113 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6433 (tt) REVERT: B 146 GLU cc_start: 0.8668 (pt0) cc_final: 0.8386 (pt0) REVERT: B 243 CYS cc_start: 0.9023 (t) cc_final: 0.8437 (t) REVERT: B 252 GLU cc_start: 0.8343 (pm20) cc_final: 0.8025 (pm20) REVERT: B 288 TYR cc_start: 0.7289 (m-80) cc_final: 0.7088 (m-80) REVERT: B 382 ASP cc_start: 0.7929 (m-30) cc_final: 0.7010 (t70) REVERT: C 126 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8344 (mm-30) REVERT: C 190 ARG cc_start: 0.8049 (mtp180) cc_final: 0.7381 (mmm160) outliers start: 55 outliers final: 44 residues processed: 163 average time/residue: 0.1869 time to fit residues: 44.9177 Evaluate side-chains 163 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 156 ILE 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 246 CYS Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 686 ASP 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 170 THR Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 231 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 301 LEU 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 46 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 178 VAL Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 189 SER 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 111 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN B 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.138677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.097522 restraints weight = 16532.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101889 restraints weight = 9058.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.104940 restraints weight = 6179.094| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9956 Z= 0.116 Angle : 0.615 11.701 13475 Z= 0.303 Chirality : 0.041 0.227 1421 Planarity : 0.004 0.067 1765 Dihedral : 5.451 47.467 1423 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.91 % Favored : 95.83 % Rotamer: Outliers : 4.04 % Allowed : 27.66 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1176 helix: 2.16 (0.20), residues: 613 sheet: -0.55 (0.62), residues: 71 loop : -1.75 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 161 HIS 0.003 0.001 HIS C 94 PHE 0.014 0.001 PHE C 153 TYR 0.027 0.001 TYR B 267 ARG 0.002 0.000 ARG A 666 Details of bonding type rmsd link_TRANS : bond 0.00002 ( 1) link_TRANS : angle 0.19897 ( 3) link_NAG-ASN : bond 0.00901 ( 4) link_NAG-ASN : angle 5.27488 ( 12) hydrogen bonds : bond 0.04408 ( 495) hydrogen bonds : angle 3.84454 ( 1497) SS BOND : bond 0.00351 ( 4) SS BOND : angle 3.14849 ( 8) covalent geometry : bond 0.00250 ( 9947) covalent geometry : angle 0.59022 (13452) *********************** 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 173 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 132 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 73 LEU cc_start: 0.7854 (tt) cc_final: 0.7647 (tp) REVERT: A 156 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7396 (tt) REVERT: A 286 LEU cc_start: 0.8479 (mt) cc_final: 0.8171 (mp) REVERT: A 322 GLU cc_start: 0.8304 (tt0) cc_final: 0.7802 (tm-30) REVERT: A 323 CYS cc_start: 0.8311 (t) cc_final: 0.7518 (t) REVERT: A 423 ASN cc_start: 0.8084 (m-40) cc_final: 0.7756 (m110) REVERT: A 461 MET cc_start: 0.7448 (mmm) cc_final: 0.7111 (tpt) REVERT: A 488 ARG cc_start: 0.8010 (mtp-110) cc_final: 0.7691 (ptp90) REVERT: B 27 GLN cc_start: 0.7688 (pm20) cc_final: 0.7044 (pp30) REVERT: B 146 GLU cc_start: 0.8486 (pt0) cc_final: 0.8161 (pt0) REVERT: B 221 ASN cc_start: 0.7370 (t0) cc_final: 0.5857 (m-40) REVERT: B 243 CYS cc_start: 0.8921 (t) cc_final: 0.8321 (t) REVERT: B 252 GLU cc_start: 0.8352 (pm20) cc_final: 0.8054 (pm20) REVERT: B 382 ASP cc_start: 0.7785 (m-30) cc_final: 0.6882 (t70) REVERT: C 59 ARG cc_start: 0.8194 (ptp-110) cc_final: 0.7917 (ptp-110) REVERT: C 190 ARG cc_start: 0.7869 (mtp180) cc_final: 0.7239 (mmm160) outliers start: 41 outliers final: 28 residues processed: 165 average time/residue: 0.1869 time to fit residues: 44.9193 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 : 1.077 ------------------------------------------------------------------------------- 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 124 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 52 LEU 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 301 LEU 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 E residue 9 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 30 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 109 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 89 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.100804 restraints weight = 16858.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105130 restraints weight = 9224.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108140 restraints weight = 6287.251| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9956 Z= 0.112 Angle : 0.606 11.845 13475 Z= 0.296 Chirality : 0.041 0.231 1421 Planarity : 0.004 0.067 1765 Dihedral : 5.121 46.865 1423 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.59 % Favored : 95.15 % Rotamer: Outliers : 3.15 % Allowed : 28.15 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1176 helix: 2.27 (0.20), residues: 615 sheet: -0.44 (0.61), residues: 71 loop : -1.75 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 161 HIS 0.004 0.000 HIS A 565 PHE 0.015 0.001 PHE C 153 TYR 0.026 0.001 TYR B 267 ARG 0.002 0.000 ARG A 666 Details of bonding type rmsd link_TRANS : bond 0.00003 ( 1) link_TRANS : angle 0.12753 ( 3) link_NAG-ASN : bond 0.00946 ( 4) link_NAG-ASN : angle 5.10732 ( 12) hydrogen bonds : bond 0.04008 ( 495) hydrogen bonds : angle 3.68584 ( 1497) SS BOND : bond 0.00304 ( 4) SS BOND : angle 2.88811 ( 8) covalent geometry : bond 0.00238 ( 9947) covalent geometry : angle 0.58272 (13452) *********************** 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 164 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.6193 (OUTLIER) cc_final: 0.5595 (mmm) REVERT: A 156 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7173 (tt) REVERT: A 218 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: A 286 LEU cc_start: 0.8379 (mt) cc_final: 0.8042 (mp) REVERT: A 322 GLU cc_start: 0.8397 (tt0) cc_final: 0.7896 (tm-30) REVERT: A 461 MET cc_start: 0.7419 (mmm) cc_final: 0.6987 (tpt) REVERT: A 471 ARG cc_start: 0.6009 (mtm-85) cc_final: 0.5630 (mtm-85) REVERT: A 488 ARG cc_start: 0.7992 (mtp-110) cc_final: 0.7670 (ptp90) REVERT: A 689 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7325 (mm-40) REVERT: B 146 GLU cc_start: 0.8448 (pt0) cc_final: 0.8030 (pt0) REVERT: B 180 MET cc_start: 0.6324 (ttt) cc_final: 0.5326 (tpt) REVERT: B 221 ASN cc_start: 0.7374 (t0) cc_final: 0.5854 (m-40) REVERT: B 243 CYS cc_start: 0.8918 (t) cc_final: 0.8323 (t) REVERT: B 252 GLU cc_start: 0.8345 (pm20) cc_final: 0.7985 (pm20) REVERT: B 288 TYR cc_start: 0.7047 (m-80) cc_final: 0.6755 (m-80) REVERT: B 382 ASP cc_start: 0.7833 (m-30) cc_final: 0.6934 (t70) REVERT: C 59 ARG cc_start: 0.8206 (ptp-110) cc_final: 0.7944 (ptp-110) REVERT: C 190 ARG cc_start: 0.7984 (mtp180) cc_final: 0.7270 (mmm160) outliers start: 32 outliers final: 24 residues processed: 156 average time/residue: 0.1877 time to fit residues: 42.4941 Evaluate side-chains 146 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 124 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE 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 246 CYS Chi-restraints excluded: chain A residue 307 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 52 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU 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 E residue 9 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 36 optimal weight: 1.9990 chunk 113 optimal weight: 0.0470 chunk 61 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 overall best weight: 0.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.140238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099223 restraints weight = 16716.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103709 restraints weight = 9018.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.106776 restraints weight = 6112.253| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9956 Z= 0.112 Angle : 0.619 11.846 13475 Z= 0.300 Chirality : 0.041 0.233 1421 Planarity : 0.004 0.069 1765 Dihedral : 4.916 47.204 1423 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.25 % Favored : 95.49 % Rotamer: Outliers : 3.05 % Allowed : 28.74 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1176 helix: 2.25 (0.20), residues: 621 sheet: -0.48 (0.59), residues: 71 loop : -1.79 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 161 HIS 0.002 0.001 HIS A 176 PHE 0.016 0.001 PHE C 153 TYR 0.025 0.001 TYR B 267 ARG 0.002 0.000 ARG A 666 Details of bonding type rmsd link_TRANS : bond 0.00002 ( 1) link_TRANS : angle 0.06262 ( 3) link_NAG-ASN : bond 0.00957 ( 4) link_NAG-ASN : angle 5.00681 ( 12) hydrogen bonds : bond 0.03934 ( 495) hydrogen bonds : angle 3.68104 ( 1497) SS BOND : bond 0.00307 ( 4) SS BOND : angle 2.74025 ( 8) covalent geometry : bond 0.00247 ( 9947) covalent geometry : angle 0.59741 (13452) *********************** 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 155 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 124 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7522 (p0) REVERT: A 156 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7309 (tt) REVERT: A 218 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: A 286 LEU cc_start: 0.8479 (mt) cc_final: 0.8155 (mp) REVERT: A 322 GLU cc_start: 0.8399 (tt0) cc_final: 0.7863 (tm-30) REVERT: A 423 ASN cc_start: 0.8068 (m110) cc_final: 0.7597 (p0) REVERT: A 471 ARG cc_start: 0.6010 (mtm-85) cc_final: 0.5626 (mtm-85) REVERT: A 488 ARG cc_start: 0.8009 (mtp-110) cc_final: 0.7725 (ptp90) REVERT: A 600 CYS cc_start: 0.7422 (m) cc_final: 0.6708 (t) REVERT: B 27 GLN cc_start: 0.7741 (pm20) cc_final: 0.7142 (pp30) REVERT: B 146 GLU cc_start: 0.8439 (pt0) cc_final: 0.8012 (pt0) REVERT: B 180 MET cc_start: 0.6313 (ttt) cc_final: 0.5334 (tpt) REVERT: B 243 CYS cc_start: 0.8896 (t) cc_final: 0.8305 (t) REVERT: B 252 GLU cc_start: 0.8360 (pm20) cc_final: 0.8027 (pm20) REVERT: B 288 TYR cc_start: 0.7071 (m-80) cc_final: 0.6780 (m-80) REVERT: B 382 ASP cc_start: 0.7745 (m-30) cc_final: 0.6894 (t70) REVERT: C 59 ARG cc_start: 0.8058 (ptp-110) cc_final: 0.7771 (ptp-110) REVERT: C 190 ARG cc_start: 0.7998 (mtp180) cc_final: 0.7326 (mmm160) outliers start: 31 outliers final: 24 residues processed: 149 average time/residue: 0.2031 time to fit residues: 44.1821 Evaluate side-chains 145 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 211 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 246 CYS Chi-restraints excluded: chain A residue 307 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 273 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU 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 E residue 9 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 56 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.139468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.105913 restraints weight = 17184.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106388 restraints weight = 11629.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.107720 restraints weight = 9618.863| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9956 Z= 0.119 Angle : 0.635 11.799 13475 Z= 0.305 Chirality : 0.041 0.240 1421 Planarity : 0.004 0.069 1765 Dihedral : 4.846 47.330 1423 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.85 % Favored : 94.90 % Rotamer: Outliers : 3.05 % Allowed : 28.84 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1176 helix: 2.23 (0.20), residues: 624 sheet: -0.49 (0.60), residues: 71 loop : -1.80 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 161 HIS 0.002 0.001 HIS A 565 PHE 0.017 0.001 PHE C 153 TYR 0.025 0.001 TYR B 267 ARG 0.002 0.000 ARG A 666 Details of bonding type rmsd link_TRANS : bond 0.00014 ( 1) link_TRANS : angle 0.07013 ( 3) link_NAG-ASN : bond 0.00936 ( 4) link_NAG-ASN : angle 4.89832 ( 12) hydrogen bonds : bond 0.04084 ( 495) hydrogen bonds : angle 3.72006 ( 1497) SS BOND : bond 0.00304 ( 4) SS BOND : angle 2.68898 ( 8) covalent geometry : bond 0.00267 ( 9947) covalent geometry : angle 0.61448 (13452) *********************** 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 160 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7486 (p0) REVERT: A 156 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7200 (tt) REVERT: A 218 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: A 286 LEU cc_start: 0.8354 (mt) cc_final: 0.8019 (mp) REVERT: A 322 GLU cc_start: 0.8411 (tt0) cc_final: 0.7912 (tm-30) REVERT: A 461 MET cc_start: 0.7676 (mmm) cc_final: 0.7358 (tpt) REVERT: A 471 ARG cc_start: 0.6142 (mtm-85) cc_final: 0.5789 (mtm-85) REVERT: A 488 ARG cc_start: 0.8030 (mtp-110) cc_final: 0.7693 (ptp90) REVERT: A 600 CYS cc_start: 0.7460 (m) cc_final: 0.6728 (t) REVERT: B 27 GLN cc_start: 0.7777 (pm20) cc_final: 0.6998 (pp30) REVERT: B 146 GLU cc_start: 0.8446 (pt0) cc_final: 0.7586 (pt0) REVERT: B 180 MET cc_start: 0.6454 (ttt) cc_final: 0.5466 (tpt) REVERT: B 243 CYS cc_start: 0.8884 (t) cc_final: 0.8274 (t) REVERT: B 252 GLU cc_start: 0.8341 (pm20) cc_final: 0.7980 (pm20) REVERT: B 288 TYR cc_start: 0.7099 (m-80) cc_final: 0.6807 (m-80) REVERT: B 382 ASP cc_start: 0.7973 (m-30) cc_final: 0.7047 (t70) REVERT: C 59 ARG cc_start: 0.8197 (ptp-110) cc_final: 0.7871 (ptp-110) REVERT: C 190 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7888 (mmm160) outliers start: 31 outliers final: 27 residues processed: 152 average time/residue: 0.1945 time to fit residues: 43.0964 Evaluate side-chains 152 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 211 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 246 CYS Chi-restraints excluded: chain A residue 307 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 253 ILE Chi-restraints excluded: chain B residue 273 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 380 MET 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 24 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.137713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100982 restraints weight = 16720.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106114 restraints weight = 10238.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106490 restraints weight = 6424.423| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9956 Z= 0.116 Angle : 0.636 11.851 13475 Z= 0.307 Chirality : 0.041 0.235 1421 Planarity : 0.004 0.069 1765 Dihedral : 4.772 47.253 1423 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.76 % Favored : 94.98 % Rotamer: Outliers : 2.95 % Allowed : 28.94 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.25), residues: 1176 helix: 2.28 (0.20), residues: 621 sheet: -0.57 (0.58), residues: 71 loop : -1.79 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 161 HIS 0.002 0.000 HIS A 565 PHE 0.016 0.001 PHE C 153 TYR 0.024 0.001 TYR B 267 ARG 0.002 0.000 ARG A 666 Details of bonding type rmsd link_TRANS : bond 0.00024 ( 1) link_TRANS : angle 0.07559 ( 3) link_NAG-ASN : bond 0.00946 ( 4) link_NAG-ASN : angle 4.86460 ( 12) hydrogen bonds : bond 0.03949 ( 495) hydrogen bonds : angle 3.70619 ( 1497) SS BOND : bond 0.00314 ( 4) SS BOND : angle 2.65577 ( 8) covalent geometry : bond 0.00259 ( 9947) covalent geometry : angle 0.61643 (13452) ********************** 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 154 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 156 ILE cc_start: 0.7703 (OUTLIER) cc_final: 0.7109 (tt) REVERT: A 218 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: A 286 LEU cc_start: 0.8165 (mt) cc_final: 0.7831 (mp) REVERT: A 322 GLU cc_start: 0.8405 (tt0) cc_final: 0.7898 (tm-30) REVERT: A 423 ASN cc_start: 0.8159 (m110) cc_final: 0.7582 (p0) REVERT: A 461 MET cc_start: 0.7786 (mmm) cc_final: 0.7283 (tpt) REVERT: A 471 ARG cc_start: 0.5842 (mtm-85) cc_final: 0.5555 (mtm-85) REVERT: A 488 ARG cc_start: 0.7984 (mtp-110) cc_final: 0.7633 (ptp90) REVERT: A 600 CYS cc_start: 0.7375 (m) cc_final: 0.6687 (t) REVERT: B 27 GLN cc_start: 0.7848 (pm20) cc_final: 0.7033 (pp30) REVERT: B 146 GLU cc_start: 0.8338 (pt0) cc_final: 0.7802 (pt0) REVERT: B 180 MET cc_start: 0.6453 (ttt) cc_final: 0.5461 (tpt) REVERT: B 243 CYS cc_start: 0.8875 (t) cc_final: 0.8297 (t) REVERT: B 252 GLU cc_start: 0.8230 (pm20) cc_final: 0.7898 (pm20) REVERT: B 288 TYR cc_start: 0.7008 (m-80) cc_final: 0.6727 (m-80) REVERT: B 382 ASP cc_start: 0.7946 (m-30) cc_final: 0.6985 (t70) REVERT: C 59 ARG cc_start: 0.8162 (ptp-110) cc_final: 0.7801 (ptp-110) REVERT: C 163 ASP cc_start: 0.8681 (t0) cc_final: 0.8211 (m-30) REVERT: C 190 ARG cc_start: 0.8088 (mtp180) cc_final: 0.7827 (mmm160) outliers start: 30 outliers final: 27 residues processed: 147 average time/residue: 0.1937 time to fit residues: 42.3114 Evaluate side-chains 148 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 124 LEU Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 211 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 246 CYS Chi-restraints excluded: chain A residue 307 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 253 ILE Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU 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 179 VAL 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 32 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101348 restraints weight = 16736.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107097 restraints weight = 10142.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107367 restraints weight = 6162.657| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9956 Z= 0.116 Angle : 0.634 11.990 13475 Z= 0.306 Chirality : 0.041 0.236 1421 Planarity : 0.004 0.069 1765 Dihedral : 4.702 46.886 1423 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.76 % Favored : 94.98 % Rotamer: Outliers : 3.05 % Allowed : 28.94 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1176 helix: 2.24 (0.20), residues: 628 sheet: -0.61 (0.58), residues: 71 loop : -1.83 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 161 HIS 0.002 0.000 HIS A 565 PHE 0.016 0.001 PHE C 153 TYR 0.024 0.001 TYR B 267 ARG 0.002 0.000 ARG A 666 Details of bonding type rmsd link_TRANS : bond 0.00031 ( 1) link_TRANS : angle 0.07648 ( 3) link_NAG-ASN : bond 0.00950 ( 4) link_NAG-ASN : angle 4.78476 ( 12) hydrogen bonds : bond 0.03896 ( 495) hydrogen bonds : angle 3.67273 ( 1497) SS BOND : bond 0.00308 ( 4) SS BOND : angle 2.62441 ( 8) covalent geometry : bond 0.00258 ( 9947) covalent geometry : angle 0.61497 (13452) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2927.06 seconds wall clock time: 52 minutes 9.28 seconds (3129.28 seconds total)