Starting phenix.real_space_refine on Fri Nov 15 21:47:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc9_37097/11_2024/8kc9_37097.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc9_37097/11_2024/8kc9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc9_37097/11_2024/8kc9_37097.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc9_37097/11_2024/8kc9_37097.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc9_37097/11_2024/8kc9_37097.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc9_37097/11_2024/8kc9_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.86, per 1000 atoms: 0.60 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: 2.82 Conformation dependent library (CDL) restraints added in 1.0 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: 0.95 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: 2.58 Time building geometry restraints manager: 3.13 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.690 Find NCS groups from input model: 0.080 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- 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 9947 Z= 0.248 Angle : 0.795 11.232 13452 Z= 0.443 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 *********************** 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 : 1.094 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: 0.2532 time to fit residues: 83.8271 Evaluate side-chains 149 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 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 9947 Z= 0.180 Angle : 0.634 9.295 13452 Z= 0.319 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 *********************** 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 : 1.098 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7501 (t0) cc_final: 0.7057 (t0) REVERT: A 156 ILE cc_start: 0.7189 (tp) cc_final: 0.6721 (tt) REVERT: A 202 THR cc_start: 0.6928 (m) cc_final: 0.6386 (p) REVERT: A 208 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6667 (tp30) REVERT: A 292 ARG cc_start: 0.8291 (ttm-80) cc_final: 0.8030 (ttm-80) REVERT: A 322 GLU cc_start: 0.8105 (tt0) cc_final: 0.7025 (tm-30) REVERT: A 323 CYS cc_start: 0.8117 (t) cc_final: 0.7495 (t) REVERT: A 374 GLU cc_start: 0.7607 (tm-30) cc_final: 0.7247 (tm-30) REVERT: A 423 ASN cc_start: 0.7705 (m-40) cc_final: 0.7189 (p0) REVERT: A 482 GLU cc_start: 0.8670 (mp0) cc_final: 0.8463 (mp0) REVERT: A 487 GLN cc_start: 0.8310 (mt0) cc_final: 0.7846 (tp-100) REVERT: A 488 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7514 (ptp90) REVERT: A 600 CYS cc_start: 0.7278 (m) cc_final: 0.6137 (t) REVERT: A 635 LYS cc_start: 0.8888 (tppt) cc_final: 0.8613 (mmtp) REVERT: B 146 GLU cc_start: 0.8469 (pt0) cc_final: 0.7530 (pt0) REVERT: B 198 ILE cc_start: 0.7927 (mm) cc_final: 0.7429 (mp) REVERT: B 199 LYS cc_start: 0.7450 (mttt) cc_final: 0.7243 (mmtm) REVERT: B 202 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7268 (mm-30) REVERT: B 215 ARG cc_start: 0.8841 (tpt-90) cc_final: 0.8620 (mmm-85) REVERT: B 242 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6773 (tm-30) REVERT: B 252 GLU cc_start: 0.7283 (pm20) cc_final: 0.7000 (pm20) REVERT: B 329 LYS cc_start: 0.9416 (mppt) cc_final: 0.9154 (mmtm) REVERT: B 344 THR cc_start: 0.8268 (m) cc_final: 0.8031 (p) REVERT: B 382 ASP cc_start: 0.7922 (m-30) cc_final: 0.6829 (p0) REVERT: C 59 ARG cc_start: 0.7372 (ttm110) cc_final: 0.6348 (ptm160) REVERT: C 174 GLU cc_start: 0.7962 (tp30) cc_final: 0.7642 (tp30) outliers start: 29 outliers final: 11 residues processed: 185 average time/residue: 0.2229 time to fit residues: 58.1036 Evaluate side-chains 141 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 60 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 0.0270 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 36 optimal weight: 0.0670 chunk 86 optimal weight: 7.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9947 Z= 0.155 Angle : 0.574 8.295 13452 Z= 0.287 Chirality : 0.041 0.247 1421 Planarity : 0.004 0.064 1765 Dihedral : 6.545 87.153 1423 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.76 % Favored : 94.98 % Rotamer: Outliers : 3.84 % Allowed : 23.52 % Favored : 72.64 % 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: 0.75 (0.25), residues: 1176 helix: 2.30 (0.21), residues: 617 sheet: -0.61 (0.66), residues: 62 loop : -1.81 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 161 HIS 0.003 0.000 HIS A 227 PHE 0.023 0.001 PHE C 123 TYR 0.019 0.001 TYR B 267 ARG 0.004 0.000 ARG A 214 *********************** 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 189 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7461 (t0) cc_final: 0.6974 (t0) REVERT: A 322 GLU cc_start: 0.8107 (tt0) cc_final: 0.7094 (tm-30) REVERT: A 347 MET cc_start: 0.8622 (tpp) cc_final: 0.8028 (mmp) REVERT: A 374 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7264 (tm-30) REVERT: A 423 ASN cc_start: 0.7789 (m-40) cc_final: 0.7063 (t0) REVERT: A 482 GLU cc_start: 0.8602 (mp0) cc_final: 0.8262 (mp0) REVERT: A 487 GLN cc_start: 0.8252 (mt0) cc_final: 0.8008 (mm-40) REVERT: A 488 ARG cc_start: 0.7828 (mtp-110) cc_final: 0.7538 (ptp90) REVERT: A 600 CYS cc_start: 0.7379 (m) cc_final: 0.6324 (t) REVERT: A 635 LYS cc_start: 0.8885 (tppt) cc_final: 0.8612 (mmtp) REVERT: B 146 GLU cc_start: 0.8230 (pt0) cc_final: 0.7644 (pt0) REVERT: B 198 ILE cc_start: 0.7921 (mm) cc_final: 0.7438 (mp) REVERT: B 199 LYS cc_start: 0.7413 (mttt) cc_final: 0.7185 (mmtt) REVERT: B 202 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7285 (mm-30) REVERT: B 215 ARG cc_start: 0.8834 (tpt-90) cc_final: 0.8616 (mmm-85) REVERT: B 242 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6906 (tm-30) REVERT: B 252 GLU cc_start: 0.7418 (pm20) cc_final: 0.7077 (pm20) REVERT: B 282 THR cc_start: 0.9226 (m) cc_final: 0.8776 (p) REVERT: B 329 LYS cc_start: 0.9415 (mppt) cc_final: 0.9124 (mmtm) REVERT: B 344 THR cc_start: 0.8252 (m) cc_final: 0.8020 (p) REVERT: B 382 ASP cc_start: 0.7953 (m-30) cc_final: 0.6785 (p0) REVERT: C 59 ARG cc_start: 0.7374 (ttm110) cc_final: 0.6308 (ptm160) REVERT: C 188 ASP cc_start: 0.5069 (OUTLIER) cc_final: 0.4858 (p0) outliers start: 39 outliers final: 26 residues processed: 173 average time/residue: 0.2153 time to fit residues: 53.1680 Evaluate side-chains 153 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 215 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 181 MET 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 347 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 188 ASP 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 106 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9947 Z= 0.173 Angle : 0.575 8.458 13452 Z= 0.286 Chirality : 0.041 0.207 1421 Planarity : 0.004 0.064 1765 Dihedral : 6.049 75.598 1423 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.93 % Favored : 94.81 % Rotamer: Outliers : 3.94 % Allowed : 24.90 % Favored : 71.16 % 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: 2.27 (0.20), residues: 620 sheet: -0.67 (0.66), residues: 63 loop : -1.76 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 161 HIS 0.004 0.001 HIS A 536 PHE 0.018 0.001 PHE C 153 TYR 0.018 0.001 TYR B 267 ARG 0.005 0.000 ARG A 354 *********************** 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 177 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 137 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7413 (t0) cc_final: 0.6968 (t0) REVERT: A 156 ILE cc_start: 0.7121 (tp) cc_final: 0.6615 (tt) REVERT: A 202 THR cc_start: 0.7032 (m) cc_final: 0.6499 (p) REVERT: A 292 ARG cc_start: 0.8143 (ttm-80) cc_final: 0.7603 (mtp85) REVERT: A 322 GLU cc_start: 0.8216 (tt0) cc_final: 0.7377 (tm-30) REVERT: A 323 CYS cc_start: 0.8900 (m) cc_final: 0.7733 (t) REVERT: A 374 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7281 (tm-30) REVERT: A 423 ASN cc_start: 0.7816 (m-40) cc_final: 0.6952 (t0) REVERT: A 482 GLU cc_start: 0.8462 (mp0) cc_final: 0.8250 (mp0) REVERT: A 487 GLN cc_start: 0.8495 (mt0) cc_final: 0.8088 (mm-40) REVERT: A 488 ARG cc_start: 0.7854 (mtp-110) cc_final: 0.7568 (ptp90) REVERT: A 594 ASN cc_start: 0.6659 (m110) cc_final: 0.6014 (p0) REVERT: A 635 LYS cc_start: 0.8866 (tppt) cc_final: 0.8610 (mmtp) REVERT: B 146 GLU cc_start: 0.8220 (pt0) cc_final: 0.7626 (pt0) REVERT: B 198 ILE cc_start: 0.7942 (mm) cc_final: 0.7449 (mp) REVERT: B 199 LYS cc_start: 0.7417 (mttt) cc_final: 0.7196 (mmtm) REVERT: B 242 GLU cc_start: 0.7511 (mm-30) cc_final: 0.6893 (tm-30) REVERT: B 252 GLU cc_start: 0.7473 (pm20) cc_final: 0.7077 (pm20) REVERT: B 329 LYS cc_start: 0.9413 (mppt) cc_final: 0.9141 (mmtm) REVERT: B 344 THR cc_start: 0.8281 (m) cc_final: 0.8061 (p) REVERT: B 382 ASP cc_start: 0.7996 (m-30) cc_final: 0.6855 (t0) REVERT: C 59 ARG cc_start: 0.7191 (ttm110) cc_final: 0.6589 (ptp-110) REVERT: C 171 LYS cc_start: 0.7700 (tttp) cc_final: 0.7428 (tttm) REVERT: C 190 ARG cc_start: 0.8152 (mtp180) cc_final: 0.7273 (mmm160) REVERT: C 195 LYS cc_start: 0.8588 (mmmm) cc_final: 0.8353 (mtmt) outliers start: 40 outliers final: 26 residues processed: 164 average time/residue: 0.2167 time to fit residues: 49.8213 Evaluate side-chains 155 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 213 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 VAL 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 B residue 181 MET Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 273 CYS 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 C residue 179 VAL Chi-restraints excluded: chain C residue 208 GLU 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 65 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9947 Z= 0.161 Angle : 0.565 9.307 13452 Z= 0.277 Chirality : 0.040 0.159 1421 Planarity : 0.004 0.065 1765 Dihedral : 5.609 62.976 1423 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.51 % Favored : 95.24 % Rotamer: Outliers : 3.94 % Allowed : 25.59 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.85 (0.25), residues: 1176 helix: 2.32 (0.20), residues: 622 sheet: -0.48 (0.66), residues: 63 loop : -1.75 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 161 HIS 0.003 0.001 HIS C 132 PHE 0.016 0.001 PHE C 153 TYR 0.020 0.001 TYR C 133 ARG 0.002 0.000 ARG A 666 *********************** 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 179 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 156 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6648 (tt) REVERT: A 322 GLU cc_start: 0.8285 (tt0) cc_final: 0.7558 (tm-30) REVERT: A 323 CYS cc_start: 0.8942 (m) cc_final: 0.7762 (t) REVERT: A 374 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7494 (tm-30) REVERT: A 423 ASN cc_start: 0.7970 (m-40) cc_final: 0.7126 (t0) REVERT: A 461 MET cc_start: 0.8061 (mmm) cc_final: 0.7798 (mmm) REVERT: A 482 GLU cc_start: 0.8472 (mp0) cc_final: 0.8208 (mp0) REVERT: A 487 GLN cc_start: 0.8504 (mt0) cc_final: 0.8076 (mm-40) REVERT: A 488 ARG cc_start: 0.7913 (mtp-110) cc_final: 0.7632 (ptp90) REVERT: A 594 ASN cc_start: 0.6828 (m110) cc_final: 0.6331 (p0) REVERT: A 635 LYS cc_start: 0.8875 (tppt) cc_final: 0.8621 (mmtp) REVERT: B 146 GLU cc_start: 0.8244 (pt0) cc_final: 0.7668 (pt0) REVERT: B 198 ILE cc_start: 0.7953 (mm) cc_final: 0.7474 (mp) REVERT: B 199 LYS cc_start: 0.7430 (mttt) cc_final: 0.7196 (mmtm) REVERT: B 242 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6806 (tm-30) REVERT: B 252 GLU cc_start: 0.7624 (pm20) cc_final: 0.7181 (pm20) REVERT: B 329 LYS cc_start: 0.9407 (mppt) cc_final: 0.9146 (mmtm) REVERT: B 344 THR cc_start: 0.8258 (m) cc_final: 0.8043 (p) REVERT: B 382 ASP cc_start: 0.7999 (m-30) cc_final: 0.6869 (t0) REVERT: C 59 ARG cc_start: 0.7210 (ttm110) cc_final: 0.6490 (ptp-110) REVERT: C 126 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8532 (mm-30) REVERT: C 171 LYS cc_start: 0.7819 (tttp) cc_final: 0.7445 (tttm) REVERT: C 190 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7108 (mmm160) REVERT: C 195 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8276 (mtmt) outliers start: 40 outliers final: 27 residues processed: 167 average time/residue: 0.2062 time to fit residues: 49.0846 Evaluate side-chains 159 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 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 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 B residue 181 MET Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 94 HIS Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 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 C residue 208 GLU 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 103 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 chunk 95 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9947 Z= 0.156 Angle : 0.577 9.806 13452 Z= 0.281 Chirality : 0.040 0.187 1421 Planarity : 0.004 0.067 1765 Dihedral : 5.189 51.466 1423 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.59 % Favored : 95.15 % Rotamer: Outliers : 4.13 % Allowed : 24.90 % Favored : 70.96 % 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: 0.92 (0.25), residues: 1176 helix: 2.39 (0.20), residues: 623 sheet: -0.39 (0.66), residues: 63 loop : -1.75 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 161 HIS 0.003 0.000 HIS C 94 PHE 0.017 0.001 PHE C 153 TYR 0.015 0.001 TYR B 267 ARG 0.005 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 138 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 156 ILE cc_start: 0.7123 (OUTLIER) cc_final: 0.6606 (tt) REVERT: A 202 THR cc_start: 0.6915 (m) cc_final: 0.6415 (p) REVERT: A 292 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7701 (mtp85) REVERT: A 322 GLU cc_start: 0.8283 (tt0) cc_final: 0.7566 (tm-30) REVERT: A 323 CYS cc_start: 0.8961 (m) cc_final: 0.7762 (t) REVERT: A 374 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7497 (tm-30) REVERT: A 423 ASN cc_start: 0.8015 (m-40) cc_final: 0.7803 (m110) REVERT: A 461 MET cc_start: 0.7910 (mmm) cc_final: 0.7682 (mmm) REVERT: A 482 GLU cc_start: 0.8465 (mp0) cc_final: 0.8208 (mp0) REVERT: A 488 ARG cc_start: 0.7893 (mtp-110) cc_final: 0.7593 (ptp90) REVERT: A 594 ASN cc_start: 0.6807 (m110) cc_final: 0.6131 (p0) REVERT: A 635 LYS cc_start: 0.8871 (tppt) cc_final: 0.8581 (mmtp) REVERT: B 146 GLU cc_start: 0.8131 (pt0) cc_final: 0.7520 (pt0) REVERT: B 180 MET cc_start: 0.6598 (ttt) cc_final: 0.5507 (tpt) REVERT: B 198 ILE cc_start: 0.7968 (mm) cc_final: 0.7490 (mp) REVERT: B 199 LYS cc_start: 0.7407 (mttt) cc_final: 0.7184 (mmtm) REVERT: B 242 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6716 (tm-30) REVERT: B 243 CYS cc_start: 0.8387 (t) cc_final: 0.8048 (t) REVERT: B 252 GLU cc_start: 0.7700 (pm20) cc_final: 0.7283 (pm20) REVERT: B 329 LYS cc_start: 0.9407 (mppt) cc_final: 0.9148 (mmtm) REVERT: B 344 THR cc_start: 0.8229 (m) cc_final: 0.8021 (p) REVERT: B 382 ASP cc_start: 0.7874 (m-30) cc_final: 0.6753 (t70) REVERT: C 48 PHE cc_start: 0.7058 (m-80) cc_final: 0.6800 (m-80) REVERT: C 59 ARG cc_start: 0.7282 (ttm110) cc_final: 0.6591 (ptp-110) REVERT: C 126 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8490 (mm-30) REVERT: C 190 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7133 (mmm160) REVERT: C 195 LYS cc_start: 0.8679 (mmmm) cc_final: 0.8302 (mtmt) outliers start: 42 outliers final: 28 residues processed: 170 average time/residue: 0.2027 time to fit residues: 49.5928 Evaluate side-chains 157 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 HIS 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 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 B residue 273 CYS Chi-restraints excluded: chain B residue 277 CYS 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 C residue 179 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain E residue 9 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 12 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 96 optimal weight: 0.1980 chunk 64 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 71 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 70 optimal weight: 0.1980 chunk 45 optimal weight: 0.0870 overall best weight: 0.3138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9947 Z= 0.139 Angle : 0.565 9.937 13452 Z= 0.273 Chirality : 0.039 0.168 1421 Planarity : 0.004 0.066 1765 Dihedral : 4.830 46.971 1423 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.25 % Favored : 95.49 % Rotamer: Outliers : 3.44 % Allowed : 26.28 % Favored : 70.28 % 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: 1.01 (0.25), residues: 1176 helix: 2.42 (0.20), residues: 626 sheet: -0.21 (0.60), residues: 73 loop : -1.72 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 161 HIS 0.003 0.000 HIS C 94 PHE 0.014 0.001 PHE C 153 TYR 0.015 0.001 TYR A 628 ARG 0.003 0.000 ARG A 292 *********************** 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 178 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 156 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6560 (tt) REVERT: A 198 LYS cc_start: 0.8333 (mmtm) cc_final: 0.8067 (mmtt) REVERT: A 286 LEU cc_start: 0.7253 (mt) cc_final: 0.6970 (mp) REVERT: A 292 ARG cc_start: 0.8140 (ttm-80) cc_final: 0.7690 (mtp85) REVERT: A 322 GLU cc_start: 0.8243 (tt0) cc_final: 0.7556 (tm-30) REVERT: A 323 CYS cc_start: 0.8965 (m) cc_final: 0.7743 (t) REVERT: A 374 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7524 (tm-30) REVERT: A 423 ASN cc_start: 0.8121 (m-40) cc_final: 0.7289 (t0) REVERT: A 461 MET cc_start: 0.7802 (mmm) cc_final: 0.7602 (mmm) REVERT: A 482 GLU cc_start: 0.8416 (mp0) cc_final: 0.8203 (mp0) REVERT: A 487 GLN cc_start: 0.8466 (mt0) cc_final: 0.8142 (mm110) REVERT: A 488 ARG cc_start: 0.7874 (mtp-110) cc_final: 0.7528 (ptp90) REVERT: A 594 ASN cc_start: 0.6597 (m110) cc_final: 0.5954 (p0) REVERT: A 600 CYS cc_start: 0.7330 (m) cc_final: 0.6724 (t) REVERT: A 635 LYS cc_start: 0.8768 (tppt) cc_final: 0.8445 (mmtp) REVERT: B 146 GLU cc_start: 0.8118 (pt0) cc_final: 0.7559 (pt0) REVERT: B 180 MET cc_start: 0.6586 (ttt) cc_final: 0.5508 (tpt) REVERT: B 198 ILE cc_start: 0.7961 (mm) cc_final: 0.7482 (mp) REVERT: B 199 LYS cc_start: 0.7410 (mttt) cc_final: 0.7185 (mmtm) REVERT: B 242 GLU cc_start: 0.7233 (mm-30) cc_final: 0.6728 (tm-30) REVERT: B 243 CYS cc_start: 0.8445 (t) cc_final: 0.8038 (t) REVERT: B 252 GLU cc_start: 0.7761 (pm20) cc_final: 0.7326 (pm20) REVERT: B 329 LYS cc_start: 0.9403 (mppt) cc_final: 0.9151 (mmtm) REVERT: B 344 THR cc_start: 0.8231 (m) cc_final: 0.8030 (p) REVERT: B 382 ASP cc_start: 0.7861 (m-30) cc_final: 0.6591 (t70) REVERT: C 48 PHE cc_start: 0.6878 (m-80) cc_final: 0.6639 (m-10) REVERT: C 59 ARG cc_start: 0.7180 (ttm110) cc_final: 0.6628 (ptp-110) REVERT: C 126 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8578 (mm-30) REVERT: C 190 ARG cc_start: 0.8045 (mtp180) cc_final: 0.7212 (mmm160) REVERT: C 195 LYS cc_start: 0.8699 (mmmm) cc_final: 0.8284 (mtmt) outliers start: 35 outliers final: 24 residues processed: 168 average time/residue: 0.2116 time to fit residues: 50.3119 Evaluate side-chains 162 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 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 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 572 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 161 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 187 THR Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain E residue 9 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 104 optimal weight: 0.0770 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6262 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9947 Z= 0.148 Angle : 0.589 10.699 13452 Z= 0.283 Chirality : 0.040 0.163 1421 Planarity : 0.004 0.067 1765 Dihedral : 4.620 47.200 1423 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.34 % Favored : 95.41 % Rotamer: Outliers : 3.15 % Allowed : 26.67 % Favored : 70.18 % 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: 1.03 (0.25), residues: 1176 helix: 2.45 (0.20), residues: 626 sheet: -0.12 (0.60), residues: 73 loop : -1.74 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 161 HIS 0.003 0.000 HIS C 94 PHE 0.016 0.001 PHE C 153 TYR 0.014 0.001 TYR A 628 ARG 0.004 0.000 ARG A 292 *********************** 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 177 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 145 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 156 ILE cc_start: 0.7135 (OUTLIER) cc_final: 0.6593 (tt) REVERT: A 198 LYS cc_start: 0.8324 (mmtm) cc_final: 0.8049 (mmtt) REVERT: A 202 THR cc_start: 0.7113 (m) cc_final: 0.6663 (p) REVERT: A 286 LEU cc_start: 0.7268 (mt) cc_final: 0.6989 (mp) REVERT: A 292 ARG cc_start: 0.8126 (ttm-80) cc_final: 0.7667 (mtp85) REVERT: A 322 GLU cc_start: 0.8281 (tt0) cc_final: 0.7558 (tm-30) REVERT: A 323 CYS cc_start: 0.8967 (m) cc_final: 0.7746 (t) REVERT: A 374 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 461 MET cc_start: 0.7755 (mmm) cc_final: 0.7535 (mmm) REVERT: A 482 GLU cc_start: 0.8485 (mp0) cc_final: 0.8246 (mp0) REVERT: A 487 GLN cc_start: 0.8472 (mt0) cc_final: 0.8143 (mm110) REVERT: A 488 ARG cc_start: 0.7880 (mtp-110) cc_final: 0.7533 (ptp90) REVERT: A 594 ASN cc_start: 0.6563 (m110) cc_final: 0.5904 (p0) REVERT: A 600 CYS cc_start: 0.7382 (m) cc_final: 0.6839 (t) REVERT: A 635 LYS cc_start: 0.8898 (tppt) cc_final: 0.8606 (mmtp) REVERT: B 146 GLU cc_start: 0.8087 (pt0) cc_final: 0.7511 (pt0) REVERT: B 180 MET cc_start: 0.6383 (ttt) cc_final: 0.5376 (tpt) REVERT: B 198 ILE cc_start: 0.7944 (mm) cc_final: 0.7483 (mp) REVERT: B 199 LYS cc_start: 0.7441 (mttt) cc_final: 0.7218 (mmtm) REVERT: B 242 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6735 (tm-30) REVERT: B 252 GLU cc_start: 0.7721 (pm20) cc_final: 0.7345 (pm20) REVERT: B 329 LYS cc_start: 0.9400 (mppt) cc_final: 0.9149 (mmtm) REVERT: B 344 THR cc_start: 0.8111 (m) cc_final: 0.7879 (p) REVERT: B 382 ASP cc_start: 0.7835 (m-30) cc_final: 0.6666 (t70) REVERT: C 48 PHE cc_start: 0.6933 (m-80) cc_final: 0.6543 (m-10) REVERT: C 59 ARG cc_start: 0.7096 (ttm110) cc_final: 0.6641 (ptp-110) REVERT: C 126 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8547 (mm-30) REVERT: C 190 ARG cc_start: 0.8024 (mtp180) cc_final: 0.7175 (mmm160) REVERT: C 195 LYS cc_start: 0.8687 (mmmm) cc_final: 0.8235 (mtmt) REVERT: C 202 CYS cc_start: 0.8699 (p) cc_final: 0.8374 (t) outliers start: 32 outliers final: 25 residues processed: 167 average time/residue: 0.2092 time to fit residues: 49.8149 Evaluate side-chains 160 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 86 PHE 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 C residue 208 GLU 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 106 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 64 optimal weight: 0.0970 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 113 optimal weight: 0.0980 chunk 68 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9947 Z= 0.161 Angle : 0.603 11.457 13452 Z= 0.289 Chirality : 0.040 0.169 1421 Planarity : 0.004 0.067 1765 Dihedral : 4.481 47.346 1423 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.51 % Favored : 95.24 % Rotamer: Outliers : 2.85 % Allowed : 26.87 % Favored : 70.28 % 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: 1.01 (0.25), residues: 1176 helix: 2.43 (0.20), residues: 626 sheet: -0.15 (0.59), residues: 73 loop : -1.73 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 161 HIS 0.003 0.001 HIS B 351 PHE 0.017 0.001 PHE C 153 TYR 0.014 0.001 TYR A 628 ARG 0.004 0.000 ARG A 292 *********************** 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 163 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 1.254 Fit side-chains revert: symmetry clash REVERT: A 156 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6605 (tt) REVERT: A 198 LYS cc_start: 0.8308 (mmtm) cc_final: 0.8035 (mmtt) REVERT: A 286 LEU cc_start: 0.7305 (mt) cc_final: 0.7010 (mp) REVERT: A 292 ARG cc_start: 0.8118 (ttm-80) cc_final: 0.7654 (mtp85) REVERT: A 322 GLU cc_start: 0.8291 (tt0) cc_final: 0.7563 (tm-30) REVERT: A 323 CYS cc_start: 0.8968 (m) cc_final: 0.7750 (t) REVERT: A 374 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 423 ASN cc_start: 0.7947 (m110) cc_final: 0.7525 (p0) REVERT: A 461 MET cc_start: 0.7680 (mmm) cc_final: 0.7430 (mmm) REVERT: A 482 GLU cc_start: 0.8514 (mp0) cc_final: 0.8224 (mp0) REVERT: A 487 GLN cc_start: 0.8479 (mt0) cc_final: 0.8136 (mm110) REVERT: A 488 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7520 (ptp90) REVERT: A 594 ASN cc_start: 0.6598 (m110) cc_final: 0.5927 (p0) REVERT: A 600 CYS cc_start: 0.7396 (m) cc_final: 0.6851 (t) REVERT: A 635 LYS cc_start: 0.8911 (tppt) cc_final: 0.8615 (mmtp) REVERT: B 146 GLU cc_start: 0.8123 (pt0) cc_final: 0.7550 (pt0) REVERT: B 180 MET cc_start: 0.6385 (ttt) cc_final: 0.5385 (tpt) REVERT: B 198 ILE cc_start: 0.7993 (mm) cc_final: 0.7544 (mp) REVERT: B 199 LYS cc_start: 0.7456 (mttt) cc_final: 0.7220 (mmtm) REVERT: B 242 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6744 (tm-30) REVERT: B 252 GLU cc_start: 0.7724 (pm20) cc_final: 0.7362 (pm20) REVERT: B 329 LYS cc_start: 0.9402 (mppt) cc_final: 0.9159 (mmtm) REVERT: B 344 THR cc_start: 0.8080 (m) cc_final: 0.7854 (p) REVERT: B 382 ASP cc_start: 0.7871 (m-30) cc_final: 0.6631 (t70) REVERT: C 48 PHE cc_start: 0.6969 (m-80) cc_final: 0.6591 (m-10) REVERT: C 59 ARG cc_start: 0.7135 (ttm110) cc_final: 0.6702 (ptp-110) REVERT: C 190 ARG cc_start: 0.8043 (mtp180) cc_final: 0.7211 (mmm160) REVERT: C 195 LYS cc_start: 0.8676 (mmmm) cc_final: 0.8196 (mtmt) REVERT: C 202 CYS cc_start: 0.8788 (p) cc_final: 0.8492 (t) outliers start: 29 outliers final: 27 residues processed: 155 average time/residue: 0.2158 time to fit residues: 48.0740 Evaluate side-chains 161 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 123 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 161 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 C residue 208 GLU 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 53 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 100 optimal weight: 0.1980 chunk 28 optimal weight: 4.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 GLN B 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9947 Z= 0.325 Angle : 0.695 12.087 13452 Z= 0.345 Chirality : 0.044 0.183 1421 Planarity : 0.004 0.068 1765 Dihedral : 4.774 47.860 1423 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.04 % Favored : 93.71 % Rotamer: Outliers : 3.15 % Allowed : 26.48 % Favored : 70.37 % 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: 0.83 (0.25), residues: 1176 helix: 2.27 (0.21), residues: 624 sheet: 0.47 (0.75), residues: 49 loop : -1.81 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 161 HIS 0.006 0.001 HIS A 565 PHE 0.022 0.002 PHE C 153 TYR 0.019 0.002 TYR C 119 ARG 0.004 0.001 ARG A 292 ********************** 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 159 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 127 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 156 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.6939 (tt) REVERT: A 202 THR cc_start: 0.7066 (m) cc_final: 0.6580 (p) REVERT: A 286 LEU cc_start: 0.7360 (mt) cc_final: 0.7088 (mp) REVERT: A 292 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7730 (ttm-80) REVERT: A 322 GLU cc_start: 0.8326 (tt0) cc_final: 0.7678 (tm-30) REVERT: A 334 ASP cc_start: 0.7660 (t0) cc_final: 0.7203 (t0) REVERT: A 374 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7561 (tm-30) REVERT: A 423 ASN cc_start: 0.7957 (m110) cc_final: 0.7445 (p0) REVERT: A 461 MET cc_start: 0.7876 (mmm) cc_final: 0.7580 (mmm) REVERT: A 482 GLU cc_start: 0.8636 (mp0) cc_final: 0.8327 (mp0) REVERT: A 488 ARG cc_start: 0.7887 (mtp-110) cc_final: 0.7527 (ptp90) REVERT: A 635 LYS cc_start: 0.8935 (tppt) cc_final: 0.8637 (mmtp) REVERT: B 27 GLN cc_start: 0.7615 (pm20) cc_final: 0.6397 (pp30) REVERT: B 146 GLU cc_start: 0.8275 (pt0) cc_final: 0.7767 (pt0) REVERT: B 180 MET cc_start: 0.6307 (ttt) cc_final: 0.5343 (tpt) REVERT: B 198 ILE cc_start: 0.7960 (mm) cc_final: 0.7481 (mp) REVERT: B 228 ASP cc_start: 0.9025 (m-30) cc_final: 0.8810 (p0) REVERT: B 242 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6780 (tm-30) REVERT: B 252 GLU cc_start: 0.7820 (pm20) cc_final: 0.7465 (pm20) REVERT: B 329 LYS cc_start: 0.9443 (mppt) cc_final: 0.9167 (mmtm) REVERT: B 344 THR cc_start: 0.7927 (m) cc_final: 0.7709 (p) REVERT: B 382 ASP cc_start: 0.8081 (m-30) cc_final: 0.7026 (t70) REVERT: C 59 ARG cc_start: 0.7207 (ttm110) cc_final: 0.6877 (ptp-110) REVERT: C 190 ARG cc_start: 0.8075 (mtp180) cc_final: 0.7818 (mmm160) REVERT: C 195 LYS cc_start: 0.8719 (mmmm) cc_final: 0.8096 (mtmt) outliers start: 32 outliers final: 25 residues processed: 150 average time/residue: 0.2158 time to fit residues: 46.2670 Evaluate side-chains 145 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.087 ------------------------------------------------------------------------------- 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 132 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 376 LEU Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain B residue 84 CYS 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 C residue 208 GLU 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 87 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 5 optimal weight: 0.0570 chunk 68 optimal weight: 0.8980 overall best weight: 0.9300 ------------------------------------------------------------------------------- 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 = 0.3754 r_free = 0.3754 target = 0.141080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.107384 restraints weight = 17000.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107434 restraints weight = 11951.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109078 restraints weight = 9690.399| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9947 Z= 0.179 Angle : 0.624 11.886 13452 Z= 0.304 Chirality : 0.041 0.197 1421 Planarity : 0.004 0.067 1765 Dihedral : 4.550 47.464 1423 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.68 % Favored : 95.07 % Rotamer: Outliers : 2.66 % Allowed : 27.36 % Favored : 69.98 % 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: 0.87 (0.25), residues: 1176 helix: 2.30 (0.21), residues: 621 sheet: -0.17 (0.60), residues: 71 loop : -1.74 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 161 HIS 0.002 0.000 HIS B 351 PHE 0.018 0.001 PHE C 153 TYR 0.029 0.001 TYR B 267 ARG 0.004 0.000 ARG B 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2007.11 seconds wall clock time: 37 minutes 31.14 seconds (2251.14 seconds total)