Starting phenix.real_space_refine on Fri Mar 6 10:11:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d46_27176/03_2026/8d46_27176.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d46_27176/03_2026/8d46_27176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d46_27176/03_2026/8d46_27176.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d46_27176/03_2026/8d46_27176.map" model { file = "/net/cci-nas-00/data/ceres_data/8d46_27176/03_2026/8d46_27176.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d46_27176/03_2026/8d46_27176.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.050 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 S 76 5.16 5 C 9640 2.51 5 N 2556 2.21 5 O 2838 1.98 5 H 15096 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30206 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7486 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 462} Chain: "C" Number of atoms: 7616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 7616 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain: "D" Number of atoms: 7618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 7618 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain: "B" Number of atoms: 7486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 7486 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 462} Time building chain proxies: 5.14, per 1000 atoms: 0.17 Number of scatterers: 30206 At special positions: 0 Unit cell: (105.93, 112.35, 100.58, 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) S 76 16.00 O 2838 8.00 N 2556 7.00 C 9640 6.00 H 15096 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 901.6 milliseconds 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 19 sheets defined 44.4% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 114 through 121 removed outlier: 3.610A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 136 Processing helix chain 'A' and resid 171 through 187 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 199 through 213 Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 283 through 297 removed outlier: 3.601A pdb=" N VAL A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 312 through 330 removed outlier: 4.469A pdb=" N ASP A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLU A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 364 Processing helix chain 'A' and resid 394 through 399 removed outlier: 3.525A pdb=" N LYS A 398 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 479 through 483 Processing helix chain 'C' and resid 56 through 71 removed outlier: 3.718A pdb=" N ALA C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 81 through 99 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 121 through 137 Processing helix chain 'C' and resid 171 through 186 Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 199 through 213 removed outlier: 3.654A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 247 through 261 Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.737A pdb=" N GLU C 325 " --> pdb=" O ARG C 321 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 365 Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 437 through 447 removed outlier: 3.688A pdb=" N ILE C 441 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 485 removed outlier: 3.634A pdb=" N GLU C 485 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 removed outlier: 3.729A pdb=" N ALA D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 81 through 99 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 121 through 137 Processing helix chain 'D' and resid 171 through 187 Proline residue: D 182 - end of helix Processing helix chain 'D' and resid 199 through 213 removed outlier: 3.654A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 247 through 261 Processing helix chain 'D' and resid 283 through 297 Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.505A pdb=" N LYS D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 365 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 413 through 422 Processing helix chain 'D' and resid 437 through 447 removed outlier: 3.683A pdb=" N ILE D 441 " --> pdb=" O ILE D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 486 Processing helix chain 'B' and resid 56 through 71 Processing helix chain 'B' and resid 81 through 99 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.610A pdb=" N ASN B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 136 Processing helix chain 'B' and resid 171 through 187 Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 199 through 213 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 283 through 297 removed outlier: 3.602A pdb=" N VAL B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 312 through 330 removed outlier: 4.469A pdb=" N ASP B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N GLU B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 394 through 399 removed outlier: 3.524A pdb=" N LYS B 398 " --> pdb=" O MET B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 422 Processing helix chain 'B' and resid 436 through 447 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 41 removed outlier: 4.361A pdb=" N CYS A 50 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 145 removed outlier: 4.221A pdb=" N THR A 153 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL B 452 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR A 491 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL B 454 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR A 493 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 219 through 221 removed outlier: 6.216A pdb=" N VAL A 190 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N CYS A 163 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS A 193 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLN A 165 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 242 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLU A 269 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE A 244 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 removed outlier: 4.123A pdb=" N THR B 153 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 385 through 386 removed outlier: 7.300A pdb=" N THR A 385 " --> pdb=" O GLN A 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 41 removed outlier: 5.663A pdb=" N PHE C 38 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN C 51 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 40 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.325A pdb=" N THR C 153 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N VAL D 452 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR C 491 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL D 454 " --> pdb=" O THR C 491 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N THR C 493 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA D 430 " --> pdb=" O TRP D 453 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N SER D 274 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N SER D 307 " --> pdb=" O GLN D 407 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N MET D 409 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE D 309 " --> pdb=" O MET D 409 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE D 411 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL D 311 " --> pdb=" O PHE D 411 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS D 410 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL D 386 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 219 through 221 removed outlier: 6.623A pdb=" N CYS C 163 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LYS C 193 " --> pdb=" O CYS C 163 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN C 165 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 367 through 368 removed outlier: 6.654A pdb=" N LYS C 410 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER C 307 " --> pdb=" O GLN C 407 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N MET C 409 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE C 309 " --> pdb=" O MET C 409 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE C 411 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N VAL C 311 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER C 274 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA C 430 " --> pdb=" O TRP C 453 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR D 153 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 23 through 25 Processing sheet with id=AB4, first strand: chain 'D' and resid 37 through 41 removed outlier: 5.632A pdb=" N PHE D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN D 51 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL D 40 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 219 through 221 removed outlier: 6.608A pdb=" N CYS D 163 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LYS D 193 " --> pdb=" O CYS D 163 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN D 165 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 374 through 375 removed outlier: 4.182A pdb=" N PHE D 381 " --> pdb=" O TRP D 375 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=AB8, first strand: chain 'B' and resid 37 through 41 removed outlier: 4.360A pdb=" N CYS B 50 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.216A pdb=" N VAL B 190 " --> pdb=" O ASN B 220 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N CYS B 163 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS B 193 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N GLN B 165 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 242 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLU B 269 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE B 244 " --> pdb=" O GLU B 269 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 385 through 386 removed outlier: 7.300A pdb=" N THR B 385 " --> pdb=" O GLN B 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 721 hydrogen bonds defined for protein. 2094 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: 8.68 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 15052 1.01 - 1.21: 54 1.21 - 1.41: 6269 1.41 - 1.61: 9049 1.61 - 1.81: 108 Bond restraints: 30532 Sorted by residual: bond pdb=" SG CYS A 303 " pdb=" HG CYS A 303 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" SG CYS A 276 " pdb=" HG CYS A 276 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" SG CYS B 303 " pdb=" HG CYS B 303 " ideal model delta sigma weight residual 1.200 1.338 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" SG CYS B 456 " pdb=" HG CYS B 456 " ideal model delta sigma weight residual 1.200 1.338 -0.138 2.00e-02 2.50e+03 4.74e+01 bond pdb=" SG CYS A 456 " pdb=" HG CYS A 456 " ideal model delta sigma weight residual 1.200 1.337 -0.137 2.00e-02 2.50e+03 4.71e+01 ... (remaining 30527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 54299 2.05 - 4.11: 923 4.11 - 6.16: 90 6.16 - 8.22: 13 8.22 - 10.27: 6 Bond angle restraints: 55331 Sorted by residual: angle pdb=" N ILE D 140 " pdb=" CA ILE D 140 " pdb=" C ILE D 140 " ideal model delta sigma weight residual 108.89 100.23 8.66 1.32e+00 5.74e-01 4.31e+01 angle pdb=" N THR C 144 " pdb=" CA THR C 144 " pdb=" C THR C 144 " ideal model delta sigma weight residual 108.73 98.46 10.27 1.63e+00 3.76e-01 3.97e+01 angle pdb=" N ILE C 140 " pdb=" CA ILE C 140 " pdb=" C ILE C 140 " ideal model delta sigma weight residual 108.89 100.66 8.23 1.32e+00 5.74e-01 3.89e+01 angle pdb=" N THR D 144 " pdb=" CA THR D 144 " pdb=" C THR D 144 " ideal model delta sigma weight residual 108.73 98.70 10.03 1.63e+00 3.76e-01 3.79e+01 angle pdb=" N LYS A 273 " pdb=" CA LYS A 273 " pdb=" C LYS A 273 " ideal model delta sigma weight residual 108.20 99.05 9.15 1.71e+00 3.42e-01 2.86e+01 ... (remaining 55326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 12444 17.94 - 35.87: 1294 35.87 - 53.81: 437 53.81 - 71.75: 131 71.75 - 89.68: 27 Dihedral angle restraints: 14333 sinusoidal: 7821 harmonic: 6512 Sorted by residual: dihedral pdb=" CA PRO A 168 " pdb=" C PRO A 168 " pdb=" N TRP A 169 " pdb=" CA TRP A 169 " ideal model delta harmonic sigma weight residual -180.00 -153.04 -26.96 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA PRO B 168 " pdb=" C PRO B 168 " pdb=" N TRP B 169 " pdb=" CA TRP B 169 " ideal model delta harmonic sigma weight residual 180.00 -153.09 -26.91 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" C THR C 14 " pdb=" N THR C 14 " pdb=" CA THR C 14 " pdb=" CB THR C 14 " ideal model delta harmonic sigma weight residual -122.00 -132.71 10.71 0 2.50e+00 1.60e-01 1.84e+01 ... (remaining 14330 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2014 0.071 - 0.143: 269 0.143 - 0.214: 13 0.214 - 0.286: 6 0.286 - 0.357: 2 Chirality restraints: 2304 Sorted by residual: chirality pdb=" CA THR C 14 " pdb=" N THR C 14 " pdb=" C THR C 14 " pdb=" CB THR C 14 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA VAL C 11 " pdb=" N VAL C 11 " pdb=" C VAL C 11 " pdb=" CB VAL C 11 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA LYS B 273 " pdb=" N LYS B 273 " pdb=" C LYS B 273 " pdb=" CB LYS B 273 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 2301 not shown) Planarity restraints: 4566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 121 " 0.308 2.00e-02 2.50e+03 4.13e-01 2.55e+03 pdb=" CG ASN D 121 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN D 121 " -0.308 2.00e-02 2.50e+03 pdb=" ND2 ASN D 121 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN D 121 " 0.657 2.00e-02 2.50e+03 pdb="HD22 ASN D 121 " -0.633 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 262 " 0.305 2.00e-02 2.50e+03 3.58e-01 1.93e+03 pdb=" CG ASN A 262 " -0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN A 262 " -0.301 2.00e-02 2.50e+03 pdb=" ND2 ASN A 262 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 262 " -0.537 2.00e-02 2.50e+03 pdb="HD22 ASN A 262 " 0.547 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 262 " -0.261 2.00e-02 2.50e+03 2.82e-01 1.19e+03 pdb=" CG ASN B 262 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN B 262 " 0.259 2.00e-02 2.50e+03 pdb=" ND2 ASN B 262 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 262 " 0.411 2.00e-02 2.50e+03 pdb="HD22 ASN B 262 " -0.414 2.00e-02 2.50e+03 ... (remaining 4563 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 1313 2.16 - 2.77: 60542 2.77 - 3.38: 90865 3.38 - 3.99: 120960 3.99 - 4.60: 190489 Nonbonded interactions: 464169 Sorted by model distance: nonbonded pdb=" HG1 THR D 442 " pdb=" HG SER B 497 " model vdw 1.554 2.100 nonbonded pdb=" O VAL C 489 " pdb="HH21 ARG D 476 " model vdw 1.615 2.450 nonbonded pdb=" H SER C 501 " pdb=" O ARG B 78 " model vdw 1.617 2.450 nonbonded pdb=" O ARG A 78 " pdb=" H SER D 501 " model vdw 1.618 2.450 nonbonded pdb="HH21 ARG C 476 " pdb=" O VAL D 489 " model vdw 1.625 2.450 ... (remaining 464164 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name H )) or resid 126 through 501)) selection = (chain 'B' and (resid 17 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name H )) or resid 126 through 501)) selection = (chain 'C' and ((resid 17 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 18 through 501)) selection = (chain 'D' and ((resid 17 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 18 through 124 or (resid 125 and (name N o \ r name CA or name C or name O or name H )) or resid 126 through 501)) } 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 individual isotropic 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: 2.600 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: 0.170 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 31.500 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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:9.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 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 0.042 15436 Z= 0.255 Angle : 0.772 10.272 20890 Z= 0.479 Chirality : 0.048 0.357 2304 Planarity : 0.005 0.092 2704 Dihedral : 17.106 89.682 5678 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.97 % Allowed : 22.40 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.20), residues: 1948 helix: 0.29 (0.18), residues: 838 sheet: -1.30 (0.28), residues: 362 loop : -0.96 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 476 TYR 0.018 0.002 TYR D 351 PHE 0.011 0.001 PHE D 483 TRP 0.022 0.001 TRP C 375 HIS 0.014 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00421 (15436) covalent geometry : angle 0.77249 (20890) hydrogen bonds : bond 0.15331 ( 721) hydrogen bonds : angle 7.20812 ( 2094) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.5511 (mmpt) cc_final: 0.5266 (mmpt) REVERT: C 46 GLU cc_start: 0.7724 (mp0) cc_final: 0.7214 (mp0) REVERT: B 65 LYS cc_start: 0.5489 (mmpt) cc_final: 0.5244 (mmpt) outliers start: 48 outliers final: 33 residues processed: 239 average time/residue: 1.0589 time to fit residues: 288.1802 Evaluate side-chains 207 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 9.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 121 ASN D 389 ASN D 474 ASN ** B 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.181025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141993 restraints weight = 45750.228| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.73 r_work: 0.3518 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15436 Z= 0.204 Angle : 0.583 5.535 20890 Z= 0.317 Chirality : 0.044 0.135 2304 Planarity : 0.006 0.086 2704 Dihedral : 7.041 82.898 2139 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.94 % Rotamer: Outliers : 3.59 % Allowed : 22.90 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.19), residues: 1948 helix: 0.53 (0.18), residues: 842 sheet: -1.41 (0.26), residues: 382 loop : -1.11 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 143 TYR 0.012 0.002 TYR C 316 PHE 0.016 0.002 PHE D 483 TRP 0.010 0.002 TRP C 453 HIS 0.013 0.002 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00462 (15436) covalent geometry : angle 0.58257 (20890) hydrogen bonds : bond 0.05023 ( 721) hydrogen bonds : angle 5.48195 ( 2094) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 189 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 436 ASP cc_start: 0.7267 (t70) cc_final: 0.6759 (t70) REVERT: C 52 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8517 (t) REVERT: C 262 ASN cc_start: 0.7486 (p0) cc_final: 0.7182 (p0) REVERT: D 143 ARG cc_start: 0.8109 (mtt180) cc_final: 0.7671 (mtp85) REVERT: B 143 ARG cc_start: 0.8266 (mtt180) cc_final: 0.7604 (mtp85) REVERT: B 436 ASP cc_start: 0.7332 (t70) cc_final: 0.6821 (t70) outliers start: 58 outliers final: 40 residues processed: 229 average time/residue: 1.0417 time to fit residues: 271.6547 Evaluate side-chains 219 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 178 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 370 CYS Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 484 HIS Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 191 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 169 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 334 ASN ** C 484 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 474 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.179309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.137542 restraints weight = 45788.543| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.78 r_work: 0.3500 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15436 Z= 0.232 Angle : 0.588 5.797 20890 Z= 0.321 Chirality : 0.045 0.143 2304 Planarity : 0.006 0.082 2704 Dihedral : 6.875 85.740 2127 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 4.27 % Allowed : 22.46 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.19), residues: 1948 helix: 0.37 (0.18), residues: 842 sheet: -1.56 (0.26), residues: 372 loop : -1.30 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 143 TYR 0.013 0.002 TYR C 457 PHE 0.014 0.002 PHE B 24 TRP 0.012 0.002 TRP D 136 HIS 0.013 0.002 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00539 (15436) covalent geometry : angle 0.58829 (20890) hydrogen bonds : bond 0.04940 ( 721) hydrogen bonds : angle 5.30752 ( 2094) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 186 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.6636 (ttmt) REVERT: C 262 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.7095 (p0) REVERT: D 46 GLU cc_start: 0.7842 (mp0) cc_final: 0.7175 (mp0) REVERT: D 284 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.6969 (tt) REVERT: D 415 ASP cc_start: 0.7571 (p0) cc_final: 0.7365 (p0) REVERT: D 484 HIS cc_start: 0.7525 (OUTLIER) cc_final: 0.6939 (p-80) REVERT: B 91 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.6643 (ttmt) outliers start: 69 outliers final: 48 residues processed: 240 average time/residue: 0.9472 time to fit residues: 260.5500 Evaluate side-chains 226 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 173 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 497 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 484 HIS Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 50 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 112 optimal weight: 0.1980 chunk 131 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 HIS A 293 HIS C 19 GLN D 117 ASN D 474 ASN B 42 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 HIS B 293 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.180637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138947 restraints weight = 45299.271| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.78 r_work: 0.3523 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15436 Z= 0.180 Angle : 0.554 5.482 20890 Z= 0.299 Chirality : 0.043 0.137 2304 Planarity : 0.005 0.084 2704 Dihedral : 6.727 84.970 2125 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 4.27 % Allowed : 22.52 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.19), residues: 1948 helix: 0.50 (0.18), residues: 842 sheet: -1.62 (0.25), residues: 372 loop : -1.26 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 TYR 0.010 0.002 TYR B 457 PHE 0.013 0.002 PHE B 24 TRP 0.012 0.002 TRP C 375 HIS 0.010 0.002 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00415 (15436) covalent geometry : angle 0.55418 (20890) hydrogen bonds : bond 0.04379 ( 721) hydrogen bonds : angle 5.10370 ( 2094) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 181 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.5558 (mm-30) cc_final: 0.5154 (mm-30) REVERT: A 91 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.6634 (ttmt) REVERT: A 106 MET cc_start: 0.6239 (tmm) cc_final: 0.5946 (tmm) REVERT: C 262 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7126 (p0) REVERT: D 46 GLU cc_start: 0.7818 (mp0) cc_final: 0.7103 (mp0) REVERT: D 284 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6958 (tp) REVERT: D 484 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.7084 (p-80) REVERT: B 46 GLU cc_start: 0.5586 (mm-30) cc_final: 0.5178 (mm-30) REVERT: B 91 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.6653 (ttmt) REVERT: B 106 MET cc_start: 0.6291 (tmm) cc_final: 0.5999 (tmm) outliers start: 69 outliers final: 56 residues processed: 237 average time/residue: 0.9836 time to fit residues: 266.6992 Evaluate side-chains 233 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 172 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 484 HIS Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 42 ASN Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 391 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 136 optimal weight: 0.0670 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN D 117 ASN D 474 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.179849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137995 restraints weight = 45719.578| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.78 r_work: 0.3519 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15436 Z= 0.217 Angle : 0.572 5.688 20890 Z= 0.312 Chirality : 0.044 0.143 2304 Planarity : 0.006 0.087 2704 Dihedral : 6.721 84.655 2123 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.03 % Favored : 94.92 % Rotamer: Outliers : 4.46 % Allowed : 22.28 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.19), residues: 1948 helix: 0.42 (0.18), residues: 842 sheet: -1.64 (0.26), residues: 370 loop : -1.31 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 143 TYR 0.012 0.002 TYR D 426 PHE 0.014 0.002 PHE B 24 TRP 0.012 0.002 TRP C 375 HIS 0.011 0.002 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00507 (15436) covalent geometry : angle 0.57163 (20890) hydrogen bonds : bond 0.04533 ( 721) hydrogen bonds : angle 5.11143 ( 2094) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 181 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.6664 (ttmt) REVERT: C 262 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7141 (p0) REVERT: C 419 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7101 (mmpt) REVERT: D 46 GLU cc_start: 0.7821 (mp0) cc_final: 0.7136 (mp0) REVERT: D 284 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6954 (tp) REVERT: D 484 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.7223 (p-80) REVERT: B 91 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.6685 (ttmt) outliers start: 72 outliers final: 61 residues processed: 240 average time/residue: 0.9795 time to fit residues: 269.5913 Evaluate side-chains 241 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 484 HIS Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 110 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 188 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN D 117 ASN D 474 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.180909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139111 restraints weight = 45399.031| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.78 r_work: 0.3530 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15436 Z= 0.172 Angle : 0.544 5.436 20890 Z= 0.294 Chirality : 0.043 0.132 2304 Planarity : 0.005 0.085 2704 Dihedral : 6.626 83.544 2123 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.17 % Rotamer: Outliers : 4.33 % Allowed : 22.34 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.19), residues: 1948 helix: 0.58 (0.18), residues: 842 sheet: -1.68 (0.25), residues: 372 loop : -1.23 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.010 0.002 TYR B 457 PHE 0.014 0.002 PHE A 24 TRP 0.014 0.002 TRP C 375 HIS 0.009 0.002 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00397 (15436) covalent geometry : angle 0.54361 (20890) hydrogen bonds : bond 0.04208 ( 721) hydrogen bonds : angle 5.00768 ( 2094) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 182 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.5410 (mm-30) cc_final: 0.5021 (mm-30) REVERT: A 91 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.6633 (ttmt) REVERT: A 106 MET cc_start: 0.6208 (tmm) cc_final: 0.5962 (tmm) REVERT: C 262 ASN cc_start: 0.7630 (OUTLIER) cc_final: 0.7052 (p0) REVERT: C 419 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7052 (mmpt) REVERT: D 284 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6948 (tp) REVERT: D 484 HIS cc_start: 0.7503 (OUTLIER) cc_final: 0.7280 (p-80) REVERT: B 91 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.6664 (ttmt) REVERT: B 106 MET cc_start: 0.6258 (tmm) cc_final: 0.6013 (tmm) REVERT: B 436 ASP cc_start: 0.7352 (t70) cc_final: 0.6862 (t70) outliers start: 70 outliers final: 55 residues processed: 243 average time/residue: 1.0020 time to fit residues: 278.3646 Evaluate side-chains 239 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 178 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain D residue 484 HIS Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 105 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 474 ASN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.181188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139356 restraints weight = 45281.751| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.82 r_work: 0.3521 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15436 Z= 0.167 Angle : 0.538 5.389 20890 Z= 0.291 Chirality : 0.043 0.133 2304 Planarity : 0.005 0.086 2704 Dihedral : 6.198 65.661 2120 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.72 % Favored : 95.23 % Rotamer: Outliers : 4.52 % Allowed : 22.40 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.19), residues: 1948 helix: 0.66 (0.18), residues: 842 sheet: -1.69 (0.25), residues: 372 loop : -1.21 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.010 0.002 TYR D 426 PHE 0.013 0.001 PHE B 24 TRP 0.015 0.002 TRP C 375 HIS 0.010 0.002 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00387 (15436) covalent geometry : angle 0.53772 (20890) hydrogen bonds : bond 0.04108 ( 721) hydrogen bonds : angle 4.96194 ( 2094) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 182 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.5535 (mm-30) cc_final: 0.5294 (mm-30) REVERT: A 91 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.6714 (ttmt) REVERT: A 106 MET cc_start: 0.6127 (tmm) cc_final: 0.5749 (tmm) REVERT: A 436 ASP cc_start: 0.7329 (t70) cc_final: 0.6864 (t70) REVERT: C 262 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7088 (p0) REVERT: C 419 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7081 (mmpt) REVERT: D 284 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7023 (tp) REVERT: D 484 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.7275 (p-80) REVERT: B 46 GLU cc_start: 0.5531 (mm-30) cc_final: 0.5283 (mm-30) REVERT: B 91 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.6741 (ttmt) REVERT: B 106 MET cc_start: 0.6170 (tmm) cc_final: 0.5792 (tmm) outliers start: 73 outliers final: 61 residues processed: 243 average time/residue: 0.9954 time to fit residues: 276.7094 Evaluate side-chains 242 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain D residue 484 HIS Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 4 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 48 optimal weight: 0.4980 chunk 154 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN D 423 ASN D 474 ASN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.181237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139279 restraints weight = 45271.066| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.81 r_work: 0.3536 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15436 Z= 0.168 Angle : 0.538 5.355 20890 Z= 0.291 Chirality : 0.043 0.134 2304 Planarity : 0.005 0.084 2704 Dihedral : 6.173 65.189 2120 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.77 % Favored : 95.17 % Rotamer: Outliers : 4.46 % Allowed : 22.65 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.19), residues: 1948 helix: 0.70 (0.18), residues: 842 sheet: -1.68 (0.25), residues: 372 loop : -1.21 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 321 TYR 0.013 0.002 TYR C 351 PHE 0.014 0.002 PHE A 402 TRP 0.018 0.002 TRP C 375 HIS 0.012 0.002 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00389 (15436) covalent geometry : angle 0.53799 (20890) hydrogen bonds : bond 0.04067 ( 721) hydrogen bonds : angle 4.93472 ( 2094) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 176 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.5595 (mm-30) cc_final: 0.5347 (mm-30) REVERT: A 91 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.6701 (ttmt) REVERT: A 106 MET cc_start: 0.6275 (tmm) cc_final: 0.5941 (tmm) REVERT: C 262 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7088 (p0) REVERT: C 419 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7071 (mmpt) REVERT: D 284 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7051 (tp) REVERT: D 320 VAL cc_start: 0.8547 (t) cc_final: 0.8249 (p) REVERT: D 484 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.7240 (p-80) REVERT: B 46 GLU cc_start: 0.5590 (mm-30) cc_final: 0.5338 (mm-30) REVERT: B 91 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.6740 (ttmt) REVERT: B 106 MET cc_start: 0.6316 (tmm) cc_final: 0.5984 (tmm) outliers start: 72 outliers final: 62 residues processed: 238 average time/residue: 0.9482 time to fit residues: 258.8730 Evaluate side-chains 244 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 176 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 262 ASN Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain D residue 484 HIS Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 497 SER Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 142 optimal weight: 0.0670 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN D 474 ASN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.183220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141528 restraints weight = 45318.302| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.78 r_work: 0.3566 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15436 Z= 0.118 Angle : 0.507 4.927 20890 Z= 0.272 Chirality : 0.042 0.140 2304 Planarity : 0.005 0.088 2704 Dihedral : 5.943 64.765 2119 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.85 % Favored : 96.10 % Rotamer: Outliers : 3.53 % Allowed : 23.39 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.19), residues: 1948 helix: 1.06 (0.18), residues: 836 sheet: -1.62 (0.25), residues: 378 loop : -1.12 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 321 TYR 0.011 0.001 TYR C 90 PHE 0.013 0.001 PHE A 24 TRP 0.020 0.001 TRP C 375 HIS 0.008 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00267 (15436) covalent geometry : angle 0.50690 (20890) hydrogen bonds : bond 0.03592 ( 721) hydrogen bonds : angle 4.76296 ( 2094) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 186 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.5503 (mm-30) cc_final: 0.5249 (mm-30) REVERT: A 91 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.6600 (ttmt) REVERT: A 368 LEU cc_start: 0.7625 (tt) cc_final: 0.6772 (mm) REVERT: A 436 ASP cc_start: 0.7165 (t70) cc_final: 0.6695 (t70) REVERT: C 419 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.6894 (mmtt) REVERT: D 284 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6970 (tp) REVERT: D 320 VAL cc_start: 0.8456 (t) cc_final: 0.8191 (p) REVERT: B 46 GLU cc_start: 0.5581 (mm-30) cc_final: 0.5324 (mm-30) REVERT: B 90 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: B 436 ASP cc_start: 0.7171 (t70) cc_final: 0.6700 (t70) outliers start: 57 outliers final: 43 residues processed: 236 average time/residue: 1.0274 time to fit residues: 276.9652 Evaluate side-chains 226 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 484 HIS Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 180 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 135 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN D 117 ASN D 474 ASN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.183277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.141162 restraints weight = 45239.133| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 1.84 r_work: 0.3550 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15436 Z= 0.131 Angle : 0.514 4.891 20890 Z= 0.276 Chirality : 0.042 0.139 2304 Planarity : 0.005 0.087 2704 Dihedral : 5.803 63.509 2111 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.41 % Favored : 95.53 % Rotamer: Outliers : 2.97 % Allowed : 24.01 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1948 helix: 1.08 (0.18), residues: 838 sheet: -1.61 (0.25), residues: 378 loop : -1.06 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 321 TYR 0.017 0.001 TYR C 351 PHE 0.016 0.001 PHE D 483 TRP 0.020 0.001 TRP C 375 HIS 0.009 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00301 (15436) covalent geometry : angle 0.51419 (20890) hydrogen bonds : bond 0.03660 ( 721) hydrogen bonds : angle 4.74596 ( 2094) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3896 Ramachandran restraints generated. 1948 Oldfield, 0 Emsley, 1948 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.5494 (mm-30) cc_final: 0.5228 (mm-30) REVERT: A 106 MET cc_start: 0.6001 (tmm) cc_final: 0.5758 (tmm) REVERT: A 368 LEU cc_start: 0.7650 (tt) cc_final: 0.6779 (mm) REVERT: A 436 ASP cc_start: 0.7189 (t70) cc_final: 0.6714 (t70) REVERT: D 284 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7027 (tp) REVERT: D 320 VAL cc_start: 0.8471 (t) cc_final: 0.8211 (p) REVERT: B 46 GLU cc_start: 0.5591 (mm-30) cc_final: 0.5329 (mm-30) REVERT: B 90 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: B 106 MET cc_start: 0.6042 (tmm) cc_final: 0.5792 (tmm) REVERT: B 436 ASP cc_start: 0.7200 (t70) cc_final: 0.6725 (t70) outliers start: 48 outliers final: 43 residues processed: 223 average time/residue: 0.9818 time to fit residues: 250.2872 Evaluate side-chains 222 residues out of total 1616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 108 SER Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 442 THR Chi-restraints excluded: chain C residue 484 HIS Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 497 SER Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 311 VAL Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 348 LYS Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 445 SER Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 497 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 138 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 474 ASN D 117 ASN D 474 ASN ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.182967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140678 restraints weight = 45573.196| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.85 r_work: 0.3552 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15436 Z= 0.141 Angle : 0.517 5.024 20890 Z= 0.278 Chirality : 0.042 0.141 2304 Planarity : 0.005 0.087 2704 Dihedral : 5.807 63.251 2111 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.97 % Allowed : 24.07 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.19), residues: 1948 helix: 1.08 (0.18), residues: 838 sheet: -1.62 (0.25), residues: 378 loop : -1.06 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 321 TYR 0.009 0.001 TYR C 90 PHE 0.023 0.001 PHE A 24 TRP 0.020 0.001 TRP C 375 HIS 0.009 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00326 (15436) covalent geometry : angle 0.51708 (20890) hydrogen bonds : bond 0.03700 ( 721) hydrogen bonds : angle 4.74394 ( 2094) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9801.51 seconds wall clock time: 166 minutes 44.68 seconds (10004.68 seconds total)