Starting phenix.real_space_refine on Sat Oct 24 10:40:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y5j_72510/10_2026/9y5j_72510.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y5j_72510/10_2026/9y5j_72510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y5j_72510/10_2026/9y5j_72510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y5j_72510/10_2026/9y5j_72510.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y5j_72510/10_2026/9y5j_72510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y5j_72510/10_2026/9y5j_72510.map" } resolution = 3.09 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= 0.003 sd= 0.039 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 8548 2.51 5 N 2068 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13036 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3259 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 4, 'TRANS': 398} Chain breaks: 3 Chain: "B" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3259 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 4, 'TRANS': 398} Chain breaks: 3 Chain: "C" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3259 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 4, 'TRANS': 398} Chain breaks: 3 Chain: "D" Number of atoms: 3259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3259 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 4, 'TRANS': 398} Chain breaks: 3 Time building chain proxies: 2.79, per 1000 atoms: 0.21 Number of scatterers: 13036 At special positions: 0 Unit cell: (110.39, 110.39, 106.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2340 8.00 N 2068 7.00 C 8548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 190 " distance=2.03 Simple disulfide: pdb=" SG CYS A 243 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 243 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 190 " distance=2.03 Simple disulfide: pdb=" SG CYS C 243 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS D 164 " - pdb=" SG CYS D 190 " distance=2.03 Simple disulfide: pdb=" SG CYS D 243 " - pdb=" SG CYS D 274 " 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: 0.98 Conformation dependent library (CDL) restraints added in 565.7 milliseconds 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3072 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 68.3% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 65 through 106 Processing helix chain 'A' and resid 123 through 140 Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 194 through 201 removed outlier: 3.604A pdb=" N GLU A 201 " --> pdb=" O VAL A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 207 removed outlier: 4.240A pdb=" N TRP A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 206 " --> pdb=" O PRO A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 removed outlier: 3.778A pdb=" N HIS A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 322 Processing helix chain 'A' and resid 346 through 371 Processing helix chain 'A' and resid 375 through 398 removed outlier: 4.023A pdb=" N VAL A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE A 394 " --> pdb=" O TRP A 390 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 440 removed outlier: 3.939A pdb=" N LEU A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR A 409 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 443 through 447 removed outlier: 4.068A pdb=" N GLU A 447 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 476 through 515 Processing helix chain 'B' and resid 66 through 106 Processing helix chain 'B' and resid 123 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 194 through 201 removed outlier: 3.604A pdb=" N GLU B 201 " --> pdb=" O VAL B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 207 removed outlier: 4.241A pdb=" N TRP B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 206 " --> pdb=" O PRO B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.780A pdb=" N HIS B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 322 Processing helix chain 'B' and resid 346 through 371 Processing helix chain 'B' and resid 375 through 398 removed outlier: 4.021A pdb=" N VAL B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE B 394 " --> pdb=" O TRP B 390 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG B 395 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 440 removed outlier: 3.939A pdb=" N LEU B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR B 409 " --> pdb=" O VAL B 405 " (cutoff:3.500A) Proline residue: B 415 - end of helix Processing helix chain 'B' and resid 443 through 447 removed outlier: 4.068A pdb=" N GLU B 447 " --> pdb=" O GLU B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 461 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 476 through 515 Processing helix chain 'C' and resid 66 through 106 Processing helix chain 'C' and resid 123 through 140 Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 194 through 201 removed outlier: 3.604A pdb=" N GLU C 201 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 207 removed outlier: 4.240A pdb=" N TRP C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 206 " --> pdb=" O PRO C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 3.778A pdb=" N HIS C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 322 Processing helix chain 'C' and resid 346 through 371 Processing helix chain 'C' and resid 375 through 398 removed outlier: 4.021A pdb=" N VAL C 393 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE C 394 " --> pdb=" O TRP C 390 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG C 395 " --> pdb=" O VAL C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 440 removed outlier: 3.939A pdb=" N LEU C 408 " --> pdb=" O ASN C 404 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR C 409 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Proline residue: C 415 - end of helix Processing helix chain 'C' and resid 443 through 447 removed outlier: 4.069A pdb=" N GLU C 447 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 461 Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 476 through 515 Processing helix chain 'D' and resid 66 through 106 Processing helix chain 'D' and resid 123 through 140 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 194 through 201 removed outlier: 3.604A pdb=" N GLU D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 207 removed outlier: 4.241A pdb=" N TRP D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 206 " --> pdb=" O PRO D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 237 removed outlier: 3.779A pdb=" N HIS D 236 " --> pdb=" O LEU D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 322 Processing helix chain 'D' and resid 346 through 371 Processing helix chain 'D' and resid 375 through 398 removed outlier: 4.021A pdb=" N VAL D 393 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE D 394 " --> pdb=" O TRP D 390 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG D 395 " --> pdb=" O VAL D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 440 removed outlier: 3.939A pdb=" N LEU D 408 " --> pdb=" O ASN D 404 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR D 409 " --> pdb=" O VAL D 405 " (cutoff:3.500A) Proline residue: D 415 - end of helix Processing helix chain 'D' and resid 443 through 447 removed outlier: 4.068A pdb=" N GLU D 447 " --> pdb=" O GLU D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 461 Processing helix chain 'D' and resid 464 through 471 Processing helix chain 'D' and resid 476 through 515 Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.584A pdb=" N CYS A 119 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP A 242 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 221 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 121 removed outlier: 3.584A pdb=" N CYS A 119 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP A 242 " --> pdb=" O ASP A 231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 221 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU A 218 " --> pdb=" O TYR A 168 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR A 168 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN A 220 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.581A pdb=" N CYS B 119 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP B 242 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 221 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 119 through 121 removed outlier: 3.581A pdb=" N CYS B 119 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP B 242 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 221 " --> pdb=" O PHE B 252 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 218 " --> pdb=" O TYR B 168 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYR B 168 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN B 220 " --> pdb=" O GLN B 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 119 through 121 removed outlier: 3.591A pdb=" N CYS C 119 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP C 242 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 221 " --> pdb=" O PHE C 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 119 through 121 removed outlier: 3.591A pdb=" N CYS C 119 " --> pdb=" O ILE C 263 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP C 242 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 221 " --> pdb=" O PHE C 252 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU C 218 " --> pdb=" O TYR C 168 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYR C 168 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN C 220 " --> pdb=" O GLN C 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.591A pdb=" N CYS D 119 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP D 242 " --> pdb=" O ASP D 231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 221 " --> pdb=" O PHE D 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 119 through 121 removed outlier: 3.591A pdb=" N CYS D 119 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP D 242 " --> pdb=" O ASP D 231 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 221 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU D 218 " --> pdb=" O TYR D 168 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYR D 168 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN D 220 " --> pdb=" O GLN D 166 " (cutoff:3.500A) 1073 hydrogen bonds defined for protein. 3159 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3980 1.34 - 1.46: 3236 1.46 - 1.58: 5972 1.58 - 1.70: 0 1.70 - 1.81: 112 Bond restraints: 13300 Sorted by residual: bond pdb=" CG LEU D 456 " pdb=" CD1 LEU D 456 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CG LEU A 456 " pdb=" CD1 LEU A 456 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" CG LEU B 456 " pdb=" CD1 LEU B 456 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.07e+00 bond pdb=" CG LEU C 456 " pdb=" CD1 LEU C 456 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" CB LEU C 456 " pdb=" CG LEU C 456 " ideal model delta sigma weight residual 1.530 1.546 -0.016 2.00e-02 2.50e+03 6.39e-01 ... (remaining 13295 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 17776 1.81 - 3.61: 176 3.61 - 5.42: 30 5.42 - 7.23: 14 7.23 - 9.03: 4 Bond angle restraints: 18000 Sorted by residual: angle pdb=" N VAL A 219 " pdb=" CA VAL A 219 " pdb=" C VAL A 219 " ideal model delta sigma weight residual 111.48 108.75 2.73 9.40e-01 1.13e+00 8.45e+00 angle pdb=" N VAL B 219 " pdb=" CA VAL B 219 " pdb=" C VAL B 219 " ideal model delta sigma weight residual 111.48 108.79 2.69 9.40e-01 1.13e+00 8.18e+00 angle pdb=" N VAL C 219 " pdb=" CA VAL C 219 " pdb=" C VAL C 219 " ideal model delta sigma weight residual 111.48 108.79 2.69 9.40e-01 1.13e+00 8.18e+00 angle pdb=" N VAL D 219 " pdb=" CA VAL D 219 " pdb=" C VAL D 219 " ideal model delta sigma weight residual 111.48 108.79 2.69 9.40e-01 1.13e+00 8.18e+00 angle pdb=" C ASN C 143 " pdb=" N ILE C 144 " pdb=" CA ILE C 144 " ideal model delta sigma weight residual 122.66 119.99 2.67 9.70e-01 1.06e+00 7.58e+00 ... (remaining 17995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 6903 16.05 - 32.10: 717 32.10 - 48.14: 180 48.14 - 64.19: 24 64.19 - 80.24: 12 Dihedral angle restraints: 7836 sinusoidal: 3084 harmonic: 4752 Sorted by residual: dihedral pdb=" CA ASP B 354 " pdb=" CB ASP B 354 " pdb=" CG ASP B 354 " pdb=" OD1 ASP B 354 " ideal model delta sinusoidal sigma weight residual -30.00 -85.59 55.59 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CA ASP C 354 " pdb=" CB ASP C 354 " pdb=" CG ASP C 354 " pdb=" OD1 ASP C 354 " ideal model delta sinusoidal sigma weight residual -30.00 -85.32 55.32 1 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" CA ASP A 354 " pdb=" CB ASP A 354 " pdb=" CG ASP A 354 " pdb=" OD1 ASP A 354 " ideal model delta sinusoidal sigma weight residual -30.00 -84.64 54.64 1 2.00e+01 2.50e-03 1.01e+01 ... (remaining 7833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1328 0.028 - 0.056: 513 0.056 - 0.084: 187 0.084 - 0.111: 73 0.111 - 0.139: 27 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CG LEU D 414 " pdb=" CB LEU D 414 " pdb=" CD1 LEU D 414 " pdb=" CD2 LEU D 414 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CG LEU B 414 " pdb=" CB LEU B 414 " pdb=" CD1 LEU B 414 " pdb=" CD2 LEU B 414 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CG LEU A 414 " pdb=" CB LEU A 414 " pdb=" CD1 LEU A 414 " pdb=" CD2 LEU A 414 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.84e-01 ... (remaining 2125 not shown) Planarity restraints: 2184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 490 " -0.003 2.00e-02 2.50e+03 1.06e-02 1.97e+00 pdb=" CG PHE C 490 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE C 490 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE C 490 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE C 490 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 490 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 490 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 490 " -0.003 2.00e-02 2.50e+03 1.06e-02 1.96e+00 pdb=" CG PHE B 490 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE B 490 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 490 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE B 490 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 490 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE B 490 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 490 " 0.003 2.00e-02 2.50e+03 1.06e-02 1.95e+00 pdb=" CG PHE D 490 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE D 490 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 490 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE D 490 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 490 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE D 490 " 0.003 2.00e-02 2.50e+03 ... (remaining 2181 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2935 2.79 - 3.32: 12866 3.32 - 3.85: 22050 3.85 - 4.37: 24851 4.37 - 4.90: 44184 Nonbonded interactions: 106886 Sorted by model distance: nonbonded pdb=" O TYR B 431 " pdb=" OH TYR B 486 " model vdw 2.266 3.040 nonbonded pdb=" O TYR D 431 " pdb=" OH TYR D 486 " model vdw 2.267 3.040 nonbonded pdb=" O TYR A 431 " pdb=" OH TYR A 486 " model vdw 2.267 3.040 nonbonded pdb=" O TYR C 431 " pdb=" OH TYR C 486 " model vdw 2.267 3.040 nonbonded pdb=" O GLN C 196 " pdb=" OG1 THR C 200 " model vdw 2.268 3.040 ... (remaining 106881 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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: 1.440 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.290 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.003 0.034 13308 Z= 0.131 Angle : 0.522 9.034 18016 Z= 0.283 Chirality : 0.038 0.139 2128 Planarity : 0.002 0.035 2184 Dihedral : 14.162 80.238 4740 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.21), residues: 1580 helix: 2.32 (0.15), residues: 992 sheet: 0.39 (0.34), residues: 236 loop : -1.81 (0.27), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 139 TYR 0.017 0.001 TYR B 428 PHE 0.018 0.001 PHE B 490 TRP 0.004 0.001 TRP B 436 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (13300) covalent geometry : angle 0.52194 / 0.28 (18000) SS BOND : bond 0.00074 / 0.05 ( 8) SS BOND : angle 0.11275 / 0.06 ( 16) hydrogen bonds : bond 0.11829 / 7.85 ( 981) hydrogen bonds : angle 6.73749 / 5.01 ( 3159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.469 Fit side-chains REVERT: A 75 MET cc_start: 0.6880 (tpp) cc_final: 0.6626 (tpt) REVERT: B 75 MET cc_start: 0.6902 (tpp) cc_final: 0.6643 (tpt) REVERT: C 75 MET cc_start: 0.6884 (tpp) cc_final: 0.6591 (tpt) REVERT: D 75 MET cc_start: 0.6881 (tpp) cc_final: 0.6586 (tpt) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.0984 time to fit residues: 28.9995 Evaluate side-chains 157 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.203341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.159674 restraints weight = 14166.912| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.12 r_work: 0.3647 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13308 Z= 0.200 Angle : 0.512 5.493 18016 Z= 0.287 Chirality : 0.039 0.140 2128 Planarity : 0.003 0.038 2184 Dihedral : 4.116 15.879 1732 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.37 % Allowed : 7.95 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.20), residues: 1580 helix: 2.01 (0.15), residues: 1024 sheet: 0.41 (0.31), residues: 236 loop : -1.97 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.014 0.001 TYR A 486 PHE 0.036 0.002 PHE B 490 TRP 0.003 0.001 TRP C 205 HIS 0.003 0.001 HIS D 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (13300) covalent geometry : angle 0.51264 / 0.29 (18000) SS BOND : bond 0.00112 / 0.06 ( 8) SS BOND : angle 0.24819 / 0.13 ( 16) hydrogen bonds : bond 0.04639 / 3.14 ( 981) hydrogen bonds : angle 4.71984 / 3.42 ( 3159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.472 Fit side-chains REVERT: A 75 MET cc_start: 0.7501 (tpp) cc_final: 0.7156 (tpt) REVERT: A 82 ARG cc_start: 0.8810 (mmm160) cc_final: 0.8582 (mtp85) REVERT: A 217 ARG cc_start: 0.8340 (mtt90) cc_final: 0.7182 (mtm180) REVERT: B 75 MET cc_start: 0.7494 (tpp) cc_final: 0.7145 (tpt) REVERT: B 82 ARG cc_start: 0.8809 (mmm160) cc_final: 0.8582 (mtp85) REVERT: B 217 ARG cc_start: 0.8331 (mtt90) cc_final: 0.7178 (mtm180) REVERT: C 75 MET cc_start: 0.7525 (tpp) cc_final: 0.7168 (tpt) REVERT: C 82 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8561 (mtp85) REVERT: C 217 ARG cc_start: 0.8348 (mtt90) cc_final: 0.7197 (mtm180) REVERT: D 75 MET cc_start: 0.7520 (tpp) cc_final: 0.7161 (tpt) REVERT: D 82 ARG cc_start: 0.8797 (mmm160) cc_final: 0.8573 (mtp85) REVERT: D 217 ARG cc_start: 0.8346 (mtt90) cc_final: 0.7200 (mtm180) outliers start: 20 outliers final: 16 residues processed: 182 average time/residue: 0.1070 time to fit residues: 28.7143 Evaluate side-chains 167 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 492 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [149, 148, 117, 81, 71, 56, 10, 136, 157, 84, 23] chunk 149 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.0670 chunk 10 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 157 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN B 471 GLN C 471 GLN D 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.207228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.163245 restraints weight = 14394.954| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.12 r_work: 0.3664 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13308 Z= 0.132 Angle : 0.436 5.398 18016 Z= 0.247 Chirality : 0.037 0.137 2128 Planarity : 0.003 0.039 2184 Dihedral : 3.871 15.087 1732 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.92 % Allowed : 9.93 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.20), residues: 1580 helix: 2.20 (0.15), residues: 1024 sheet: 0.73 (0.31), residues: 236 loop : -1.95 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 217 TYR 0.014 0.001 TYR C 428 PHE 0.025 0.001 PHE B 490 TRP 0.002 0.000 TRP B 346 HIS 0.003 0.001 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (13300) covalent geometry : angle 0.43630 / 0.25 (18000) SS BOND : bond 0.00084 / 0.04 ( 8) SS BOND : angle 0.21488 / 0.11 ( 16) hydrogen bonds : bond 0.04159 / 2.81 ( 981) hydrogen bonds : angle 4.33836 / 3.13 ( 3159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.378 Fit side-chains REVERT: A 75 MET cc_start: 0.7441 (tpp) cc_final: 0.7105 (tpt) REVERT: A 217 ARG cc_start: 0.8304 (mtt90) cc_final: 0.7178 (mtm180) REVERT: A 410 MET cc_start: 0.4870 (mmm) cc_final: 0.4252 (mmm) REVERT: B 75 MET cc_start: 0.7442 (tpp) cc_final: 0.7109 (tpt) REVERT: B 185 ASP cc_start: 0.7018 (m-30) cc_final: 0.6632 (m-30) REVERT: B 217 ARG cc_start: 0.8289 (mtt90) cc_final: 0.7157 (mtm180) REVERT: B 410 MET cc_start: 0.4867 (mmm) cc_final: 0.4256 (mmm) REVERT: C 75 MET cc_start: 0.7406 (tpp) cc_final: 0.7073 (tpt) REVERT: C 185 ASP cc_start: 0.6996 (m-30) cc_final: 0.6612 (m-30) REVERT: C 217 ARG cc_start: 0.8318 (mtt90) cc_final: 0.7178 (mtm180) REVERT: C 410 MET cc_start: 0.4876 (mmm) cc_final: 0.4262 (mmm) REVERT: D 75 MET cc_start: 0.7416 (tpp) cc_final: 0.7077 (tpt) REVERT: D 185 ASP cc_start: 0.6995 (m-30) cc_final: 0.6606 (m-30) REVERT: D 217 ARG cc_start: 0.8319 (mtt90) cc_final: 0.7176 (mtm180) REVERT: D 410 MET cc_start: 0.4892 (mmm) cc_final: 0.4275 (mmm) outliers start: 28 outliers final: 12 residues processed: 203 average time/residue: 0.1056 time to fit residues: 31.6062 Evaluate side-chains 184 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 492 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [138, 145, 32, 86, 143, 65, 22, 84, 120, 159, 7] chunk 138 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 chunk 84 optimal weight: 0.9980 chunk 120 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.202597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.157374 restraints weight = 14329.419| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.22 r_work: 0.3608 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13308 Z= 0.194 Angle : 0.494 5.385 18016 Z= 0.277 Chirality : 0.039 0.136 2128 Planarity : 0.003 0.042 2184 Dihedral : 4.103 15.966 1732 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.01 % Allowed : 11.23 % Favored : 85.75 % 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: 1.43 (0.20), residues: 1580 helix: 1.87 (0.15), residues: 1024 sheet: 0.70 (0.30), residues: 236 loop : -1.95 (0.29), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 395 TYR 0.014 0.001 TYR B 428 PHE 0.022 0.002 PHE D 490 TRP 0.003 0.001 TRP B 346 HIS 0.004 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 (13300) covalent geometry : angle 0.49401 / 0.28 (18000) SS BOND : bond 0.00152 / 0.08 ( 8) SS BOND : angle 0.27757 / 0.15 ( 16) hydrogen bonds : bond 0.04413 / 3.00 ( 981) hydrogen bonds : angle 4.47925 / 3.22 ( 3159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.408 Fit side-chains REVERT: A 75 MET cc_start: 0.7461 (tpp) cc_final: 0.7183 (tpt) REVERT: A 217 ARG cc_start: 0.8364 (mtt90) cc_final: 0.7137 (mtm180) REVERT: B 75 MET cc_start: 0.7473 (tpp) cc_final: 0.7131 (tpt) REVERT: B 217 ARG cc_start: 0.8350 (mtt90) cc_final: 0.7169 (mtm180) REVERT: C 75 MET cc_start: 0.7462 (tpp) cc_final: 0.7149 (tpt) REVERT: C 217 ARG cc_start: 0.8367 (mtt90) cc_final: 0.7141 (mtm180) REVERT: D 75 MET cc_start: 0.7469 (tpp) cc_final: 0.7152 (tpt) REVERT: D 217 ARG cc_start: 0.8367 (mtt90) cc_final: 0.7143 (mtm180) outliers start: 44 outliers final: 26 residues processed: 195 average time/residue: 0.1069 time to fit residues: 30.5079 Evaluate side-chains 189 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [148, 12, 4, 118, 146, 133, 109, 84, 97, 25, 120] chunk 148 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.201253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.156399 restraints weight = 14476.596| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.19 r_work: 0.3589 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13308 Z= 0.212 Angle : 0.513 5.777 18016 Z= 0.288 Chirality : 0.040 0.137 2128 Planarity : 0.003 0.043 2184 Dihedral : 4.171 15.861 1732 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.47 % Allowed : 12.95 % Favored : 84.59 % 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: 1.27 (0.20), residues: 1580 helix: 1.71 (0.15), residues: 1024 sheet: 0.67 (0.31), residues: 236 loop : -1.89 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 310 TYR 0.014 0.002 TYR C 428 PHE 0.019 0.002 PHE B 490 TRP 0.003 0.001 TRP A 346 HIS 0.004 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (13300) covalent geometry : angle 0.51333 / 0.29 (18000) SS BOND : bond 0.00150 / 0.08 ( 8) SS BOND : angle 0.26479 / 0.14 ( 16) hydrogen bonds : bond 0.04485 / 3.05 ( 981) hydrogen bonds : angle 4.55425 / 3.28 ( 3159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.535 Fit side-chains REVERT: A 75 MET cc_start: 0.7499 (tpp) cc_final: 0.7229 (tpt) REVERT: A 217 ARG cc_start: 0.8408 (mtt90) cc_final: 0.7145 (mtm180) REVERT: A 410 MET cc_start: 0.5078 (mmm) cc_final: 0.4405 (mmm) REVERT: B 75 MET cc_start: 0.7482 (tpp) cc_final: 0.7216 (tpt) REVERT: B 217 ARG cc_start: 0.8400 (mtt90) cc_final: 0.7133 (mtm180) REVERT: B 410 MET cc_start: 0.5038 (mmm) cc_final: 0.4380 (mmm) REVERT: C 75 MET cc_start: 0.7451 (tpp) cc_final: 0.7046 (tpt) REVERT: C 217 ARG cc_start: 0.8408 (mtt90) cc_final: 0.7139 (mtm180) REVERT: C 410 MET cc_start: 0.5051 (mmm) cc_final: 0.4386 (mmm) REVERT: D 75 MET cc_start: 0.7460 (tpp) cc_final: 0.7045 (tpt) REVERT: D 217 ARG cc_start: 0.8406 (mtt90) cc_final: 0.7148 (mtm180) REVERT: D 410 MET cc_start: 0.5066 (mmm) cc_final: 0.4400 (mmm) outliers start: 36 outliers final: 29 residues processed: 196 average time/residue: 0.1236 time to fit residues: 34.4294 Evaluate side-chains 201 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 224 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 224 SER Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [68, 121, 145, 98, 85, 3, 11, 154, 128, 147, 125] chunk 68 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 128 optimal weight: 0.0870 chunk 147 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.207948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.165113 restraints weight = 14301.884| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 2.18 r_work: 0.3655 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 13308 Z= 0.117 Angle : 0.443 7.097 18016 Z= 0.249 Chirality : 0.037 0.136 2128 Planarity : 0.003 0.041 2184 Dihedral : 3.814 13.792 1732 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.60 % Allowed : 13.56 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.20), residues: 1580 helix: 2.12 (0.15), residues: 1024 sheet: 0.86 (0.31), residues: 236 loop : -1.86 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 139 TYR 0.015 0.001 TYR A 428 PHE 0.015 0.001 PHE D 490 TRP 0.004 0.001 TRP B 205 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (13300) covalent geometry : angle 0.44295 / 0.25 (18000) SS BOND : bond 0.00054 / 0.03 ( 8) SS BOND : angle 0.19678 / 0.10 ( 16) hydrogen bonds : bond 0.04018 / 2.71 ( 981) hydrogen bonds : angle 4.24401 / 3.05 ( 3159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 175 time to evaluate : 0.460 Fit side-chains REVERT: A 75 MET cc_start: 0.7482 (tpp) cc_final: 0.7103 (tpt) REVERT: A 185 ASP cc_start: 0.6994 (m-30) cc_final: 0.6553 (m-30) REVERT: A 410 MET cc_start: 0.4846 (mmm) cc_final: 0.4646 (mmm) REVERT: B 75 MET cc_start: 0.7496 (tpp) cc_final: 0.7123 (tpt) REVERT: B 185 ASP cc_start: 0.6964 (m-30) cc_final: 0.6532 (m-30) REVERT: C 75 MET cc_start: 0.7417 (tpp) cc_final: 0.7076 (tpt) REVERT: C 185 ASP cc_start: 0.6955 (m-30) cc_final: 0.6524 (m-30) REVERT: D 75 MET cc_start: 0.7424 (tpp) cc_final: 0.7081 (tpt) REVERT: D 185 ASP cc_start: 0.6930 (m-30) cc_final: 0.6494 (m-30) outliers start: 38 outliers final: 20 residues processed: 195 average time/residue: 0.0854 time to fit residues: 26.6167 Evaluate side-chains 184 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 164 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [12, 40, 107, 75, 113, 91, 23, 16, 86, 140, 8] chunk 12 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 0.0470 chunk 86 optimal weight: 0.1980 chunk 140 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN B 471 GLN C 471 GLN D 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.205720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.162047 restraints weight = 14447.358| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.14 r_work: 0.3666 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 13308 Z= 0.141 Angle : 0.465 8.114 18016 Z= 0.259 Chirality : 0.038 0.134 2128 Planarity : 0.003 0.041 2184 Dihedral : 3.863 13.964 1732 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.19 % Allowed : 14.11 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.20), residues: 1580 helix: 2.07 (0.15), residues: 1024 sheet: 0.84 (0.31), residues: 236 loop : -1.86 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 217 TYR 0.015 0.001 TYR B 428 PHE 0.014 0.001 PHE B 490 TRP 0.004 0.001 TRP B 346 HIS 0.002 0.001 HIS C 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (13300) covalent geometry : angle 0.46549 / 0.26 (18000) SS BOND : bond 0.00088 / 0.05 ( 8) SS BOND : angle 0.20283 / 0.11 ( 16) hydrogen bonds : bond 0.04099 / 2.78 ( 981) hydrogen bonds : angle 4.27811 / 3.07 ( 3159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.400 Fit side-chains REVERT: A 75 MET cc_start: 0.7454 (tpp) cc_final: 0.7123 (tpt) REVERT: B 75 MET cc_start: 0.7463 (tpp) cc_final: 0.7141 (tpt) REVERT: B 185 ASP cc_start: 0.7033 (m-30) cc_final: 0.6601 (m-30) REVERT: C 75 MET cc_start: 0.7461 (tpp) cc_final: 0.7070 (tpt) REVERT: C 185 ASP cc_start: 0.7023 (m-30) cc_final: 0.6596 (m-30) REVERT: D 75 MET cc_start: 0.7477 (tpp) cc_final: 0.7083 (tpt) REVERT: D 185 ASP cc_start: 0.7023 (m-30) cc_final: 0.6585 (m-30) outliers start: 32 outliers final: 27 residues processed: 180 average time/residue: 0.0864 time to fit residues: 24.6724 Evaluate side-chains 188 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [33, 46, 83, 10, 40, 12, 93, 58, 122, 64, 3] chunk 33 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.206475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.164300 restraints weight = 14100.806| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.13 r_work: 0.3700 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13308 Z= 0.121 Angle : 0.460 7.863 18016 Z= 0.255 Chirality : 0.038 0.133 2128 Planarity : 0.003 0.041 2184 Dihedral : 3.790 13.345 1732 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.05 % Allowed : 14.79 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.20), residues: 1580 helix: 2.16 (0.15), residues: 1024 sheet: 0.91 (0.31), residues: 236 loop : -1.90 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 139 TYR 0.015 0.001 TYR B 428 PHE 0.013 0.001 PHE C 490 TRP 0.004 0.001 TRP B 346 HIS 0.004 0.001 HIS D 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13300) covalent geometry : angle 0.46039 / 0.26 (18000) SS BOND : bond 0.00065 / 0.04 ( 8) SS BOND : angle 0.16275 / 0.09 ( 16) hydrogen bonds : bond 0.03987 / 2.69 ( 981) hydrogen bonds : angle 4.22554 / 3.04 ( 3159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.439 Fit side-chains REVERT: A 75 MET cc_start: 0.7424 (tpp) cc_final: 0.7017 (tpt) REVERT: A 185 ASP cc_start: 0.7000 (m-30) cc_final: 0.6585 (m-30) REVERT: B 185 ASP cc_start: 0.7015 (m-30) cc_final: 0.6598 (m-30) REVERT: C 185 ASP cc_start: 0.7002 (m-30) cc_final: 0.6596 (m-30) REVERT: D 185 ASP cc_start: 0.6986 (m-30) cc_final: 0.6572 (m-30) outliers start: 30 outliers final: 27 residues processed: 180 average time/residue: 0.0842 time to fit residues: 24.1416 Evaluate side-chains 188 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 153 GLU Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [143, 129, 1, 26, 67, 88, 48, 70, 55, 131, 117] chunk 143 optimal weight: 2.9990 chunk 129 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 chunk 131 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 471 GLN B 471 GLN C 471 GLN D 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.207085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.163392 restraints weight = 14450.082| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.27 r_work: 0.3688 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13308 Z= 0.129 Angle : 0.474 7.309 18016 Z= 0.259 Chirality : 0.038 0.133 2128 Planarity : 0.003 0.041 2184 Dihedral : 3.796 13.538 1732 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.85 % Allowed : 14.86 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.20), residues: 1580 helix: 2.12 (0.15), residues: 1024 sheet: 0.90 (0.31), residues: 236 loop : -1.95 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 139 TYR 0.015 0.001 TYR A 428 PHE 0.013 0.001 PHE C 490 TRP 0.004 0.001 TRP A 346 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (13300) covalent geometry : angle 0.47400 / 0.26 (18000) SS BOND : bond 0.00068 / 0.04 ( 8) SS BOND : angle 0.16548 / 0.09 ( 16) hydrogen bonds : bond 0.04058 / 2.74 ( 981) hydrogen bonds : angle 4.21798 / 3.03 ( 3159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.490 Fit side-chains REVERT: A 75 MET cc_start: 0.7489 (tpp) cc_final: 0.7066 (tpt) REVERT: A 185 ASP cc_start: 0.6999 (m-30) cc_final: 0.6600 (m-30) REVERT: B 75 MET cc_start: 0.7328 (tpp) cc_final: 0.6924 (tpt) REVERT: B 185 ASP cc_start: 0.7019 (m-30) cc_final: 0.6619 (m-30) REVERT: C 75 MET cc_start: 0.7288 (tpp) cc_final: 0.6932 (tpt) REVERT: C 185 ASP cc_start: 0.7020 (m-30) cc_final: 0.6622 (m-30) REVERT: D 75 MET cc_start: 0.7291 (tpp) cc_final: 0.6928 (tpt) REVERT: D 185 ASP cc_start: 0.7007 (m-30) cc_final: 0.6605 (m-30) outliers start: 27 outliers final: 25 residues processed: 183 average time/residue: 0.0856 time to fit residues: 24.9638 Evaluate side-chains 188 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [98, 62, 80, 122, 21, 46, 133, 19, 53, 13, 152] chunk 98 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 0.0170 chunk 152 optimal weight: 2.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.202885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.159693 restraints weight = 14556.589| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 2.22 r_work: 0.3618 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13308 Z= 0.186 Angle : 0.515 9.549 18016 Z= 0.286 Chirality : 0.040 0.145 2128 Planarity : 0.003 0.042 2184 Dihedral : 4.034 14.869 1732 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.78 % Allowed : 15.34 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.20), residues: 1580 helix: 1.81 (0.15), residues: 1024 sheet: 0.81 (0.31), residues: 236 loop : -2.01 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 217 TYR 0.018 0.002 TYR A 151 PHE 0.014 0.002 PHE A 482 TRP 0.004 0.001 TRP C 346 HIS 0.003 0.001 HIS C 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (13300) covalent geometry : angle 0.51469 / 0.29 (18000) SS BOND : bond 0.00113 / 0.06 ( 8) SS BOND : angle 0.23204 / 0.12 ( 16) hydrogen bonds : bond 0.04314 / 2.93 ( 981) hydrogen bonds : angle 4.44104 / 3.19 ( 3159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3160 Ramachandran restraints generated. 1580 Oldfield, 0 Emsley, 1580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 175 time to evaluate : 0.502 Fit side-chains REVERT: A 75 MET cc_start: 0.7424 (tpp) cc_final: 0.7146 (tpt) REVERT: A 185 ASP cc_start: 0.6887 (m-30) cc_final: 0.6545 (m-30) REVERT: A 217 ARG cc_start: 0.8319 (mtt90) cc_final: 0.7230 (mtm180) REVERT: B 185 ASP cc_start: 0.6894 (m-30) cc_final: 0.6550 (m-30) REVERT: B 217 ARG cc_start: 0.8293 (mtt90) cc_final: 0.7205 (mtm180) REVERT: C 75 MET cc_start: 0.7315 (tpp) cc_final: 0.6953 (tpt) REVERT: C 185 ASP cc_start: 0.6909 (m-30) cc_final: 0.6567 (m-30) REVERT: C 217 ARG cc_start: 0.8288 (mtt90) cc_final: 0.7203 (mtm180) REVERT: D 75 MET cc_start: 0.7342 (tpp) cc_final: 0.6970 (tpt) REVERT: D 185 ASP cc_start: 0.6908 (m-30) cc_final: 0.6562 (m-30) REVERT: D 217 ARG cc_start: 0.8297 (mtt90) cc_final: 0.7216 (mtm180) outliers start: 26 outliers final: 26 residues processed: 190 average time/residue: 0.1205 time to fit residues: 32.1926 Evaluate side-chains 202 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain B residue 88 GLN Chi-restraints excluded: chain B residue 196 GLN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 492 SER Chi-restraints excluded: chain C residue 494 PHE Chi-restraints excluded: chain D residue 88 GLN Chi-restraints excluded: chain D residue 196 GLN Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 494 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [112, 72, 93, 142, 25, 117, 54, 37, 73, 20, 148] chunk 112 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 93 optimal weight: 0.4980 chunk 142 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.208223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.165840 restraints weight = 14442.689| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.09 r_work: 0.3707 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 13308 Z= 0.115 Angle : 0.472 11.556 18016 Z= 0.254 Chirality : 0.038 0.168 2128 Planarity : 0.003 0.041 2184 Dihedral : 3.772 13.237 1732 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.58 % Allowed : 15.68 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.20), residues: 1580 helix: 2.16 (0.15), residues: 1020 sheet: 0.89 (0.31), residues: 236 loop : -1.94 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 217 TYR 0.016 0.001 TYR A 151 PHE 0.013 0.001 PHE D 490 TRP 0.005 0.001 TRP C 205 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (13300) covalent geometry : angle 0.47207 / 0.25 (18000) SS BOND : bond 0.00056 / 0.03 ( 8) SS BOND : angle 0.12856 / 0.07 ( 16) hydrogen bonds : bond 0.04023 / 2.72 ( 981) hydrogen bonds : angle 4.22157 / 3.03 ( 3159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3395.59 seconds wall clock time: 58 minutes 53.28 seconds (3533.28 seconds total)