Starting phenix.real_space_refine on Fri Aug 7 02:53:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s7s_54649/08_2026/9s7s_54649.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s7s_54649/08_2026/9s7s_54649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s7s_54649/08_2026/9s7s_54649.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s7s_54649/08_2026/9s7s_54649.map" model { file = "/net/cci-nas-00/data/ceres_data/9s7s_54649/08_2026/9s7s_54649.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s7s_54649/08_2026/9s7s_54649.cif" } resolution = 3.3 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= 0.001 sd= 0.025 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 40 5.16 5 C 5895 2.51 5 N 1534 2.21 5 O 1611 1.98 5 H 9113 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18193 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 7356 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 11, 'TRANS': 435} Chain breaks: 2 Chain: "B" Number of atoms: 7356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 7356 Classifications: {'peptide': 447} Link IDs: {'PTRANS': 11, 'TRANS': 435} Chain breaks: 2 Chain: "C" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1802 Classifications: {'peptide': 117} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain breaks: 1 Chain: "D" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1679 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain breaks: 1 Time building chain proxies: 2.75, per 1000 atoms: 0.15 Number of scatterers: 18193 At special positions: 0 Unit cell: (125.424, 117.92, 94.336, 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 40 16.00 O 1611 8.00 N 1534 7.00 C 5895 6.00 H 9113 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 407 " - pdb=" SG CYS C 481 " distance=2.03 Simple disulfide: pdb=" SG CYS D 407 " - pdb=" SG CYS D 481 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 642.8 milliseconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 8 sheets defined 51.6% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 3 through 37 removed outlier: 4.062A pdb=" N ASN A 7 " --> pdb=" O HIS A 3 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 8 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LEU A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 27 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 48 through 70 removed outlier: 4.372A pdb=" N TRP A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 106 Processing helix chain 'A' and resid 110 through 139 removed outlier: 4.045A pdb=" N MET A 116 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 152 through 165 removed outlier: 3.531A pdb=" N GLU A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 204 removed outlier: 3.679A pdb=" N LEU A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR A 203 " --> pdb=" O LYS A 199 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 204' Processing helix chain 'A' and resid 219 through 233 removed outlier: 4.043A pdb=" N ARG A 223 " --> pdb=" O GLN A 219 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASN A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 308 Proline residue: A 297 - end of helix Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 373 through 380 Processing helix chain 'A' and resid 381 through 384 removed outlier: 3.850A pdb=" N LEU A 384 " --> pdb=" O LEU A 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 381 through 384' Processing helix chain 'A' and resid 385 through 392 removed outlier: 3.873A pdb=" N ASN A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 392 " --> pdb=" O PHE A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 392' Processing helix chain 'A' and resid 404 through 411 removed outlier: 4.095A pdb=" N GLU A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 4.055A pdb=" N TYR A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.582A pdb=" N VAL A 431 " --> pdb=" O GLY A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 452 removed outlier: 4.134A pdb=" N TYR A 444 " --> pdb=" O ASP A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 473 removed outlier: 3.544A pdb=" N ASP A 458 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 459 " --> pdb=" O MET A 455 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 37 removed outlier: 4.279A pdb=" N VAL B 8 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 49 through 70 removed outlier: 3.543A pdb=" N TRP B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 106 Processing helix chain 'B' and resid 110 through 139 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 152 through 165 Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 219 through 234 Processing helix chain 'B' and resid 273 through 308 Proline residue: B 297 - end of helix removed outlier: 3.692A pdb=" N LYS B 308 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 380 Processing helix chain 'B' and resid 381 through 384 Processing helix chain 'B' and resid 385 through 392 removed outlier: 3.874A pdb=" N ASN B 389 " --> pdb=" O PRO B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.561A pdb=" N GLU B 409 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 removed outlier: 3.759A pdb=" N TYR B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 3.725A pdb=" N VAL B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.786A pdb=" N ARG B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 474 removed outlier: 3.509A pdb=" N ILE B 459 " --> pdb=" O MET B 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 441 removed outlier: 3.718A pdb=" N SER C 441 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.961A pdb=" N ASP C 475 " --> pdb=" O LYS C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 497 Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 447 through 450 Processing helix chain 'D' and resid 492 through 496 Processing sheet with id=AA1, first strand: chain 'A' and resid 193 through 196 removed outlier: 3.908A pdb=" N GLN A 193 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG A 144 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 173 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR A 146 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHE A 175 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE A 148 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASP A 177 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN A 210 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL B 262 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 257 removed outlier: 3.665A pdb=" N VAL A 262 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE B 211 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASP B 145 " --> pdb=" O GLN B 210 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE B 212 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N TRP B 147 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ARG B 144 " --> pdb=" O ASN B 171 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B 173 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR B 146 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE B 175 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N GLN B 193 " --> pdb=" O ASN B 171 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL B 173 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ILE B 195 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE B 175 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 320 Processing sheet with id=AA5, first strand: chain 'B' and resid 318 through 320 Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 6 removed outlier: 4.159A pdb=" N LEU C 405 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 444 through 445 removed outlier: 6.754A pdb=" N TRP C 421 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER C 435 " --> pdb=" O MET C 419 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N MET C 419 " --> pdb=" O SER C 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 434 through 436 414 hydrogen bonds defined for protein. 1179 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: 3.21 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9105 1.03 - 1.23: 10 1.23 - 1.42: 4033 1.42 - 1.62: 5201 1.62 - 1.81: 68 Bond restraints: 18417 Sorted by residual: bond pdb=" N HIS B 3 " pdb=" CA HIS B 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 bond pdb=" N VAL D 2 " pdb=" CA VAL D 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 bond pdb=" N HIS A 3 " pdb=" CA HIS A 3 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N HIS B 3 " pdb=" H HIS B 3 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" N HIS A 3 " pdb=" H HIS A 3 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.22e+00 ... (remaining 18412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 32831 1.73 - 3.47: 320 3.47 - 5.20: 31 5.20 - 6.94: 2 6.94 - 8.67: 1 Bond angle restraints: 33185 Sorted by residual: angle pdb=" N LYS D 450 " pdb=" CA LYS D 450 " pdb=" C LYS D 450 " ideal model delta sigma weight residual 113.55 108.36 5.19 1.26e+00 6.30e-01 1.69e+01 angle pdb=" CB LYS D 450 " pdb=" CG LYS D 450 " pdb=" CD LYS D 450 " ideal model delta sigma weight residual 111.30 119.97 -8.67 2.30e+00 1.89e-01 1.42e+01 angle pdb=" N GLY D 451 " pdb=" CA GLY D 451 " pdb=" C GLY D 451 " ideal model delta sigma weight residual 112.73 108.55 4.18 1.20e+00 6.94e-01 1.21e+01 angle pdb=" N SER D 470 " pdb=" CA SER D 470 " pdb=" CB SER D 470 " ideal model delta sigma weight residual 114.27 109.70 4.57 1.64e+00 3.72e-01 7.76e+00 angle pdb=" N ASP B 413 " pdb=" CA ASP B 413 " pdb=" C ASP B 413 " ideal model delta sigma weight residual 114.39 110.72 3.67 1.45e+00 4.76e-01 6.40e+00 ... (remaining 33180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 7731 17.71 - 35.42: 644 35.42 - 53.13: 177 53.13 - 70.84: 57 70.84 - 88.55: 13 Dihedral angle restraints: 8622 sinusoidal: 4587 harmonic: 4035 Sorted by residual: dihedral pdb=" CA ASN D 469 " pdb=" C ASN D 469 " pdb=" N SER D 470 " pdb=" CA SER D 470 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA VAL D 478 " pdb=" C VAL D 478 " pdb=" N TYR D 479 " pdb=" CA TYR D 479 " ideal model delta harmonic sigma weight residual -180.00 -159.18 -20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CB CYS C 407 " pdb=" SG CYS C 407 " pdb=" SG CYS C 481 " pdb=" CB CYS C 481 " ideal model delta sinusoidal sigma weight residual 93.00 58.24 34.76 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 8619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 916 0.030 - 0.060: 303 0.060 - 0.090: 95 0.090 - 0.119: 62 0.119 - 0.149: 13 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CA ILE B 241 " pdb=" N ILE B 241 " pdb=" C ILE B 241 " pdb=" CB ILE B 241 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA VAL D 5 " pdb=" N VAL D 5 " pdb=" C VAL D 5 " pdb=" CB VAL D 5 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CG LEU A 58 " pdb=" CB LEU A 58 " pdb=" CD1 LEU A 58 " pdb=" CD2 LEU A 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1386 not shown) Planarity restraints: 2635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 424 " -0.036 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO D 425 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 425 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 425 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 425 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.54e+00 pdb=" N PRO D 426 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO D 426 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 426 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 366 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO A 367 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " -0.019 5.00e-02 4.00e+02 ... (remaining 2632 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.16: 834 2.16 - 2.77: 35391 2.77 - 3.38: 51800 3.38 - 3.99: 63509 3.99 - 4.60: 99458 Nonbonded interactions: 250992 Sorted by model distance: nonbonded pdb=" O ASN B 270 " pdb=" HG SER B 276 " model vdw 1.555 2.450 nonbonded pdb=" HZ3 LYS C 472 " pdb=" OE2 GLU C 474 " model vdw 1.561 2.450 nonbonded pdb=" O ASN A 270 " pdb=" HG SER A 276 " model vdw 1.611 2.450 nonbonded pdb="HD21 ASN A 225 " pdb=" O PRO C 487 " model vdw 1.612 2.450 nonbonded pdb=" O ASP B 438 " pdb=" H THR B 441 " model vdw 1.613 2.450 ... (remaining 250987 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 2 through 403 or resid 406 through 507)) selection = chain 'D' } 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: 1.210 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: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.370 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 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 : 0.002 0.039 9306 Z= 0.121 Angle : 0.563 8.669 12611 Z= 0.326 Chirality : 0.039 0.149 1389 Planarity : 0.003 0.054 1556 Dihedral : 14.041 88.551 3349 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 0.10 % Allowed : 12.21 % Favored : 87.69 % 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: 0.64 (0.26), residues: 1101 helix: 1.81 (0.25), residues: 462 sheet: -0.92 (0.42), residues: 160 loop : -0.40 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 497 TYR 0.010 0.001 TYR B 315 PHE 0.005 0.001 PHE C 414 TRP 0.007 0.001 TRP A 66 HIS 0.002 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 9304) covalent geometry : angle 0.56287 / 0.33 (12607) SS BOND : bond 0.00281 / 0.14 ( 2) SS BOND : angle 0.36490 / 0.26 ( 4) hydrogen bonds : bond 0.15320 / 10.73 ( 414) hydrogen bonds : angle 5.27645 / 3.92 ( 1179) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 0.291 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 VAL cc_start: 0.6808 (t) cc_final: 0.6521 (m) REVERT: A 72 ARG cc_start: 0.6797 (mtp85) cc_final: 0.6067 (mtp85) REVERT: A 104 PHE cc_start: 0.7451 (t80) cc_final: 0.7211 (t80) REVERT: A 153 LYS cc_start: 0.7801 (tppt) cc_final: 0.7185 (tppt) REVERT: A 196 SER cc_start: 0.8237 (p) cc_final: 0.7687 (p) REVERT: A 219 GLN cc_start: 0.8166 (mt0) cc_final: 0.7789 (mt0) REVERT: A 233 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.6729 (ttm170) REVERT: A 250 ASP cc_start: 0.7249 (m-30) cc_final: 0.6794 (m-30) REVERT: A 254 MET cc_start: 0.6600 (tmm) cc_final: 0.6324 (tmm) REVERT: A 261 GLU cc_start: 0.6384 (mp0) cc_final: 0.5583 (mp0) REVERT: A 262 VAL cc_start: 0.7383 (p) cc_final: 0.7079 (m) REVERT: A 392 LYS cc_start: 0.7713 (mttt) cc_final: 0.7317 (mttt) REVERT: A 394 GLU cc_start: 0.5977 (mp0) cc_final: 0.5705 (mp0) REVERT: A 401 ARG cc_start: 0.7290 (ttp80) cc_final: 0.6914 (ttm-80) REVERT: A 438 ASP cc_start: 0.6134 (t0) cc_final: 0.5876 (t0) REVERT: B 8 VAL cc_start: 0.6751 (t) cc_final: 0.6525 (p) REVERT: B 33 LEU cc_start: 0.7836 (mm) cc_final: 0.7516 (tp) REVERT: B 37 LEU cc_start: 0.7438 (tp) cc_final: 0.7120 (tp) REVERT: B 48 GLN cc_start: 0.5024 (mm110) cc_final: 0.4213 (pt0) REVERT: B 50 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6748 (mt-10) REVERT: B 98 GLU cc_start: 0.7583 (tt0) cc_final: 0.7301 (tt0) REVERT: B 110 SER cc_start: 0.7860 (t) cc_final: 0.7541 (p) REVERT: B 203 THR cc_start: 0.8379 (t) cc_final: 0.8119 (p) REVERT: B 237 TYR cc_start: 0.7820 (m-80) cc_final: 0.7613 (m-10) REVERT: C 412 ARG cc_start: 0.5886 (mtm-85) cc_final: 0.5627 (mtm-85) REVERT: C 419 MET cc_start: 0.6874 (mmp) cc_final: 0.6186 (mmp) REVERT: C 442 ASN cc_start: 0.8307 (m110) cc_final: 0.7978 (m-40) REVERT: D 4 LEU cc_start: 0.8308 (pt) cc_final: 0.8062 (mt) outliers start: 1 outliers final: 0 residues processed: 334 average time/residue: 0.2289 time to fit residues: 101.7009 Evaluate side-chains 278 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.0020 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS A 224 ASN B 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.152078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.130243 restraints weight = 44957.169| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.92 r_work: 0.3588 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9306 Z= 0.155 Angle : 0.570 6.270 12611 Z= 0.307 Chirality : 0.041 0.168 1389 Planarity : 0.004 0.051 1556 Dihedral : 4.646 20.266 1240 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 1.22 % Allowed : 17.19 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.56 (0.26), residues: 1101 helix: 1.69 (0.24), residues: 470 sheet: -0.88 (0.44), residues: 152 loop : -0.47 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 266 TYR 0.017 0.001 TYR B 315 PHE 0.012 0.001 PHE B 265 TRP 0.011 0.001 TRP A 81 HIS 0.005 0.001 HIS A 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 9304) covalent geometry : angle 0.56966 / 0.31 (12607) SS BOND : bond 0.00524 / 0.26 ( 2) SS BOND : angle 0.44362 / 0.28 ( 4) hydrogen bonds : bond 0.04608 / 3.18 ( 414) hydrogen bonds : angle 4.39267 / 3.29 ( 1179) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 297 time to evaluate : 0.482 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8106 (m) cc_final: 0.7538 (p) REVERT: A 18 ASP cc_start: 0.7079 (p0) cc_final: 0.6867 (p0) REVERT: A 46 GLN cc_start: 0.7025 (tp-100) cc_final: 0.6558 (tp-100) REVERT: A 72 ARG cc_start: 0.7809 (mtp85) cc_final: 0.7310 (mtp85) REVERT: A 81 TRP cc_start: 0.8323 (m100) cc_final: 0.7986 (m100) REVERT: A 130 MET cc_start: 0.7596 (mmm) cc_final: 0.7384 (mmt) REVERT: A 219 GLN cc_start: 0.8843 (mt0) cc_final: 0.8621 (mt0) REVERT: A 229 GLU cc_start: 0.7627 (tp30) cc_final: 0.7107 (tp30) REVERT: A 250 ASP cc_start: 0.7001 (m-30) cc_final: 0.6709 (m-30) REVERT: A 254 MET cc_start: 0.7732 (tmm) cc_final: 0.7443 (tmm) REVERT: A 261 GLU cc_start: 0.7172 (mp0) cc_final: 0.6948 (mp0) REVERT: A 262 VAL cc_start: 0.8916 (p) cc_final: 0.8566 (m) REVERT: A 401 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7873 (ttm-80) REVERT: A 463 PHE cc_start: 0.7856 (m-10) cc_final: 0.7546 (m-10) REVERT: B 33 LEU cc_start: 0.8347 (mm) cc_final: 0.8089 (tp) REVERT: B 50 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7286 (mt-10) REVERT: B 69 ILE cc_start: 0.7843 (pt) cc_final: 0.7617 (mp) REVERT: B 98 GLU cc_start: 0.8252 (tt0) cc_final: 0.8016 (tt0) REVERT: B 110 SER cc_start: 0.8557 (t) cc_final: 0.8065 (p) REVERT: B 116 MET cc_start: 0.6731 (mmm) cc_final: 0.6488 (mmm) REVERT: B 176 VAL cc_start: 0.8348 (t) cc_final: 0.8135 (t) REVERT: B 207 LYS cc_start: 0.8574 (mttm) cc_final: 0.8218 (mtpp) REVERT: B 266 ARG cc_start: 0.7816 (ttp-170) cc_final: 0.7605 (ttp80) REVERT: B 335 MET cc_start: 0.4547 (mmp) cc_final: 0.4313 (mmp) REVERT: B 383 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 434 ARG cc_start: 0.7551 (ptp-170) cc_final: 0.6879 (ptp-170) REVERT: C 414 PHE cc_start: 0.7254 (t80) cc_final: 0.6883 (t80) REVERT: C 442 ASN cc_start: 0.8633 (m110) cc_final: 0.8278 (m110) REVERT: D 437 MET cc_start: 0.2269 (mmp) cc_final: 0.2033 (mmt) outliers start: 12 outliers final: 10 residues processed: 302 average time/residue: 0.2318 time to fit residues: 92.8941 Evaluate side-chains 297 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 287 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 416 SER Chi-restraints excluded: chain C residue 462 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 412 ASN C 509 GLN D 442 ASN D 467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.143301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121869 restraints weight = 44480.266| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.82 r_work: 0.3455 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9306 Z= 0.228 Angle : 0.612 4.748 12611 Z= 0.337 Chirality : 0.043 0.181 1389 Planarity : 0.005 0.055 1556 Dihedral : 4.969 21.057 1240 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.28 % Rotamer: Outliers : 2.03 % Allowed : 20.04 % Favored : 77.92 % 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: 0.13 (0.26), residues: 1101 helix: 1.48 (0.23), residues: 472 sheet: -1.22 (0.42), residues: 164 loop : -0.82 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 333 TYR 0.017 0.002 TYR B 418 PHE 0.023 0.002 PHE B 120 TRP 0.012 0.002 TRP A 81 HIS 0.004 0.001 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 ( 9304) covalent geometry : angle 0.61128 / 0.34 (12607) SS BOND : bond 0.01051 / 0.53 ( 2) SS BOND : angle 1.22310 / 0.70 ( 4) hydrogen bonds : bond 0.04986 / 3.40 ( 414) hydrogen bonds : angle 4.41110 / 3.31 ( 1179) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 339 time to evaluate : 0.458 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: 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 11 SER cc_start: 0.8769 (m) cc_final: 0.8315 (p) REVERT: A 12 ILE cc_start: 0.8561 (tp) cc_final: 0.8327 (mt) REVERT: A 46 GLN cc_start: 0.7335 (tp-100) cc_final: 0.6946 (tp-100) REVERT: A 72 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7572 (mtp85) REVERT: A 130 MET cc_start: 0.7945 (mmm) cc_final: 0.7708 (mmt) REVERT: A 153 LYS cc_start: 0.8482 (tppt) cc_final: 0.8073 (tppt) REVERT: A 180 ASP cc_start: 0.7951 (t0) cc_final: 0.7666 (t0) REVERT: A 198 ASP cc_start: 0.7575 (m-30) cc_final: 0.7297 (m-30) REVERT: A 203 THR cc_start: 0.8880 (t) cc_final: 0.8650 (p) REVERT: A 229 GLU cc_start: 0.8381 (tp30) cc_final: 0.8010 (tp30) REVERT: A 254 MET cc_start: 0.7817 (tmm) cc_final: 0.7554 (tmm) REVERT: A 265 PHE cc_start: 0.8224 (m-10) cc_final: 0.7938 (m-10) REVERT: A 318 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7134 (tm-30) REVERT: A 389 ASN cc_start: 0.8681 (t0) cc_final: 0.8253 (t0) REVERT: A 401 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7714 (ttm-80) REVERT: A 438 ASP cc_start: 0.7393 (t0) cc_final: 0.6967 (t0) REVERT: A 441 THR cc_start: 0.8182 (m) cc_final: 0.7710 (m) REVERT: A 463 PHE cc_start: 0.8239 (m-10) cc_final: 0.7872 (m-10) REVERT: B 23 THR cc_start: 0.8485 (m) cc_final: 0.8157 (p) REVERT: B 33 LEU cc_start: 0.8341 (mm) cc_final: 0.8063 (tp) REVERT: B 50 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7515 (mt-10) REVERT: B 110 SER cc_start: 0.8672 (t) cc_final: 0.8409 (m) REVERT: B 135 ILE cc_start: 0.8469 (pt) cc_final: 0.8091 (mm) REVERT: B 171 ASN cc_start: 0.8284 (t0) cc_final: 0.7983 (t0) REVERT: B 177 ASP cc_start: 0.8173 (t0) cc_final: 0.7885 (t0) REVERT: B 205 VAL cc_start: 0.8509 (t) cc_final: 0.8290 (p) REVERT: B 207 LYS cc_start: 0.8795 (mttm) cc_final: 0.8396 (mtpp) REVERT: B 265 PHE cc_start: 0.8323 (m-80) cc_final: 0.7966 (m-80) REVERT: B 284 ASP cc_start: 0.7602 (m-30) cc_final: 0.7158 (m-30) REVERT: B 317 HIS cc_start: 0.6341 (t-90) cc_final: 0.5572 (t-90) REVERT: B 328 LYS cc_start: 0.7148 (ptpp) cc_final: 0.6937 (mtpp) REVERT: B 383 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7319 (mt-10) REVERT: B 446 ASP cc_start: 0.8408 (m-30) cc_final: 0.8122 (m-30) REVERT: B 448 TRP cc_start: 0.8609 (t60) cc_final: 0.8399 (t60) outliers start: 20 outliers final: 14 residues processed: 348 average time/residue: 0.2326 time to fit residues: 107.2587 Evaluate side-chains 325 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 311 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 453 TRP Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 462 ASN Chi-restraints excluded: chain D residue 442 ASN Chi-restraints excluded: chain D residue 476 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN B 208 HIS ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 424 GLN ** C 509 GLN ** 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 = 0.3864 r_free = 0.3864 target = 0.141497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120129 restraints weight = 44534.613| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.85 r_work: 0.3427 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9306 Z= 0.201 Angle : 0.565 5.118 12611 Z= 0.309 Chirality : 0.041 0.200 1389 Planarity : 0.004 0.050 1556 Dihedral : 4.836 22.410 1240 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % Rotamer: Outliers : 2.14 % Allowed : 22.89 % Favored : 74.97 % 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: 0.20 (0.26), residues: 1101 helix: 1.62 (0.23), residues: 474 sheet: -1.30 (0.42), residues: 162 loop : -0.85 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 233 TYR 0.014 0.001 TYR C 444 PHE 0.013 0.001 PHE D 432 TRP 0.014 0.001 TRP B 114 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.20 ( 9304) covalent geometry : angle 0.56431 / 0.31 (12607) SS BOND : bond 0.00668 / 0.34 ( 2) SS BOND : angle 0.99980 / 0.72 ( 4) hydrogen bonds : bond 0.04521 / 3.08 ( 414) hydrogen bonds : angle 4.25006 / 3.20 ( 1179) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 325 time to evaluate : 0.485 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: 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 11 SER cc_start: 0.8780 (m) cc_final: 0.8348 (p) REVERT: A 12 ILE cc_start: 0.8536 (tp) cc_final: 0.8299 (mt) REVERT: A 46 GLN cc_start: 0.7372 (tp-100) cc_final: 0.6979 (tp-100) REVERT: A 72 ARG cc_start: 0.8157 (mtp85) cc_final: 0.7442 (mtp85) REVERT: A 130 MET cc_start: 0.7977 (mmm) cc_final: 0.7735 (mmt) REVERT: A 180 ASP cc_start: 0.7958 (t0) cc_final: 0.7704 (t0) REVERT: A 199 LYS cc_start: 0.8344 (mmmt) cc_final: 0.8104 (tppp) REVERT: A 203 THR cc_start: 0.8886 (t) cc_final: 0.8675 (p) REVERT: A 254 MET cc_start: 0.7896 (tmm) cc_final: 0.7579 (tmm) REVERT: A 265 PHE cc_start: 0.8140 (m-10) cc_final: 0.7868 (m-10) REVERT: A 317 HIS cc_start: 0.7804 (m90) cc_final: 0.7448 (m170) REVERT: A 318 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7115 (tm-30) REVERT: A 325 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8072 (mmmm) REVERT: A 401 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7739 (ttm-80) REVERT: A 438 ASP cc_start: 0.7457 (t0) cc_final: 0.6998 (t0) REVERT: A 441 THR cc_start: 0.8169 (m) cc_final: 0.7697 (m) REVERT: A 463 PHE cc_start: 0.8301 (m-10) cc_final: 0.7909 (m-10) REVERT: B 16 VAL cc_start: 0.8616 (t) cc_final: 0.8307 (p) REVERT: B 23 THR cc_start: 0.8444 (m) cc_final: 0.8054 (p) REVERT: B 50 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7505 (mt-10) REVERT: B 110 SER cc_start: 0.8676 (t) cc_final: 0.8195 (p) REVERT: B 135 ILE cc_start: 0.8447 (pt) cc_final: 0.8114 (mm) REVERT: B 162 ILE cc_start: 0.8885 (mm) cc_final: 0.8612 (mt) REVERT: B 177 ASP cc_start: 0.8185 (t0) cc_final: 0.7906 (t0) REVERT: B 207 LYS cc_start: 0.8781 (mttm) cc_final: 0.8323 (mtpp) REVERT: B 253 ASP cc_start: 0.6895 (t0) cc_final: 0.6549 (t0) REVERT: B 265 PHE cc_start: 0.8328 (m-80) cc_final: 0.8091 (m-80) REVERT: B 266 ARG cc_start: 0.7859 (ttp-170) cc_final: 0.7612 (ttp80) REVERT: B 317 HIS cc_start: 0.6605 (t-90) cc_final: 0.5993 (t-90) REVERT: B 328 LYS cc_start: 0.7335 (ptpp) cc_final: 0.7130 (mtpp) REVERT: B 383 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7250 (mt-10) REVERT: B 430 GLN cc_start: 0.8214 (tt0) cc_final: 0.7723 (tt0) REVERT: B 448 TRP cc_start: 0.8612 (t60) cc_final: 0.8355 (t60) REVERT: C 485 PRO cc_start: 0.8775 (Cg_endo) cc_final: 0.8461 (Cg_exo) outliers start: 21 outliers final: 16 residues processed: 334 average time/residue: 0.2434 time to fit residues: 110.1189 Evaluate side-chains 334 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 318 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 432 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 462 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 92 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.0770 chunk 18 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 386 GLN B 208 HIS ** B 452 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 = 0.3871 r_free = 0.3871 target = 0.142122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.121032 restraints weight = 44359.860| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.77 r_work: 0.3443 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9306 Z= 0.136 Angle : 0.532 4.552 12611 Z= 0.286 Chirality : 0.040 0.151 1389 Planarity : 0.004 0.051 1556 Dihedral : 4.638 21.015 1240 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 1.73 % Allowed : 23.80 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.26), residues: 1101 helix: 2.04 (0.24), residues: 463 sheet: -1.29 (0.43), residues: 162 loop : -0.73 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 442 TYR 0.014 0.001 TYR C 444 PHE 0.012 0.001 PHE D 432 TRP 0.009 0.001 TRP A 52 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 ( 9304) covalent geometry : angle 0.53127 / 0.29 (12607) SS BOND : bond 0.01165 / 0.61 ( 2) SS BOND : angle 1.38184 / 0.87 ( 4) hydrogen bonds : bond 0.04031 / 2.72 ( 414) hydrogen bonds : angle 4.03967 / 3.06 ( 1179) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 322 time to evaluate : 0.616 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8744 (m) cc_final: 0.8327 (p) REVERT: A 12 ILE cc_start: 0.8444 (tp) cc_final: 0.8232 (mt) REVERT: A 46 GLN cc_start: 0.7308 (tp-100) cc_final: 0.6926 (tp-100) REVERT: A 62 CYS cc_start: 0.8213 (p) cc_final: 0.7937 (p) REVERT: A 72 ARG cc_start: 0.8160 (mtp85) cc_final: 0.7491 (mtp85) REVERT: A 130 MET cc_start: 0.7921 (mmm) cc_final: 0.7676 (mmt) REVERT: A 180 ASP cc_start: 0.8021 (t0) cc_final: 0.7735 (t0) REVERT: A 206 ASP cc_start: 0.7699 (t0) cc_final: 0.7455 (t0) REVERT: A 254 MET cc_start: 0.7909 (tmm) cc_final: 0.7627 (tmm) REVERT: A 265 PHE cc_start: 0.8053 (m-10) cc_final: 0.7807 (m-10) REVERT: A 317 HIS cc_start: 0.7815 (m90) cc_final: 0.7471 (m170) REVERT: A 318 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7137 (tm-30) REVERT: A 325 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8069 (mmmm) REVERT: A 374 GLN cc_start: 0.7818 (mm110) cc_final: 0.7599 (mm-40) REVERT: A 389 ASN cc_start: 0.8694 (t0) cc_final: 0.8479 (t0) REVERT: A 401 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7463 (ttm-80) REVERT: A 429 TRP cc_start: 0.8325 (p-90) cc_final: 0.7960 (p-90) REVERT: A 463 PHE cc_start: 0.8322 (m-10) cc_final: 0.7902 (m-10) REVERT: B 16 VAL cc_start: 0.8570 (t) cc_final: 0.8260 (p) REVERT: B 23 THR cc_start: 0.8464 (m) cc_final: 0.8057 (p) REVERT: B 50 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7498 (mt-10) REVERT: B 98 GLU cc_start: 0.8432 (tt0) cc_final: 0.8155 (tt0) REVERT: B 110 SER cc_start: 0.8667 (t) cc_final: 0.8169 (p) REVERT: B 135 ILE cc_start: 0.8410 (pt) cc_final: 0.8085 (mm) REVERT: B 162 ILE cc_start: 0.8828 (mm) cc_final: 0.8566 (mt) REVERT: B 177 ASP cc_start: 0.8155 (t0) cc_final: 0.7854 (t0) REVERT: B 207 LYS cc_start: 0.8826 (mttm) cc_final: 0.8343 (mtpp) REVERT: B 265 PHE cc_start: 0.8301 (m-80) cc_final: 0.8086 (m-80) REVERT: B 276 SER cc_start: 0.8656 (m) cc_final: 0.8352 (p) REVERT: B 317 HIS cc_start: 0.6637 (t-90) cc_final: 0.5978 (t-90) REVERT: B 328 LYS cc_start: 0.7403 (ptpp) cc_final: 0.7193 (mtpp) REVERT: B 335 MET cc_start: 0.4954 (mmp) cc_final: 0.4738 (mmt) REVERT: B 383 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7230 (mt-10) REVERT: B 430 GLN cc_start: 0.8187 (tt0) cc_final: 0.7689 (tt0) REVERT: B 448 TRP cc_start: 0.8574 (t60) cc_final: 0.8301 (t60) REVERT: C 417 TYR cc_start: 0.7933 (m-80) cc_final: 0.7509 (m-80) REVERT: C 421 TRP cc_start: 0.8214 (m100) cc_final: 0.7809 (m100) REVERT: C 437 MET cc_start: 0.7786 (ttt) cc_final: 0.7322 (ttm) REVERT: C 485 PRO cc_start: 0.8690 (Cg_endo) cc_final: 0.8325 (Cg_exo) REVERT: C 500 SER cc_start: 0.8536 (m) cc_final: 0.8269 (p) outliers start: 17 outliers final: 15 residues processed: 328 average time/residue: 0.2434 time to fit residues: 107.5177 Evaluate side-chains 328 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 313 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 462 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 67 optimal weight: 0.0040 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN B 208 HIS ** B 452 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 = 0.3853 r_free = 0.3853 target = 0.140531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119910 restraints weight = 43921.234| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.74 r_work: 0.3437 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9306 Z= 0.157 Angle : 0.527 4.564 12611 Z= 0.287 Chirality : 0.040 0.150 1389 Planarity : 0.004 0.053 1556 Dihedral : 4.566 21.042 1240 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 2.44 % Allowed : 23.80 % Favored : 73.75 % 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: 0.55 (0.26), residues: 1101 helix: 2.15 (0.24), residues: 463 sheet: -1.27 (0.44), residues: 162 loop : -0.83 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 442 TYR 0.012 0.001 TYR A 112 PHE 0.016 0.001 PHE A 388 TRP 0.011 0.001 TRP A 52 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 ( 9304) covalent geometry : angle 0.52649 / 0.29 (12607) SS BOND : bond 0.00582 / 0.30 ( 2) SS BOND : angle 1.64359 / 0.98 ( 4) hydrogen bonds : bond 0.04104 / 2.80 ( 414) hydrogen bonds : angle 4.03351 / 3.05 ( 1179) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 325 time to evaluate : 0.484 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: 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 8 VAL cc_start: 0.8553 (p) cc_final: 0.8143 (t) REVERT: A 11 SER cc_start: 0.8865 (m) cc_final: 0.8411 (p) REVERT: A 12 ILE cc_start: 0.8537 (tp) cc_final: 0.8300 (mt) REVERT: A 46 GLN cc_start: 0.7275 (tp-100) cc_final: 0.6933 (tp-100) REVERT: A 62 CYS cc_start: 0.8315 (p) cc_final: 0.7984 (p) REVERT: A 72 ARG cc_start: 0.8237 (mtp85) cc_final: 0.7591 (mtp85) REVERT: A 130 MET cc_start: 0.7912 (mmm) cc_final: 0.7664 (mmt) REVERT: A 180 ASP cc_start: 0.7975 (t0) cc_final: 0.7684 (t0) REVERT: A 254 MET cc_start: 0.7908 (tmm) cc_final: 0.7651 (tmm) REVERT: A 265 PHE cc_start: 0.8036 (m-10) cc_final: 0.7807 (m-10) REVERT: A 317 HIS cc_start: 0.7810 (m90) cc_final: 0.7526 (m170) REVERT: A 318 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7204 (tm-30) REVERT: A 325 LYS cc_start: 0.8615 (mtmm) cc_final: 0.8125 (mmmm) REVERT: A 374 GLN cc_start: 0.7878 (mm110) cc_final: 0.7609 (mm-40) REVERT: A 389 ASN cc_start: 0.8690 (t0) cc_final: 0.8474 (t0) REVERT: A 401 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7339 (ttm-80) REVERT: A 429 TRP cc_start: 0.8330 (p-90) cc_final: 0.7956 (p-90) REVERT: A 463 PHE cc_start: 0.8389 (m-10) cc_final: 0.7980 (m-10) REVERT: A 464 LYS cc_start: 0.7228 (mmtt) cc_final: 0.6889 (mptt) REVERT: B 16 VAL cc_start: 0.8618 (t) cc_final: 0.8268 (p) REVERT: B 18 ASP cc_start: 0.8120 (t0) cc_final: 0.7850 (m-30) REVERT: B 23 THR cc_start: 0.8465 (m) cc_final: 0.8138 (p) REVERT: B 33 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8032 (tp) REVERT: B 50 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7555 (mt-10) REVERT: B 98 GLU cc_start: 0.8360 (tt0) cc_final: 0.8049 (tt0) REVERT: B 102 ILE cc_start: 0.8597 (mm) cc_final: 0.8133 (mt) REVERT: B 110 SER cc_start: 0.8691 (t) cc_final: 0.8369 (m) REVERT: B 177 ASP cc_start: 0.8158 (t0) cc_final: 0.7889 (t0) REVERT: B 207 LYS cc_start: 0.8898 (mttm) cc_final: 0.8455 (mtpp) REVERT: B 265 PHE cc_start: 0.8299 (m-80) cc_final: 0.8073 (m-80) REVERT: B 266 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7338 (ttp80) REVERT: B 273 LYS cc_start: 0.8091 (ttmm) cc_final: 0.7829 (mtpt) REVERT: B 276 SER cc_start: 0.8704 (m) cc_final: 0.8407 (p) REVERT: B 317 HIS cc_start: 0.6665 (t-90) cc_final: 0.6095 (t-90) REVERT: B 383 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7380 (mt-10) REVERT: B 394 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7037 (mt-10) REVERT: B 430 GLN cc_start: 0.8263 (tt0) cc_final: 0.7799 (tt0) REVERT: B 448 TRP cc_start: 0.8642 (t60) cc_final: 0.8354 (t60) REVERT: C 417 TYR cc_start: 0.8003 (m-80) cc_final: 0.7648 (m-80) REVERT: C 421 TRP cc_start: 0.8211 (m100) cc_final: 0.7875 (m100) REVERT: C 485 PRO cc_start: 0.8708 (Cg_endo) cc_final: 0.8350 (Cg_exo) outliers start: 24 outliers final: 17 residues processed: 337 average time/residue: 0.2518 time to fit residues: 113.1404 Evaluate side-chains 335 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 317 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 479 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 99 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 386 GLN B 208 HIS ** B 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.141735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.120592 restraints weight = 43252.207| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.80 r_work: 0.3428 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9306 Z= 0.135 Angle : 0.520 5.762 12611 Z= 0.280 Chirality : 0.039 0.146 1389 Planarity : 0.004 0.056 1556 Dihedral : 4.459 21.020 1240 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 2.64 % Allowed : 23.40 % Favored : 73.96 % 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: 0.63 (0.26), residues: 1101 helix: 2.29 (0.24), residues: 461 sheet: -1.21 (0.43), residues: 162 loop : -0.86 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 442 TYR 0.013 0.001 TYR C 494 PHE 0.022 0.001 PHE A 388 TRP 0.012 0.001 TRP A 52 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 9304) covalent geometry : angle 0.51945 / 0.28 (12607) SS BOND : bond 0.00632 / 0.32 ( 2) SS BOND : angle 1.00114 / 0.63 ( 4) hydrogen bonds : bond 0.03901 / 2.64 ( 414) hydrogen bonds : angle 3.91011 / 2.97 ( 1179) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 327 time to evaluate : 0.482 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: 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 7 ASN cc_start: 0.8195 (m-40) cc_final: 0.7963 (m-40) REVERT: A 8 VAL cc_start: 0.8546 (p) cc_final: 0.8119 (t) REVERT: A 11 SER cc_start: 0.8849 (m) cc_final: 0.8422 (p) REVERT: A 17 VAL cc_start: 0.8474 (t) cc_final: 0.8157 (p) REVERT: A 46 GLN cc_start: 0.7285 (tp-100) cc_final: 0.6957 (tp-100) REVERT: A 62 CYS cc_start: 0.8459 (p) cc_final: 0.8239 (p) REVERT: A 72 ARG cc_start: 0.8278 (mtp85) cc_final: 0.7661 (mtp85) REVERT: A 130 MET cc_start: 0.7916 (mmm) cc_final: 0.7665 (mmt) REVERT: A 180 ASP cc_start: 0.8075 (t0) cc_final: 0.7788 (t0) REVERT: A 254 MET cc_start: 0.7918 (tmm) cc_final: 0.7658 (tmm) REVERT: A 265 PHE cc_start: 0.8010 (m-10) cc_final: 0.7772 (m-10) REVERT: A 317 HIS cc_start: 0.7821 (m90) cc_final: 0.7524 (m170) REVERT: A 318 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7210 (tm-30) REVERT: A 325 LYS cc_start: 0.8625 (mtmm) cc_final: 0.8111 (mmmm) REVERT: A 401 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7573 (ttm-80) REVERT: A 429 TRP cc_start: 0.8296 (p-90) cc_final: 0.8037 (p-90) REVERT: A 463 PHE cc_start: 0.8451 (m-10) cc_final: 0.8019 (m-10) REVERT: A 464 LYS cc_start: 0.7143 (mmtt) cc_final: 0.6851 (mptt) REVERT: B 16 VAL cc_start: 0.8626 (t) cc_final: 0.8284 (p) REVERT: B 18 ASP cc_start: 0.8119 (t0) cc_final: 0.7839 (m-30) REVERT: B 23 THR cc_start: 0.8488 (m) cc_final: 0.8162 (p) REVERT: B 50 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7547 (mt-10) REVERT: B 98 GLU cc_start: 0.8319 (tt0) cc_final: 0.8036 (tt0) REVERT: B 110 SER cc_start: 0.8659 (t) cc_final: 0.8174 (p) REVERT: B 177 ASP cc_start: 0.8179 (t0) cc_final: 0.7898 (t0) REVERT: B 207 LYS cc_start: 0.8929 (mttm) cc_final: 0.8470 (mtpp) REVERT: B 266 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7596 (ttp80) REVERT: B 273 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7827 (mtpt) REVERT: B 276 SER cc_start: 0.8645 (m) cc_final: 0.8354 (p) REVERT: B 317 HIS cc_start: 0.6690 (t-90) cc_final: 0.6075 (t-90) REVERT: B 383 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7459 (mt-10) REVERT: B 394 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7190 (mt-10) REVERT: B 430 GLN cc_start: 0.8238 (tt0) cc_final: 0.7814 (tt0) REVERT: B 448 TRP cc_start: 0.8640 (t60) cc_final: 0.8334 (t60) REVERT: C 417 TYR cc_start: 0.7987 (m-80) cc_final: 0.7716 (m-80) REVERT: C 421 TRP cc_start: 0.8202 (m100) cc_final: 0.7917 (m100) REVERT: C 430 ARG cc_start: 0.8226 (ptp90) cc_final: 0.8019 (ptp90) outliers start: 26 outliers final: 19 residues processed: 338 average time/residue: 0.2333 time to fit residues: 106.1466 Evaluate side-chains 336 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 317 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 386 GLN Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain D residue 469 ASN Chi-restraints excluded: chain D residue 479 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN A 386 GLN B 208 HIS ** B 452 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 = 0.3835 r_free = 0.3835 target = 0.139607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118581 restraints weight = 43078.700| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.78 r_work: 0.3395 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.6776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9306 Z= 0.187 Angle : 0.539 5.009 12611 Z= 0.294 Chirality : 0.040 0.149 1389 Planarity : 0.004 0.064 1556 Dihedral : 4.532 21.527 1240 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 2.64 % Allowed : 24.92 % Favored : 72.43 % 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 (0.26), residues: 1101 helix: 2.15 (0.24), residues: 463 sheet: -1.18 (0.44), residues: 162 loop : -0.97 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 442 TYR 0.015 0.001 TYR A 112 PHE 0.028 0.001 PHE A 388 TRP 0.017 0.001 TRP A 52 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 ( 9304) covalent geometry : angle 0.53839 / 0.29 (12607) SS BOND : bond 0.00448 / 0.21 ( 2) SS BOND : angle 1.65089 / 1.03 ( 4) hydrogen bonds : bond 0.04214 / 2.86 ( 414) hydrogen bonds : angle 4.02548 / 3.04 ( 1179) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 325 time to evaluate : 0.491 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: 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 7 ASN cc_start: 0.8187 (m-40) cc_final: 0.7984 (m-40) REVERT: A 8 VAL cc_start: 0.8554 (p) cc_final: 0.8127 (t) REVERT: A 11 SER cc_start: 0.8882 (m) cc_final: 0.8537 (p) REVERT: A 17 VAL cc_start: 0.8572 (t) cc_final: 0.8319 (p) REVERT: A 46 GLN cc_start: 0.7433 (tp-100) cc_final: 0.7102 (tp-100) REVERT: A 62 CYS cc_start: 0.8397 (p) cc_final: 0.8097 (p) REVERT: A 72 ARG cc_start: 0.8351 (mtp85) cc_final: 0.7809 (mtp85) REVERT: A 130 MET cc_start: 0.7893 (mmm) cc_final: 0.7653 (mmt) REVERT: A 160 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8417 (mtmm) REVERT: A 180 ASP cc_start: 0.7992 (t0) cc_final: 0.7714 (t0) REVERT: A 254 MET cc_start: 0.7955 (tmm) cc_final: 0.7685 (tmm) REVERT: A 265 PHE cc_start: 0.7997 (m-10) cc_final: 0.7763 (m-10) REVERT: A 317 HIS cc_start: 0.7845 (m90) cc_final: 0.7575 (m170) REVERT: A 318 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7190 (tm-30) REVERT: A 325 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8128 (mmmm) REVERT: A 463 PHE cc_start: 0.8485 (m-10) cc_final: 0.8063 (m-10) REVERT: B 16 VAL cc_start: 0.8632 (t) cc_final: 0.8288 (p) REVERT: B 18 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: B 23 THR cc_start: 0.8488 (m) cc_final: 0.8155 (p) REVERT: B 33 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7966 (tp) REVERT: B 50 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7651 (mt-10) REVERT: B 110 SER cc_start: 0.8681 (t) cc_final: 0.8250 (p) REVERT: B 177 ASP cc_start: 0.8221 (t0) cc_final: 0.7967 (t0) REVERT: B 207 LYS cc_start: 0.8956 (mttm) cc_final: 0.8562 (mtpp) REVERT: B 265 PHE cc_start: 0.8239 (m-80) cc_final: 0.7891 (m-10) REVERT: B 273 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7923 (mtpt) REVERT: B 276 SER cc_start: 0.8622 (m) cc_final: 0.8379 (p) REVERT: B 317 HIS cc_start: 0.6770 (t-90) cc_final: 0.6182 (t-90) REVERT: B 383 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7503 (mt-10) REVERT: B 394 GLU cc_start: 0.7520 (mt-10) cc_final: 0.7157 (mt-10) REVERT: B 430 GLN cc_start: 0.8293 (tt0) cc_final: 0.7903 (tt0) REVERT: B 448 TRP cc_start: 0.8689 (t60) cc_final: 0.8478 (t60) REVERT: C 417 TYR cc_start: 0.8032 (m-80) cc_final: 0.7769 (m-80) REVERT: C 421 TRP cc_start: 0.8216 (m100) cc_final: 0.7923 (m100) outliers start: 26 outliers final: 20 residues processed: 336 average time/residue: 0.2321 time to fit residues: 104.8349 Evaluate side-chains 337 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 314 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain D residue 469 ASN Chi-restraints excluded: chain D residue 476 THR Chi-restraints excluded: chain D residue 479 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 71 optimal weight: 0.3980 chunk 108 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS ** B 452 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 = 0.3852 r_free = 0.3852 target = 0.140728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.119616 restraints weight = 43120.502| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.78 r_work: 0.3406 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.6937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9306 Z= 0.142 Angle : 0.526 4.926 12611 Z= 0.284 Chirality : 0.039 0.149 1389 Planarity : 0.004 0.061 1556 Dihedral : 4.435 21.667 1240 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 2.14 % Allowed : 25.64 % Favored : 72.23 % 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: 0.58 (0.26), residues: 1101 helix: 2.31 (0.24), residues: 461 sheet: -1.18 (0.44), residues: 162 loop : -0.99 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 442 TYR 0.013 0.001 TYR B 315 PHE 0.018 0.001 PHE A 388 TRP 0.014 0.001 TRP A 52 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 9304) covalent geometry : angle 0.52498 / 0.28 (12607) SS BOND : bond 0.00564 / 0.29 ( 2) SS BOND : angle 1.63888 / 0.97 ( 4) hydrogen bonds : bond 0.03958 / 2.69 ( 414) hydrogen bonds : angle 3.90668 / 2.96 ( 1179) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 320 time to evaluate : 0.414 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: 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 7 ASN cc_start: 0.8107 (m-40) cc_final: 0.7884 (m-40) REVERT: A 8 VAL cc_start: 0.8520 (p) cc_final: 0.8095 (t) REVERT: A 11 SER cc_start: 0.8885 (m) cc_final: 0.8525 (p) REVERT: A 17 VAL cc_start: 0.8530 (t) cc_final: 0.8291 (p) REVERT: A 46 GLN cc_start: 0.7417 (tp-100) cc_final: 0.7096 (tp-100) REVERT: A 72 ARG cc_start: 0.8336 (mtp85) cc_final: 0.7788 (mtp85) REVERT: A 130 MET cc_start: 0.7886 (mmm) cc_final: 0.7668 (mmt) REVERT: A 160 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8396 (mtmm) REVERT: A 180 ASP cc_start: 0.7998 (t0) cc_final: 0.7716 (t0) REVERT: A 254 MET cc_start: 0.7955 (tmm) cc_final: 0.7676 (tmm) REVERT: A 265 PHE cc_start: 0.7971 (m-10) cc_final: 0.7751 (m-10) REVERT: A 317 HIS cc_start: 0.7849 (m90) cc_final: 0.7546 (m170) REVERT: A 318 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7251 (tm-30) REVERT: A 325 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8160 (mmmm) REVERT: A 380 SER cc_start: 0.8377 (t) cc_final: 0.8168 (m) REVERT: A 429 TRP cc_start: 0.8306 (p-90) cc_final: 0.8046 (p-90) REVERT: A 463 PHE cc_start: 0.8493 (m-10) cc_final: 0.8060 (m-10) REVERT: A 464 LYS cc_start: 0.7232 (mmtt) cc_final: 0.7017 (mptt) REVERT: B 16 VAL cc_start: 0.8641 (t) cc_final: 0.8284 (p) REVERT: B 18 ASP cc_start: 0.8139 (t0) cc_final: 0.7848 (m-30) REVERT: B 23 THR cc_start: 0.8499 (m) cc_final: 0.8161 (p) REVERT: B 33 LEU cc_start: 0.8299 (mm) cc_final: 0.7964 (tp) REVERT: B 50 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7598 (mt-10) REVERT: B 110 SER cc_start: 0.8701 (t) cc_final: 0.8242 (p) REVERT: B 153 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8136 (ttpp) REVERT: B 177 ASP cc_start: 0.8238 (t0) cc_final: 0.7969 (t0) REVERT: B 207 LYS cc_start: 0.8954 (mttm) cc_final: 0.8560 (mtpp) REVERT: B 265 PHE cc_start: 0.8245 (m-80) cc_final: 0.7898 (m-10) REVERT: B 273 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7920 (mtpt) REVERT: B 276 SER cc_start: 0.8605 (m) cc_final: 0.8345 (p) REVERT: B 317 HIS cc_start: 0.6711 (t-90) cc_final: 0.6107 (t-90) REVERT: B 327 PHE cc_start: 0.8273 (p90) cc_final: 0.7488 (p90) REVERT: B 383 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7397 (mt-10) REVERT: B 394 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7084 (mt-10) REVERT: B 430 GLN cc_start: 0.8284 (tt0) cc_final: 0.7904 (tt0) REVERT: C 417 TYR cc_start: 0.8041 (m-80) cc_final: 0.7824 (m-80) REVERT: C 421 TRP cc_start: 0.8210 (m100) cc_final: 0.7947 (m100) REVERT: C 428 LYS cc_start: 0.8463 (tptt) cc_final: 0.8203 (tptt) REVERT: D 412 ARG cc_start: 0.5370 (OUTLIER) cc_final: 0.4324 (ptt-90) outliers start: 21 outliers final: 18 residues processed: 332 average time/residue: 0.2351 time to fit residues: 105.0720 Evaluate side-chains 336 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 315 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain D residue 412 ARG Chi-restraints excluded: chain D residue 469 ASN Chi-restraints excluded: chain D residue 479 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 56 optimal weight: 0.0770 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.138349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.117472 restraints weight = 43268.785| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.74 r_work: 0.3377 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.7226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9306 Z= 0.225 Angle : 0.562 5.278 12611 Z= 0.310 Chirality : 0.041 0.149 1389 Planarity : 0.005 0.056 1556 Dihedral : 4.591 22.145 1240 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.72 % Favored : 94.19 % Rotamer: Outliers : 2.75 % Allowed : 25.33 % Favored : 71.92 % 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: 0.37 (0.26), residues: 1101 helix: 2.09 (0.24), residues: 463 sheet: -1.04 (0.47), residues: 143 loop : -1.19 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 442 TYR 0.017 0.001 TYR A 112 PHE 0.017 0.002 PHE D 432 TRP 0.016 0.002 TRP A 52 HIS 0.003 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.23 ( 9304) covalent geometry : angle 0.56134 / 0.31 (12607) SS BOND : bond 0.00894 / 0.45 ( 2) SS BOND : angle 2.09303 / 1.32 ( 4) hydrogen bonds : bond 0.04459 / 3.03 ( 414) hydrogen bonds : angle 4.08770 / 3.07 ( 1179) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 337 time to evaluate : 0.472 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ASN cc_start: 0.8128 (m-40) cc_final: 0.7923 (m-40) REVERT: A 8 VAL cc_start: 0.8547 (p) cc_final: 0.8189 (t) REVERT: A 11 SER cc_start: 0.8904 (m) cc_final: 0.8668 (p) REVERT: A 17 VAL cc_start: 0.8563 (t) cc_final: 0.8327 (p) REVERT: A 46 GLN cc_start: 0.7512 (tp-100) cc_final: 0.7205 (tp-100) REVERT: A 130 MET cc_start: 0.7898 (mmm) cc_final: 0.7626 (mmt) REVERT: A 160 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8427 (mtmm) REVERT: A 180 ASP cc_start: 0.7996 (t0) cc_final: 0.7713 (t0) REVERT: A 254 MET cc_start: 0.7990 (tmm) cc_final: 0.7724 (tmm) REVERT: A 265 PHE cc_start: 0.7976 (m-10) cc_final: 0.7773 (m-10) REVERT: A 270 ASN cc_start: 0.7957 (m-40) cc_final: 0.7746 (m110) REVERT: A 312 SER cc_start: 0.8244 (t) cc_final: 0.7970 (p) REVERT: A 317 HIS cc_start: 0.7889 (m90) cc_final: 0.7614 (m170) REVERT: A 318 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7245 (tm-30) REVERT: A 325 LYS cc_start: 0.8730 (mtmm) cc_final: 0.8203 (mmmm) REVERT: A 375 PHE cc_start: 0.6808 (m-80) cc_final: 0.6542 (m-80) REVERT: A 380 SER cc_start: 0.8470 (t) cc_final: 0.8261 (m) REVERT: A 438 ASP cc_start: 0.7459 (t0) cc_final: 0.7146 (t0) REVERT: A 463 PHE cc_start: 0.8545 (m-10) cc_final: 0.8104 (m-80) REVERT: A 464 LYS cc_start: 0.7317 (mmtt) cc_final: 0.7077 (mptt) REVERT: B 16 VAL cc_start: 0.8661 (t) cc_final: 0.8316 (p) REVERT: B 23 THR cc_start: 0.8497 (m) cc_final: 0.8177 (p) REVERT: B 50 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7659 (mt-10) REVERT: B 98 GLU cc_start: 0.8358 (tt0) cc_final: 0.8132 (tt0) REVERT: B 110 SER cc_start: 0.8730 (t) cc_final: 0.8270 (p) REVERT: B 111 ARG cc_start: 0.6933 (mtm-85) cc_final: 0.6025 (mtm-85) REVERT: B 153 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8205 (ttpp) REVERT: B 177 ASP cc_start: 0.8263 (t0) cc_final: 0.8034 (t0) REVERT: B 207 LYS cc_start: 0.8954 (mttm) cc_final: 0.8564 (mtpp) REVERT: B 265 PHE cc_start: 0.8282 (m-80) cc_final: 0.7942 (m-10) REVERT: B 273 LYS cc_start: 0.8280 (ttmm) cc_final: 0.7926 (mtpt) REVERT: B 276 SER cc_start: 0.8612 (m) cc_final: 0.8384 (p) REVERT: B 290 SER cc_start: 0.8528 (m) cc_final: 0.8009 (p) REVERT: B 317 HIS cc_start: 0.6773 (t-90) cc_final: 0.6375 (t-90) REVERT: B 319 ARG cc_start: 0.8070 (mtt90) cc_final: 0.7462 (mpt-90) REVERT: B 327 PHE cc_start: 0.8451 (p90) cc_final: 0.7691 (p90) REVERT: B 394 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7118 (mt-10) REVERT: B 421 ILE cc_start: 0.8663 (mm) cc_final: 0.8354 (pt) REVERT: B 430 GLN cc_start: 0.8335 (tt0) cc_final: 0.7954 (tt0) REVERT: C 421 TRP cc_start: 0.8265 (m100) cc_final: 0.8005 (m100) REVERT: C 428 LYS cc_start: 0.8500 (tptt) cc_final: 0.8231 (tptt) REVERT: C 437 MET cc_start: 0.7819 (ttt) cc_final: 0.7540 (ttp) REVERT: D 412 ARG cc_start: 0.5467 (OUTLIER) cc_final: 0.4302 (ptt-90) outliers start: 27 outliers final: 21 residues processed: 352 average time/residue: 0.2440 time to fit residues: 114.9145 Evaluate side-chains 358 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 334 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 274 TRP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 40 PHE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 160 LYS Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 250 ASP Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 325 LYS Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain D residue 412 ARG Chi-restraints excluded: chain D residue 469 ASN Chi-restraints excluded: chain D residue 479 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN ** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.138944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.118692 restraints weight = 43349.424| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.68 r_work: 0.3410 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.7371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9306 Z= 0.156 Angle : 0.534 5.325 12611 Z= 0.290 Chirality : 0.040 0.150 1389 Planarity : 0.004 0.060 1556 Dihedral : 4.479 22.275 1240 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 2.14 % Allowed : 26.45 % Favored : 71.41 % 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 (0.26), residues: 1101 helix: 2.25 (0.24), residues: 461 sheet: -1.02 (0.49), residues: 130 loop : -1.16 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 442 TYR 0.012 0.001 TYR A 112 PHE 0.016 0.001 PHE D 432 TRP 0.019 0.001 TRP A 52 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 9304) covalent geometry : angle 0.53330 / 0.29 (12607) SS BOND : bond 0.00664 / 0.34 ( 2) SS BOND : angle 1.62324 / 0.97 ( 4) hydrogen bonds : bond 0.04127 / 2.83 ( 414) hydrogen bonds : angle 3.95396 / 2.98 ( 1179) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4270.54 seconds wall clock time: 73 minutes 7.57 seconds (4387.57 seconds total)