Starting phenix.real_space_refine on Fri Mar 14 00:09:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cr3_45831/03_2025/9cr3_45831.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cr3_45831/03_2025/9cr3_45831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cr3_45831/03_2025/9cr3_45831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cr3_45831/03_2025/9cr3_45831.map" model { file = "/net/cci-nas-00/data/ceres_data/9cr3_45831/03_2025/9cr3_45831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cr3_45831/03_2025/9cr3_45831.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 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 60 5.16 5 C 5950 2.51 5 N 1581 2.21 5 O 1708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9299 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2315 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 18, 'TRANS': 280} Chain breaks: 2 Chain: "D" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2314 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 280} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2335 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 18, 'TRANS': 282} Chain breaks: 2 Chain: "B" Number of atoms: 2335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2335 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 18, 'TRANS': 282} Chain breaks: 2 Time building chain proxies: 6.34, per 1000 atoms: 0.68 Number of scatterers: 9299 At special positions: 0 Unit cell: (90.47, 101.26, 95.45, 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 60 16.00 O 1708 8.00 N 1581 7.00 C 5950 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 16 sheets defined 25.8% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 118 through 132 Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.584A pdb=" N GLU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 151 removed outlier: 3.611A pdb=" N ASP A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 3.625A pdb=" N LYS A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 219 through 230 removed outlier: 3.680A pdb=" N GLN A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.971A pdb=" N THR A 325 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.787A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 425 removed outlier: 3.600A pdb=" N LEU A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 118 through 132 removed outlier: 3.853A pdb=" N GLU D 132 " --> pdb=" O HIS D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 151 Processing helix chain 'D' and resid 154 through 159 Processing helix chain 'D' and resid 185 through 194 Processing helix chain 'D' and resid 219 through 229 removed outlier: 4.020A pdb=" N GLN D 223 " --> pdb=" O ASN D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.958A pdb=" N THR D 325 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.905A pdb=" N ALA D 330 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 331 " --> pdb=" O TYR D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 331' Processing helix chain 'D' and resid 412 through 425 removed outlier: 3.631A pdb=" N LEU D 425 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 118 through 132 removed outlier: 3.580A pdb=" N GLU C 132 " --> pdb=" O HIS C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 151 removed outlier: 3.527A pdb=" N ASP C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 185 through 194 Processing helix chain 'C' and resid 219 through 229 removed outlier: 4.056A pdb=" N GLN C 223 " --> pdb=" O ASN C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 removed outlier: 3.793A pdb=" N THR C 325 " --> pdb=" O THR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.940A pdb=" N ALA C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 326 through 331' Processing helix chain 'C' and resid 412 through 425 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 118 through 132 Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.880A pdb=" N LYS B 160 " --> pdb=" O ALA B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 219 through 230 removed outlier: 3.915A pdb=" N GLN B 223 " --> pdb=" O ASN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.807A pdb=" N THR B 325 " --> pdb=" O THR B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.770A pdb=" N ALA B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 425 Processing sheet with id=AA1, first strand: chain 'A' and resid 162 through 163 removed outlier: 6.406A pdb=" N VAL A 136 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 107 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE A 179 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU A 108 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU A 181 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE A 110 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 178 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N PHE A 204 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N CYS A 180 " --> pdb=" O PHE A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 237 removed outlier: 4.335A pdb=" N ALA A 233 " --> pdb=" O CYS A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 278 through 282 removed outlier: 3.584A pdb=" N GLY A 313 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 309 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 303 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 390 removed outlier: 3.646A pdb=" N GLY A 315 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.814A pdb=" N MET A 335 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 315 " --> pdb=" O ILE B 348 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 162 through 163 removed outlier: 6.086A pdb=" N VAL D 136 " --> pdb=" O CYS D 162 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL D 107 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE D 178 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N PHE D 204 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYS D 180 " --> pdb=" O PHE D 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 233 through 237 removed outlier: 4.103A pdb=" N ALA D 233 " --> pdb=" O CYS D 409 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 280 through 282 removed outlier: 3.570A pdb=" N THR D 309 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU D 303 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU D 307 " --> pdb=" O LEU D 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 387 through 390 removed outlier: 3.605A pdb=" N GLY D 315 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 335 through 336 removed outlier: 6.934A pdb=" N MET D 335 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 315 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 163 removed outlier: 6.279A pdb=" N VAL C 107 " --> pdb=" O TYR C 137 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE C 179 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU C 108 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU C 181 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE C 110 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE C 178 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE C 204 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N CYS C 180 " --> pdb=" O PHE C 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 233 through 237 removed outlier: 4.545A pdb=" N ALA C 233 " --> pdb=" O CYS C 409 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 280 through 282 removed outlier: 3.561A pdb=" N THR C 309 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 303 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LEU C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 162 through 164 removed outlier: 3.572A pdb=" N CYS B 162 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL B 107 " --> pdb=" O TYR B 137 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLU B 139 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N VAL B 109 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER B 106 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N ILE B 179 " --> pdb=" O SER B 106 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU B 108 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU B 181 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE B 110 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE B 178 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N PHE B 204 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N CYS B 180 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 215 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 233 through 237 removed outlier: 4.303A pdb=" N ALA B 233 " --> pdb=" O CYS B 409 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 280 through 282 removed outlier: 3.571A pdb=" N THR B 309 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 303 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 948 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: 2.89 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3001 1.34 - 1.46: 2036 1.46 - 1.58: 4374 1.58 - 1.70: 0 1.70 - 1.82: 92 Bond restraints: 9503 Sorted by residual: bond pdb=" N ARG C 356 " pdb=" CA ARG C 356 " ideal model delta sigma weight residual 1.454 1.479 -0.025 1.44e-02 4.82e+03 3.06e+00 bond pdb=" CA LYS B 102 " pdb=" CB LYS B 102 " ideal model delta sigma weight residual 1.532 1.549 -0.017 1.36e-02 5.41e+03 1.62e+00 bond pdb=" CA ARG C 356 " pdb=" C ARG C 356 " ideal model delta sigma weight residual 1.526 1.511 0.014 1.25e-02 6.40e+03 1.30e+00 bond pdb=" CB VAL D 359 " pdb=" CG2 VAL D 359 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.75e-01 bond pdb=" CB VAL B 359 " pdb=" CG2 VAL B 359 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.24e-01 ... (remaining 9498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 12469 1.51 - 3.01: 348 3.01 - 4.52: 79 4.52 - 6.03: 7 6.03 - 7.53: 4 Bond angle restraints: 12907 Sorted by residual: angle pdb=" C ARG C 356 " pdb=" N PRO C 357 " pdb=" CA PRO C 357 " ideal model delta sigma weight residual 119.78 123.16 -3.38 1.03e+00 9.43e-01 1.08e+01 angle pdb=" CA LYS B 102 " pdb=" CB LYS B 102 " pdb=" CG LYS B 102 " ideal model delta sigma weight residual 114.10 120.56 -6.46 2.00e+00 2.50e-01 1.04e+01 angle pdb=" C TRP D 427 " pdb=" N ASN D 428 " pdb=" CA ASN D 428 " ideal model delta sigma weight residual 120.38 124.65 -4.27 1.46e+00 4.69e-01 8.55e+00 angle pdb=" CA ARG C 356 " pdb=" C ARG C 356 " pdb=" O ARG C 356 " ideal model delta sigma weight residual 120.60 118.08 2.52 9.00e-01 1.23e+00 7.82e+00 angle pdb=" CA PHE C 355 " pdb=" C PHE C 355 " pdb=" N ARG C 356 " ideal model delta sigma weight residual 115.84 112.00 3.84 1.49e+00 4.50e-01 6.64e+00 ... (remaining 12902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5384 17.92 - 35.85: 312 35.85 - 53.77: 23 53.77 - 71.69: 13 71.69 - 89.62: 7 Dihedral angle restraints: 5739 sinusoidal: 2259 harmonic: 3480 Sorted by residual: dihedral pdb=" CA TYR B 295 " pdb=" C TYR B 295 " pdb=" N LEU B 296 " pdb=" CA LEU B 296 " ideal model delta harmonic sigma weight residual 180.00 157.04 22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA SER B 103 " pdb=" C SER B 103 " pdb=" N PRO B 104 " pdb=" CA PRO B 104 " ideal model delta harmonic sigma weight residual 180.00 -158.32 -21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA SER B 294 " pdb=" C SER B 294 " pdb=" N TYR B 295 " pdb=" CA TYR B 295 " ideal model delta harmonic sigma weight residual 180.00 -158.90 -21.10 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 5736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1047 0.044 - 0.088: 292 0.088 - 0.132: 150 0.132 - 0.176: 8 0.176 - 0.220: 3 Chirality restraints: 1500 Sorted by residual: chirality pdb=" CA ARG C 356 " pdb=" N ARG C 356 " pdb=" C ARG C 356 " pdb=" CB ARG C 356 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR C 310 " pdb=" CA THR C 310 " pdb=" OG1 THR C 310 " pdb=" CG2 THR C 310 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB THR C 127 " pdb=" CA THR C 127 " pdb=" OG1 THR C 127 " pdb=" CG2 THR C 127 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 1497 not shown) Planarity restraints: 1640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 220 " 0.014 2.00e-02 2.50e+03 1.38e-02 3.34e+00 pdb=" CG PHE A 220 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 220 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 220 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 220 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 220 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 220 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 337 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO C 338 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 338 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 338 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 337 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 338 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " -0.020 5.00e-02 4.00e+02 ... (remaining 1637 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 86 2.62 - 3.19: 8196 3.19 - 3.76: 13482 3.76 - 4.33: 19178 4.33 - 4.90: 32078 Nonbonded interactions: 73020 Sorted by model distance: nonbonded pdb=" OD1 ASP A 412 " pdb=" OG SER A 415 " model vdw 2.045 3.040 nonbonded pdb=" OD1 ASP B 412 " pdb=" OG SER B 415 " model vdw 2.179 3.040 nonbonded pdb=" OD1 ASP C 412 " pdb=" OG SER C 415 " model vdw 2.203 3.040 nonbonded pdb=" OG SER D 334 " pdb=" OG SER C 334 " model vdw 2.246 3.040 nonbonded pdb=" OD2 ASP A 314 " pdb=" OH TYR D 327 " model vdw 2.257 3.040 ... (remaining 73015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 96 through 164 or resid 173 or (resid 174 and (name N or n \ ame CA or name C or name O or name CB )) or resid 175 through 430)) selection = (chain 'B' and (resid 96 through 164 or resid 173 or (resid 174 and (name N or n \ ame CA or name C or name O or name CB )) or resid 175 through 430)) selection = (chain 'C' and (resid 96 through 164 or resid 173 or (resid 174 and (name N or n \ ame CA or name C or name O or name CB )) or resid 175 through 430)) selection = (chain 'D' and (resid 96 through 246 or resid 276 through 430)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.160 Find NCS groups from input model: 0.470 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 0.029 9503 Z= 0.199 Angle : 0.620 7.534 12907 Z= 0.330 Chirality : 0.049 0.220 1500 Planarity : 0.005 0.055 1640 Dihedral : 11.750 89.616 3475 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.26), residues: 1176 helix: 0.94 (0.36), residues: 237 sheet: 0.19 (0.27), residues: 373 loop : -1.30 (0.28), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 427 HIS 0.002 0.001 HIS B 128 PHE 0.031 0.002 PHE A 220 TYR 0.010 0.001 TYR D 280 ARG 0.003 0.000 ARG C 387 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.8347 (tmtt) cc_final: 0.8040 (tmtt) REVERT: A 105 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7418 (mmmt) REVERT: A 108 LEU cc_start: 0.8705 (tp) cc_final: 0.8268 (tt) REVERT: A 111 LYS cc_start: 0.8866 (ttpp) cc_final: 0.8524 (ttpp) REVERT: A 120 GLN cc_start: 0.8459 (tt0) cc_final: 0.7710 (tm-30) REVERT: A 122 PHE cc_start: 0.8762 (t80) cc_final: 0.8489 (t80) REVERT: A 123 LYS cc_start: 0.8696 (mtmm) cc_final: 0.8466 (mtmm) REVERT: A 124 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7797 (mt-10) REVERT: A 130 MET cc_start: 0.7651 (tpp) cc_final: 0.7404 (tpp) REVERT: A 134 MET cc_start: 0.8110 (ttt) cc_final: 0.7816 (ttt) REVERT: A 159 LYS cc_start: 0.8494 (mptt) cc_final: 0.8166 (mptt) REVERT: A 195 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7639 (mm-40) REVERT: A 202 MET cc_start: 0.8573 (ptt) cc_final: 0.8331 (ptm) REVERT: A 204 PHE cc_start: 0.8744 (m-80) cc_final: 0.8440 (m-80) REVERT: A 219 ASN cc_start: 0.8426 (t0) cc_final: 0.7929 (t0) REVERT: A 241 LYS cc_start: 0.8383 (ttpp) cc_final: 0.8049 (ttpp) REVERT: A 245 VAL cc_start: 0.8397 (t) cc_final: 0.8055 (m) REVERT: A 281 GLN cc_start: 0.8319 (mm-40) cc_final: 0.7886 (mm-40) REVERT: A 382 PHE cc_start: 0.8721 (m-80) cc_final: 0.8373 (m-80) REVERT: A 386 LYS cc_start: 0.7617 (mtmm) cc_final: 0.7343 (mtmm) REVERT: A 392 HIS cc_start: 0.8248 (m90) cc_final: 0.8033 (m90) REVERT: A 394 ASP cc_start: 0.7688 (m-30) cc_final: 0.7378 (m-30) REVERT: A 397 SER cc_start: 0.8632 (m) cc_final: 0.7977 (p) REVERT: A 416 ASP cc_start: 0.8137 (t0) cc_final: 0.7909 (t0) REVERT: D 98 LEU cc_start: 0.8202 (tp) cc_final: 0.7906 (mt) REVERT: D 105 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7834 (mmmt) REVERT: D 109 VAL cc_start: 0.9095 (t) cc_final: 0.8762 (m) REVERT: D 120 GLN cc_start: 0.8402 (tt0) cc_final: 0.7677 (tm-30) REVERT: D 122 PHE cc_start: 0.8883 (t80) cc_final: 0.8545 (t80) REVERT: D 123 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8005 (mmmm) REVERT: D 124 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7672 (mt-10) REVERT: D 127 THR cc_start: 0.9008 (p) cc_final: 0.8738 (p) REVERT: D 130 MET cc_start: 0.7880 (tpp) cc_final: 0.7474 (tpp) REVERT: D 134 MET cc_start: 0.7856 (ttt) cc_final: 0.7647 (ttt) REVERT: D 154 PHE cc_start: 0.8214 (t80) cc_final: 0.7320 (t80) REVERT: D 158 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8386 (mtpt) REVERT: D 176 ASP cc_start: 0.8144 (m-30) cc_final: 0.7743 (m-30) REVERT: D 193 LEU cc_start: 0.8237 (mm) cc_final: 0.7992 (mm) REVERT: D 194 PHE cc_start: 0.8353 (m-80) cc_final: 0.8087 (m-80) REVERT: D 211 PHE cc_start: 0.8392 (m-80) cc_final: 0.8077 (m-80) REVERT: D 215 PHE cc_start: 0.8607 (m-80) cc_final: 0.7948 (m-80) REVERT: D 218 GLU cc_start: 0.8004 (pp20) cc_final: 0.7746 (pp20) REVERT: D 219 ASN cc_start: 0.8465 (t0) cc_final: 0.8073 (t0) REVERT: D 221 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8249 (mm-40) REVERT: D 226 GLN cc_start: 0.8229 (tt0) cc_final: 0.7908 (tt0) REVERT: D 245 VAL cc_start: 0.8358 (t) cc_final: 0.8015 (p) REVERT: D 278 MET cc_start: 0.7871 (mmm) cc_final: 0.7551 (mmm) REVERT: D 279 GLN cc_start: 0.8372 (tt0) cc_final: 0.8161 (tt0) REVERT: D 285 GLU cc_start: 0.7904 (pm20) cc_final: 0.7289 (pm20) REVERT: D 325 THR cc_start: 0.8653 (p) cc_final: 0.8386 (p) REVERT: D 335 MET cc_start: 0.8388 (mmm) cc_final: 0.7748 (mmm) REVERT: D 395 SER cc_start: 0.8538 (t) cc_final: 0.8021 (p) REVERT: D 397 SER cc_start: 0.8604 (m) cc_final: 0.7902 (p) REVERT: D 425 LEU cc_start: 0.8426 (mt) cc_final: 0.8218 (mp) REVERT: C 109 VAL cc_start: 0.9081 (t) cc_final: 0.8722 (m) REVERT: C 112 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8040 (ttmt) REVERT: C 120 GLN cc_start: 0.8336 (tt0) cc_final: 0.7605 (tm-30) REVERT: C 122 PHE cc_start: 0.8776 (t80) cc_final: 0.8548 (t80) REVERT: C 123 LYS cc_start: 0.8709 (mmtm) cc_final: 0.8377 (mmtm) REVERT: C 124 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7678 (mt-10) REVERT: C 134 MET cc_start: 0.7955 (ttt) cc_final: 0.7634 (ttt) REVERT: C 154 PHE cc_start: 0.7996 (t80) cc_final: 0.7391 (t80) REVERT: C 158 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8066 (mtpt) REVERT: C 159 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8006 (mmmt) REVERT: C 176 ASP cc_start: 0.7903 (m-30) cc_final: 0.7609 (m-30) REVERT: C 218 GLU cc_start: 0.7998 (pp20) cc_final: 0.7642 (pp20) REVERT: C 226 GLN cc_start: 0.8365 (tt0) cc_final: 0.8111 (tt0) REVERT: C 245 VAL cc_start: 0.8461 (t) cc_final: 0.8160 (p) REVERT: C 281 GLN cc_start: 0.8065 (mm-40) cc_final: 0.7827 (mm-40) REVERT: C 285 GLU cc_start: 0.7930 (pm20) cc_final: 0.7366 (pm20) REVERT: C 319 SER cc_start: 0.8830 (p) cc_final: 0.8413 (t) REVERT: C 352 SER cc_start: 0.8657 (t) cc_final: 0.8425 (t) REVERT: C 355 PHE cc_start: 0.8569 (t80) cc_final: 0.8211 (t80) REVERT: C 365 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6805 (tm-30) REVERT: C 397 SER cc_start: 0.8610 (m) cc_final: 0.7947 (p) REVERT: B 98 LEU cc_start: 0.8034 (tp) cc_final: 0.7705 (mt) REVERT: B 105 LYS cc_start: 0.7656 (mmmt) cc_final: 0.7336 (mmmt) REVERT: B 110 ILE cc_start: 0.9142 (mt) cc_final: 0.8847 (mm) REVERT: B 111 LYS cc_start: 0.8773 (ttpp) cc_final: 0.8411 (ttpp) REVERT: B 113 MET cc_start: 0.7753 (ttm) cc_final: 0.7404 (ttm) REVERT: B 124 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7652 (mt-10) REVERT: B 125 LEU cc_start: 0.8897 (tp) cc_final: 0.8687 (tt) REVERT: B 134 MET cc_start: 0.7580 (tpp) cc_final: 0.7257 (tpt) REVERT: B 154 PHE cc_start: 0.7801 (t80) cc_final: 0.7135 (t80) REVERT: B 158 LYS cc_start: 0.8908 (mtpt) cc_final: 0.8397 (mtpt) REVERT: B 194 PHE cc_start: 0.8315 (m-80) cc_final: 0.8002 (m-80) REVERT: B 195 GLN cc_start: 0.7884 (mm-40) cc_final: 0.7481 (mm-40) REVERT: B 218 GLU cc_start: 0.8043 (pp20) cc_final: 0.7830 (pp20) REVERT: B 239 ARG cc_start: 0.8641 (mtm180) cc_final: 0.8341 (mtp180) REVERT: B 278 MET cc_start: 0.7835 (mmm) cc_final: 0.7523 (mmm) REVERT: B 279 GLN cc_start: 0.8481 (tt0) cc_final: 0.8197 (tt0) REVERT: B 285 GLU cc_start: 0.7874 (pm20) cc_final: 0.7345 (pm20) REVERT: B 294 SER cc_start: 0.8114 (m) cc_final: 0.7646 (p) REVERT: B 311 VAL cc_start: 0.8521 (p) cc_final: 0.8166 (m) REVERT: B 335 MET cc_start: 0.8575 (mpp) cc_final: 0.8260 (mmm) REVERT: B 397 SER cc_start: 0.8521 (m) cc_final: 0.8084 (p) REVERT: B 416 ASP cc_start: 0.8215 (t0) cc_final: 0.7992 (t0) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2576 time to fit residues: 131.3262 Evaluate side-chains 346 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.0010 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 60 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.124796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109337 restraints weight = 14596.747| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.86 r_work: 0.3291 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9503 Z= 0.282 Angle : 0.589 7.899 12907 Z= 0.308 Chirality : 0.049 0.207 1500 Planarity : 0.005 0.039 1640 Dihedral : 4.731 21.558 1270 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 1.52 % Allowed : 10.28 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.26), residues: 1176 helix: 0.41 (0.34), residues: 251 sheet: 0.39 (0.27), residues: 383 loop : -1.29 (0.29), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 427 HIS 0.004 0.001 HIS A 128 PHE 0.032 0.002 PHE D 220 TYR 0.013 0.001 TYR B 137 ARG 0.004 0.000 ARG D 391 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 370 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7819 (mmmt) REVERT: A 107 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.7991 (m) REVERT: A 111 LYS cc_start: 0.9009 (ttpp) cc_final: 0.8748 (ttpp) REVERT: A 120 GLN cc_start: 0.8692 (tt0) cc_final: 0.7951 (tm-30) REVERT: A 122 PHE cc_start: 0.8746 (t80) cc_final: 0.8518 (t80) REVERT: A 123 LYS cc_start: 0.8730 (mtmm) cc_final: 0.8485 (mtmm) REVERT: A 124 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8105 (mt-10) REVERT: A 130 MET cc_start: 0.8000 (tpp) cc_final: 0.7795 (tpp) REVERT: A 131 GLU cc_start: 0.8272 (tt0) cc_final: 0.7935 (tt0) REVERT: A 159 LYS cc_start: 0.8609 (mptt) cc_final: 0.8289 (mptt) REVERT: A 202 MET cc_start: 0.8715 (ptt) cc_final: 0.8465 (ptm) REVERT: A 204 PHE cc_start: 0.8692 (m-80) cc_final: 0.8397 (m-80) REVERT: A 219 ASN cc_start: 0.8525 (t0) cc_final: 0.8067 (t0) REVERT: A 228 ILE cc_start: 0.9011 (mt) cc_final: 0.8778 (tp) REVERT: A 245 VAL cc_start: 0.8551 (t) cc_final: 0.8286 (p) REVERT: A 365 GLU cc_start: 0.7407 (tm-30) cc_final: 0.6892 (tm-30) REVERT: A 392 HIS cc_start: 0.8458 (m90) cc_final: 0.8230 (m90) REVERT: A 397 SER cc_start: 0.8638 (m) cc_final: 0.7936 (p) REVERT: D 98 LEU cc_start: 0.8401 (tp) cc_final: 0.8025 (mt) REVERT: D 103 SER cc_start: 0.8814 (t) cc_final: 0.8548 (t) REVERT: D 105 LYS cc_start: 0.8225 (mmmt) cc_final: 0.7839 (mmmt) REVERT: D 109 VAL cc_start: 0.9015 (t) cc_final: 0.8732 (m) REVERT: D 120 GLN cc_start: 0.8744 (tt0) cc_final: 0.8054 (tm-30) REVERT: D 122 PHE cc_start: 0.8847 (t80) cc_final: 0.8542 (t80) REVERT: D 123 LYS cc_start: 0.8727 (mmtm) cc_final: 0.8045 (mmmm) REVERT: D 124 GLU cc_start: 0.8561 (mt-10) cc_final: 0.7949 (mt-10) REVERT: D 130 MET cc_start: 0.8124 (tpp) cc_final: 0.7800 (tpp) REVERT: D 134 MET cc_start: 0.7669 (ttt) cc_final: 0.7372 (ttt) REVERT: D 154 PHE cc_start: 0.7963 (t80) cc_final: 0.7039 (t80) REVERT: D 158 LYS cc_start: 0.8861 (mtpt) cc_final: 0.8361 (mtpt) REVERT: D 176 ASP cc_start: 0.8246 (m-30) cc_final: 0.7912 (m-30) REVERT: D 193 LEU cc_start: 0.8470 (mm) cc_final: 0.8263 (mm) REVERT: D 211 PHE cc_start: 0.8402 (m-80) cc_final: 0.8089 (m-80) REVERT: D 215 PHE cc_start: 0.8457 (m-80) cc_final: 0.7773 (m-80) REVERT: D 218 GLU cc_start: 0.8033 (pp20) cc_final: 0.7743 (pp20) REVERT: D 219 ASN cc_start: 0.8516 (t0) cc_final: 0.8081 (t0) REVERT: D 221 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8321 (mm-40) REVERT: D 245 VAL cc_start: 0.8311 (t) cc_final: 0.7983 (p) REVERT: D 278 MET cc_start: 0.7981 (mmm) cc_final: 0.7707 (mmm) REVERT: D 285 GLU cc_start: 0.8049 (pm20) cc_final: 0.7485 (pm20) REVERT: D 335 MET cc_start: 0.8502 (mmm) cc_final: 0.7605 (mmm) REVERT: D 397 SER cc_start: 0.8633 (m) cc_final: 0.7971 (p) REVERT: D 425 LEU cc_start: 0.8480 (mt) cc_final: 0.8251 (mp) REVERT: C 105 LYS cc_start: 0.8240 (mmpt) cc_final: 0.7906 (mmpt) REVERT: C 106 SER cc_start: 0.7804 (p) cc_final: 0.7522 (p) REVERT: C 109 VAL cc_start: 0.9011 (t) cc_final: 0.8685 (m) REVERT: C 112 LYS cc_start: 0.8364 (ttmt) cc_final: 0.8093 (ttmt) REVERT: C 122 PHE cc_start: 0.8730 (t80) cc_final: 0.8505 (t80) REVERT: C 123 LYS cc_start: 0.8739 (mmtm) cc_final: 0.8455 (mmtm) REVERT: C 134 MET cc_start: 0.7787 (ttt) cc_final: 0.7563 (ttt) REVERT: C 154 PHE cc_start: 0.7625 (t80) cc_final: 0.6936 (t80) REVERT: C 158 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8064 (mtpt) REVERT: C 159 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8049 (mmmt) REVERT: C 174 GLN cc_start: 0.8078 (mt0) cc_final: 0.7803 (mt0) REVERT: C 176 ASP cc_start: 0.8068 (m-30) cc_final: 0.7676 (m-30) REVERT: C 198 VAL cc_start: 0.8609 (t) cc_final: 0.8332 (p) REVERT: C 204 PHE cc_start: 0.8689 (m-80) cc_final: 0.8345 (m-80) REVERT: C 218 GLU cc_start: 0.8112 (pp20) cc_final: 0.7805 (pp20) REVERT: C 226 GLN cc_start: 0.8396 (tt0) cc_final: 0.8144 (tt0) REVERT: C 243 ARG cc_start: 0.8206 (ttp-170) cc_final: 0.7737 (ptm160) REVERT: C 245 VAL cc_start: 0.8486 (t) cc_final: 0.8082 (m) REVERT: C 278 MET cc_start: 0.7571 (mmm) cc_final: 0.7187 (mmm) REVERT: C 281 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7929 (mm-40) REVERT: C 285 GLU cc_start: 0.7938 (pm20) cc_final: 0.7532 (pm20) REVERT: C 319 SER cc_start: 0.8742 (p) cc_final: 0.8322 (t) REVERT: C 324 SER cc_start: 0.8446 (m) cc_final: 0.8240 (p) REVERT: C 335 MET cc_start: 0.8745 (mpp) cc_final: 0.8422 (mmm) REVERT: C 346 THR cc_start: 0.8601 (m) cc_final: 0.8134 (p) REVERT: C 352 SER cc_start: 0.8569 (t) cc_final: 0.8325 (t) REVERT: C 365 GLU cc_start: 0.7469 (tm-30) cc_final: 0.6900 (tm-30) REVERT: C 397 SER cc_start: 0.8688 (m) cc_final: 0.7744 (p) REVERT: B 98 LEU cc_start: 0.8230 (tp) cc_final: 0.7751 (mt) REVERT: B 105 LYS cc_start: 0.7828 (mmmt) cc_final: 0.7303 (mmmt) REVERT: B 111 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8560 (ttpp) REVERT: B 113 MET cc_start: 0.7827 (ttm) cc_final: 0.7477 (ttm) REVERT: B 124 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7874 (mt-10) REVERT: B 125 LEU cc_start: 0.8968 (tp) cc_final: 0.8753 (tt) REVERT: B 128 HIS cc_start: 0.8583 (t70) cc_final: 0.8200 (t70) REVERT: B 132 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8150 (mt-10) REVERT: B 154 PHE cc_start: 0.7898 (t80) cc_final: 0.7116 (t80) REVERT: B 158 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8471 (mtpt) REVERT: B 202 MET cc_start: 0.8593 (ptt) cc_final: 0.8267 (ptm) REVERT: B 204 PHE cc_start: 0.8605 (m-80) cc_final: 0.8247 (m-80) REVERT: B 218 GLU cc_start: 0.8103 (pp20) cc_final: 0.7821 (pp20) REVERT: B 221 GLN cc_start: 0.8635 (mm-40) cc_final: 0.8290 (mm-40) REVERT: B 226 GLN cc_start: 0.8575 (tt0) cc_final: 0.8287 (tt0) REVERT: B 239 ARG cc_start: 0.8630 (mtm180) cc_final: 0.8349 (mtp180) REVERT: B 279 GLN cc_start: 0.8504 (tt0) cc_final: 0.8250 (tt0) REVERT: B 285 GLU cc_start: 0.7974 (pm20) cc_final: 0.7574 (pm20) REVERT: B 294 SER cc_start: 0.8196 (m) cc_final: 0.7692 (p) REVERT: B 335 MET cc_start: 0.8584 (mpp) cc_final: 0.8311 (mmm) REVERT: B 367 LYS cc_start: 0.8357 (ttmm) cc_final: 0.8022 (ttmm) REVERT: B 397 SER cc_start: 0.8607 (m) cc_final: 0.7885 (p) outliers start: 16 outliers final: 6 residues processed: 373 average time/residue: 0.3523 time to fit residues: 176.9885 Evaluate side-chains 370 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 363 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 310 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 90 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 102 optimal weight: 0.0870 chunk 20 optimal weight: 0.0020 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 overall best weight: 0.5768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS A 221 GLN D 392 HIS ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.126473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111003 restraints weight = 14530.497| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.75 r_work: 0.3318 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9503 Z= 0.194 Angle : 0.570 8.945 12907 Z= 0.298 Chirality : 0.047 0.168 1500 Planarity : 0.005 0.035 1640 Dihedral : 4.627 22.618 1270 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 2.00 % Allowed : 14.27 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.26), residues: 1176 helix: 0.43 (0.34), residues: 248 sheet: 0.47 (0.27), residues: 373 loop : -1.16 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 427 HIS 0.006 0.001 HIS A 128 PHE 0.036 0.002 PHE D 220 TYR 0.008 0.001 TYR C 280 ARG 0.002 0.000 ARG D 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 366 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8205 (tp) cc_final: 0.7418 (mt) REVERT: A 105 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7648 (mmmt) REVERT: A 111 LYS cc_start: 0.8989 (ttpp) cc_final: 0.8746 (ttpp) REVERT: A 120 GLN cc_start: 0.8689 (tt0) cc_final: 0.7950 (tm-30) REVERT: A 122 PHE cc_start: 0.8692 (t80) cc_final: 0.8420 (t80) REVERT: A 123 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8446 (mtmm) REVERT: A 124 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8146 (mt-10) REVERT: A 131 GLU cc_start: 0.8175 (tt0) cc_final: 0.7882 (tt0) REVERT: A 159 LYS cc_start: 0.8518 (mptt) cc_final: 0.8162 (mptt) REVERT: A 202 MET cc_start: 0.8718 (ptt) cc_final: 0.8485 (ptm) REVERT: A 204 PHE cc_start: 0.8683 (m-80) cc_final: 0.8427 (m-80) REVERT: A 219 ASN cc_start: 0.8404 (t0) cc_final: 0.7963 (t0) REVERT: A 228 ILE cc_start: 0.8927 (mt) cc_final: 0.8711 (tp) REVERT: A 245 VAL cc_start: 0.8559 (t) cc_final: 0.8193 (m) REVERT: A 365 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6720 (tm-30) REVERT: A 392 HIS cc_start: 0.8436 (m90) cc_final: 0.8224 (m90) REVERT: A 397 SER cc_start: 0.8638 (m) cc_final: 0.7974 (p) REVERT: A 423 GLN cc_start: 0.8532 (tp40) cc_final: 0.8308 (tt0) REVERT: D 98 LEU cc_start: 0.8352 (tp) cc_final: 0.8013 (mt) REVERT: D 103 SER cc_start: 0.8818 (t) cc_final: 0.8574 (t) REVERT: D 105 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7711 (mmmt) REVERT: D 109 VAL cc_start: 0.9021 (t) cc_final: 0.8745 (m) REVERT: D 120 GLN cc_start: 0.8813 (tt0) cc_final: 0.8134 (tm-30) REVERT: D 122 PHE cc_start: 0.8793 (t80) cc_final: 0.8470 (t80) REVERT: D 123 LYS cc_start: 0.8649 (mmtm) cc_final: 0.7986 (mmmm) REVERT: D 124 GLU cc_start: 0.8512 (mt-10) cc_final: 0.7897 (mt-10) REVERT: D 130 MET cc_start: 0.8049 (tpp) cc_final: 0.7814 (tpp) REVERT: D 134 MET cc_start: 0.7661 (ttt) cc_final: 0.7342 (ttt) REVERT: D 154 PHE cc_start: 0.7769 (t80) cc_final: 0.6882 (t80) REVERT: D 158 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8305 (mtpt) REVERT: D 176 ASP cc_start: 0.8152 (m-30) cc_final: 0.7855 (m-30) REVERT: D 194 PHE cc_start: 0.8304 (m-80) cc_final: 0.8102 (m-80) REVERT: D 211 PHE cc_start: 0.8371 (m-80) cc_final: 0.8021 (m-80) REVERT: D 213 THR cc_start: 0.7974 (p) cc_final: 0.7712 (p) REVERT: D 218 GLU cc_start: 0.7877 (pp20) cc_final: 0.7506 (pp20) REVERT: D 221 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8210 (mm-40) REVERT: D 245 VAL cc_start: 0.8355 (t) cc_final: 0.7985 (p) REVERT: D 278 MET cc_start: 0.7810 (mmm) cc_final: 0.7518 (mmm) REVERT: D 285 GLU cc_start: 0.8000 (pm20) cc_final: 0.7499 (pm20) REVERT: D 395 SER cc_start: 0.8538 (t) cc_final: 0.8319 (p) REVERT: D 397 SER cc_start: 0.8639 (m) cc_final: 0.7975 (p) REVERT: D 425 LEU cc_start: 0.8487 (mt) cc_final: 0.8255 (mp) REVERT: C 105 LYS cc_start: 0.8181 (mmpt) cc_final: 0.7776 (mmpt) REVERT: C 106 SER cc_start: 0.7863 (p) cc_final: 0.7654 (p) REVERT: C 109 VAL cc_start: 0.9007 (t) cc_final: 0.8687 (m) REVERT: C 112 LYS cc_start: 0.8312 (ttmt) cc_final: 0.8036 (ttmt) REVERT: C 122 PHE cc_start: 0.8700 (t80) cc_final: 0.8465 (t80) REVERT: C 123 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8423 (mmtm) REVERT: C 154 PHE cc_start: 0.7532 (t80) cc_final: 0.6826 (t80) REVERT: C 158 LYS cc_start: 0.8997 (mtpt) cc_final: 0.8009 (mtpt) REVERT: C 159 LYS cc_start: 0.8508 (mmmt) cc_final: 0.7994 (mmmt) REVERT: C 174 GLN cc_start: 0.8092 (mt0) cc_final: 0.7855 (mt0) REVERT: C 176 ASP cc_start: 0.8027 (m-30) cc_final: 0.7673 (m-30) REVERT: C 204 PHE cc_start: 0.8685 (m-80) cc_final: 0.8366 (m-80) REVERT: C 218 GLU cc_start: 0.8004 (pp20) cc_final: 0.7664 (pp20) REVERT: C 226 GLN cc_start: 0.8371 (tt0) cc_final: 0.8124 (tt0) REVERT: C 243 ARG cc_start: 0.8209 (ttp-170) cc_final: 0.7768 (ptm160) REVERT: C 245 VAL cc_start: 0.8522 (t) cc_final: 0.8151 (m) REVERT: C 278 MET cc_start: 0.7366 (mmm) cc_final: 0.7123 (mmm) REVERT: C 281 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7825 (mm-40) REVERT: C 285 GLU cc_start: 0.7874 (pm20) cc_final: 0.7502 (pm20) REVERT: C 319 SER cc_start: 0.8687 (p) cc_final: 0.8282 (t) REVERT: C 335 MET cc_start: 0.8724 (mpp) cc_final: 0.8429 (mmm) REVERT: C 346 THR cc_start: 0.8569 (m) cc_final: 0.8107 (p) REVERT: C 352 SER cc_start: 0.8522 (t) cc_final: 0.8274 (t) REVERT: C 365 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6871 (tm-30) REVERT: C 397 SER cc_start: 0.8682 (m) cc_final: 0.7882 (p) REVERT: B 98 LEU cc_start: 0.8219 (tp) cc_final: 0.7733 (mt) REVERT: B 105 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7164 (mmmt) REVERT: B 111 LYS cc_start: 0.8849 (ttpp) cc_final: 0.8505 (ttpp) REVERT: B 113 MET cc_start: 0.7707 (ttm) cc_final: 0.7361 (ttm) REVERT: B 125 LEU cc_start: 0.8958 (tp) cc_final: 0.8745 (tt) REVERT: B 154 PHE cc_start: 0.7770 (t80) cc_final: 0.6928 (t80) REVERT: B 158 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8441 (mtpt) REVERT: B 202 MET cc_start: 0.8580 (ptt) cc_final: 0.8286 (ptm) REVERT: B 221 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8104 (mm-40) REVERT: B 226 GLN cc_start: 0.8577 (tt0) cc_final: 0.8308 (tt0) REVERT: B 228 ILE cc_start: 0.9135 (mm) cc_final: 0.8902 (tp) REVERT: B 239 ARG cc_start: 0.8602 (mtm180) cc_final: 0.8304 (mtp180) REVERT: B 278 MET cc_start: 0.7767 (mmm) cc_final: 0.7350 (mmm) REVERT: B 285 GLU cc_start: 0.7911 (pm20) cc_final: 0.7597 (pm20) REVERT: B 294 SER cc_start: 0.8195 (m) cc_final: 0.7705 (p) REVERT: B 311 VAL cc_start: 0.8562 (p) cc_final: 0.8227 (m) REVERT: B 335 MET cc_start: 0.8567 (mpp) cc_final: 0.8325 (mmm) REVERT: B 356 ARG cc_start: 0.8478 (tpp-160) cc_final: 0.8245 (tpp80) REVERT: B 365 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7137 (tm-30) REVERT: B 367 LYS cc_start: 0.8339 (ttmm) cc_final: 0.8035 (ttmm) REVERT: B 397 SER cc_start: 0.8612 (m) cc_final: 0.7937 (p) outliers start: 21 outliers final: 14 residues processed: 371 average time/residue: 0.2341 time to fit residues: 115.5168 Evaluate side-chains 370 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 356 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 364 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.124328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.109012 restraints weight = 14433.197| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.71 r_work: 0.3298 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9503 Z= 0.291 Angle : 0.591 10.610 12907 Z= 0.307 Chirality : 0.048 0.166 1500 Planarity : 0.005 0.039 1640 Dihedral : 4.645 21.999 1270 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 2.66 % Allowed : 16.94 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1176 helix: 0.57 (0.34), residues: 251 sheet: 0.47 (0.27), residues: 384 loop : -1.15 (0.30), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 427 HIS 0.002 0.001 HIS A 337 PHE 0.035 0.002 PHE D 220 TYR 0.008 0.001 TYR C 280 ARG 0.002 0.000 ARG D 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 371 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7183 (mmmt) REVERT: A 111 LYS cc_start: 0.8976 (ttpp) cc_final: 0.8724 (ttpp) REVERT: A 120 GLN cc_start: 0.8706 (tt0) cc_final: 0.7969 (tm-30) REVERT: A 122 PHE cc_start: 0.8747 (t80) cc_final: 0.8496 (t80) REVERT: A 123 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8443 (mtmm) REVERT: A 124 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8143 (mt-10) REVERT: A 131 GLU cc_start: 0.8084 (tt0) cc_final: 0.7800 (tt0) REVERT: A 159 LYS cc_start: 0.8585 (mptt) cc_final: 0.8248 (mptt) REVERT: A 202 MET cc_start: 0.8747 (ptt) cc_final: 0.8504 (ptm) REVERT: A 204 PHE cc_start: 0.8722 (m-80) cc_final: 0.8333 (m-80) REVERT: A 213 THR cc_start: 0.7836 (p) cc_final: 0.7576 (p) REVERT: A 219 ASN cc_start: 0.8444 (t0) cc_final: 0.7992 (t0) REVERT: A 228 ILE cc_start: 0.8915 (mt) cc_final: 0.8666 (tp) REVERT: A 245 VAL cc_start: 0.8574 (t) cc_final: 0.8286 (p) REVERT: A 365 GLU cc_start: 0.7504 (tm-30) cc_final: 0.6720 (tm-30) REVERT: A 392 HIS cc_start: 0.8400 (m90) cc_final: 0.8199 (m90) REVERT: A 397 SER cc_start: 0.8619 (m) cc_final: 0.7954 (p) REVERT: A 423 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8306 (tt0) REVERT: D 103 SER cc_start: 0.8832 (t) cc_final: 0.8601 (t) REVERT: D 105 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7622 (mmmt) REVERT: D 109 VAL cc_start: 0.9024 (t) cc_final: 0.8744 (m) REVERT: D 120 GLN cc_start: 0.8800 (tt0) cc_final: 0.8182 (tt0) REVERT: D 122 PHE cc_start: 0.8841 (t80) cc_final: 0.8511 (t80) REVERT: D 123 LYS cc_start: 0.8678 (mmtm) cc_final: 0.7998 (mmmm) REVERT: D 124 GLU cc_start: 0.8529 (mt-10) cc_final: 0.7961 (mt-10) REVERT: D 130 MET cc_start: 0.8046 (tpp) cc_final: 0.7806 (tpp) REVERT: D 134 MET cc_start: 0.7802 (ttt) cc_final: 0.7444 (ttt) REVERT: D 154 PHE cc_start: 0.7792 (t80) cc_final: 0.6888 (t80) REVERT: D 158 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8332 (mtpt) REVERT: D 211 PHE cc_start: 0.8422 (m-80) cc_final: 0.8098 (m-80) REVERT: D 215 PHE cc_start: 0.8461 (m-80) cc_final: 0.8039 (m-80) REVERT: D 218 GLU cc_start: 0.7922 (pp20) cc_final: 0.7565 (pp20) REVERT: D 221 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8313 (mm-40) REVERT: D 245 VAL cc_start: 0.8360 (t) cc_final: 0.7970 (p) REVERT: D 278 MET cc_start: 0.7801 (mmm) cc_final: 0.7502 (mmm) REVERT: D 285 GLU cc_start: 0.7996 (pm20) cc_final: 0.7618 (pm20) REVERT: D 335 MET cc_start: 0.8494 (mmm) cc_final: 0.7669 (mmm) REVERT: D 395 SER cc_start: 0.8579 (t) cc_final: 0.8294 (p) REVERT: D 397 SER cc_start: 0.8665 (m) cc_final: 0.7976 (p) REVERT: D 425 LEU cc_start: 0.8553 (mt) cc_final: 0.8302 (mp) REVERT: C 105 LYS cc_start: 0.8085 (mmpt) cc_final: 0.7693 (mmtt) REVERT: C 109 VAL cc_start: 0.8989 (t) cc_final: 0.8677 (m) REVERT: C 112 LYS cc_start: 0.8323 (ttmt) cc_final: 0.8028 (ttmt) REVERT: C 120 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8173 (tm-30) REVERT: C 122 PHE cc_start: 0.8759 (t80) cc_final: 0.8534 (t80) REVERT: C 123 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8429 (mmtm) REVERT: C 154 PHE cc_start: 0.7625 (t80) cc_final: 0.6871 (t80) REVERT: C 158 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8003 (mtpt) REVERT: C 159 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8004 (mmmt) REVERT: C 174 GLN cc_start: 0.8035 (mt0) cc_final: 0.7759 (mt0) REVERT: C 176 ASP cc_start: 0.8074 (m-30) cc_final: 0.7702 (m-30) REVERT: C 198 VAL cc_start: 0.8601 (t) cc_final: 0.8312 (p) REVERT: C 218 GLU cc_start: 0.8062 (pp20) cc_final: 0.7711 (pp20) REVERT: C 226 GLN cc_start: 0.8403 (tt0) cc_final: 0.8161 (tt0) REVERT: C 243 ARG cc_start: 0.8262 (ttp-170) cc_final: 0.7742 (ptm160) REVERT: C 245 VAL cc_start: 0.8508 (t) cc_final: 0.8074 (m) REVERT: C 278 MET cc_start: 0.7465 (mmm) cc_final: 0.7259 (mmm) REVERT: C 281 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7831 (mm-40) REVERT: C 285 GLU cc_start: 0.7884 (pm20) cc_final: 0.7520 (pm20) REVERT: C 319 SER cc_start: 0.8751 (p) cc_final: 0.8358 (t) REVERT: C 335 MET cc_start: 0.8707 (mpp) cc_final: 0.8456 (mmm) REVERT: C 346 THR cc_start: 0.8552 (m) cc_final: 0.8107 (p) REVERT: C 352 SER cc_start: 0.8589 (t) cc_final: 0.8346 (t) REVERT: C 365 GLU cc_start: 0.7526 (tm-30) cc_final: 0.6919 (tm-30) REVERT: C 397 SER cc_start: 0.8673 (m) cc_final: 0.7810 (p) REVERT: B 105 LYS cc_start: 0.7880 (mmmt) cc_final: 0.7329 (mmmt) REVERT: B 113 MET cc_start: 0.7788 (ttm) cc_final: 0.7559 (ttm) REVERT: B 125 LEU cc_start: 0.8959 (tp) cc_final: 0.8730 (tt) REVERT: B 154 PHE cc_start: 0.7793 (t80) cc_final: 0.6994 (t80) REVERT: B 158 LYS cc_start: 0.8989 (mtpt) cc_final: 0.8501 (mtpt) REVERT: B 202 MET cc_start: 0.8602 (ptt) cc_final: 0.8374 (ptm) REVERT: B 226 GLN cc_start: 0.8597 (tt0) cc_final: 0.8365 (tt0) REVERT: B 228 ILE cc_start: 0.9137 (mm) cc_final: 0.8917 (tp) REVERT: B 239 ARG cc_start: 0.8627 (mtm180) cc_final: 0.8334 (mtp180) REVERT: B 285 GLU cc_start: 0.8014 (pm20) cc_final: 0.7692 (pm20) REVERT: B 335 MET cc_start: 0.8559 (mpp) cc_final: 0.8294 (mmm) REVERT: B 356 ARG cc_start: 0.8477 (tpp-160) cc_final: 0.8247 (tpp80) REVERT: B 365 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7183 (tm-30) REVERT: B 397 SER cc_start: 0.8604 (m) cc_final: 0.7999 (p) REVERT: B 412 ASP cc_start: 0.7773 (p0) cc_final: 0.7549 (p0) outliers start: 28 outliers final: 22 residues processed: 377 average time/residue: 0.2396 time to fit residues: 120.7759 Evaluate side-chains 381 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 358 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 386 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.123450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108058 restraints weight = 14473.869| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.71 r_work: 0.3279 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9503 Z= 0.337 Angle : 0.609 8.262 12907 Z= 0.319 Chirality : 0.049 0.183 1500 Planarity : 0.005 0.042 1640 Dihedral : 4.749 22.245 1270 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 3.43 % Allowed : 16.84 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.26), residues: 1176 helix: 0.55 (0.34), residues: 251 sheet: 0.40 (0.27), residues: 384 loop : -1.27 (0.29), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 427 HIS 0.004 0.001 HIS B 128 PHE 0.041 0.003 PHE D 220 TYR 0.008 0.001 TYR C 280 ARG 0.002 0.000 ARG D 391 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 366 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8266 (mmmt) cc_final: 0.7849 (mmmt) REVERT: A 107 VAL cc_start: 0.8349 (t) cc_final: 0.8008 (m) REVERT: A 111 LYS cc_start: 0.8973 (ttpp) cc_final: 0.8717 (ttpp) REVERT: A 120 GLN cc_start: 0.8720 (tt0) cc_final: 0.7970 (tm-30) REVERT: A 122 PHE cc_start: 0.8785 (t80) cc_final: 0.8538 (t80) REVERT: A 123 LYS cc_start: 0.8709 (mtmm) cc_final: 0.8481 (mtmm) REVERT: A 124 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8128 (mt-10) REVERT: A 131 GLU cc_start: 0.8085 (tt0) cc_final: 0.7788 (tt0) REVERT: A 134 MET cc_start: 0.7758 (mmm) cc_final: 0.7477 (tpt) REVERT: A 159 LYS cc_start: 0.8615 (mptt) cc_final: 0.8300 (mptt) REVERT: A 202 MET cc_start: 0.8741 (ptt) cc_final: 0.8486 (ptm) REVERT: A 213 THR cc_start: 0.7890 (p) cc_final: 0.7651 (p) REVERT: A 219 ASN cc_start: 0.8446 (t0) cc_final: 0.8022 (t0) REVERT: A 228 ILE cc_start: 0.8945 (mt) cc_final: 0.8700 (tp) REVERT: A 245 VAL cc_start: 0.8590 (t) cc_final: 0.8285 (p) REVERT: A 365 GLU cc_start: 0.7486 (tm-30) cc_final: 0.6724 (tm-30) REVERT: A 397 SER cc_start: 0.8610 (m) cc_final: 0.7937 (p) REVERT: A 423 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: D 103 SER cc_start: 0.8846 (t) cc_final: 0.8615 (t) REVERT: D 105 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7640 (mmmt) REVERT: D 109 VAL cc_start: 0.9023 (t) cc_final: 0.8751 (m) REVERT: D 122 PHE cc_start: 0.8826 (t80) cc_final: 0.8526 (t80) REVERT: D 123 LYS cc_start: 0.8665 (mmtm) cc_final: 0.7984 (mmmm) REVERT: D 124 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8069 (mt-10) REVERT: D 130 MET cc_start: 0.8043 (tpp) cc_final: 0.7732 (tpp) REVERT: D 134 MET cc_start: 0.7821 (ttt) cc_final: 0.7425 (ttt) REVERT: D 154 PHE cc_start: 0.7816 (t80) cc_final: 0.6949 (t80) REVERT: D 158 LYS cc_start: 0.8882 (mtpt) cc_final: 0.8356 (mtpt) REVERT: D 211 PHE cc_start: 0.8456 (m-80) cc_final: 0.8137 (m-80) REVERT: D 218 GLU cc_start: 0.7795 (pp20) cc_final: 0.7372 (pp20) REVERT: D 221 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8314 (mm-40) REVERT: D 245 VAL cc_start: 0.8366 (t) cc_final: 0.8025 (p) REVERT: D 278 MET cc_start: 0.7816 (mmm) cc_final: 0.7521 (mmm) REVERT: D 285 GLU cc_start: 0.7992 (pm20) cc_final: 0.7655 (pm20) REVERT: D 335 MET cc_start: 0.8508 (mmm) cc_final: 0.7608 (mmm) REVERT: D 397 SER cc_start: 0.8677 (m) cc_final: 0.8024 (p) REVERT: D 425 LEU cc_start: 0.8595 (mt) cc_final: 0.8342 (mp) REVERT: C 109 VAL cc_start: 0.8998 (t) cc_final: 0.8689 (m) REVERT: C 111 LYS cc_start: 0.8901 (ttpp) cc_final: 0.8615 (ttpp) REVERT: C 118 LEU cc_start: 0.8789 (mt) cc_final: 0.8588 (mt) REVERT: C 120 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8207 (tm-30) REVERT: C 122 PHE cc_start: 0.8728 (t80) cc_final: 0.8484 (t80) REVERT: C 123 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8417 (mmtm) REVERT: C 134 MET cc_start: 0.7767 (tpp) cc_final: 0.7293 (tpt) REVERT: C 144 GLU cc_start: 0.7636 (pt0) cc_final: 0.7361 (pt0) REVERT: C 154 PHE cc_start: 0.7689 (t80) cc_final: 0.6812 (t80) REVERT: C 158 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8009 (mtpt) REVERT: C 159 LYS cc_start: 0.8534 (mmmt) cc_final: 0.7987 (mmmt) REVERT: C 174 GLN cc_start: 0.8039 (mt0) cc_final: 0.7732 (mt0) REVERT: C 176 ASP cc_start: 0.8031 (m-30) cc_final: 0.7685 (m-30) REVERT: C 198 VAL cc_start: 0.8602 (t) cc_final: 0.8319 (p) REVERT: C 218 GLU cc_start: 0.8014 (pp20) cc_final: 0.7614 (pp20) REVERT: C 226 GLN cc_start: 0.8418 (tt0) cc_final: 0.8182 (tt0) REVERT: C 228 ILE cc_start: 0.8983 (mt) cc_final: 0.8672 (tp) REVERT: C 243 ARG cc_start: 0.8240 (ttp-170) cc_final: 0.7691 (ptm160) REVERT: C 245 VAL cc_start: 0.8516 (t) cc_final: 0.8116 (p) REVERT: C 281 GLN cc_start: 0.8066 (mm-40) cc_final: 0.7813 (mm-40) REVERT: C 285 GLU cc_start: 0.7851 (pm20) cc_final: 0.7475 (pm20) REVERT: C 335 MET cc_start: 0.8695 (mpp) cc_final: 0.8431 (mmm) REVERT: C 346 THR cc_start: 0.8537 (m) cc_final: 0.8111 (p) REVERT: C 352 SER cc_start: 0.8628 (t) cc_final: 0.8403 (t) REVERT: C 365 GLU cc_start: 0.7570 (tm-30) cc_final: 0.6767 (tm-30) REVERT: C 397 SER cc_start: 0.8664 (m) cc_final: 0.7799 (p) REVERT: B 105 LYS cc_start: 0.7952 (mmmt) cc_final: 0.7423 (mmmt) REVERT: B 113 MET cc_start: 0.7814 (ttm) cc_final: 0.7577 (ttm) REVERT: B 124 GLU cc_start: 0.8447 (mt-10) cc_final: 0.7912 (mt-10) REVERT: B 125 LEU cc_start: 0.8953 (tp) cc_final: 0.8721 (tt) REVERT: B 128 HIS cc_start: 0.8672 (t70) cc_final: 0.8250 (t-90) REVERT: B 132 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8035 (mt-10) REVERT: B 154 PHE cc_start: 0.7864 (t80) cc_final: 0.7134 (t80) REVERT: B 158 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8530 (mtpt) REVERT: B 181 LEU cc_start: 0.8879 (mt) cc_final: 0.8657 (mp) REVERT: B 218 GLU cc_start: 0.8007 (pp20) cc_final: 0.7558 (pp20) REVERT: B 228 ILE cc_start: 0.9152 (mm) cc_final: 0.8933 (tp) REVERT: B 278 MET cc_start: 0.7742 (mmm) cc_final: 0.7539 (mmm) REVERT: B 285 GLU cc_start: 0.8006 (pm20) cc_final: 0.7644 (pm20) REVERT: B 335 MET cc_start: 0.8575 (mpp) cc_final: 0.8303 (mmm) REVERT: B 356 ARG cc_start: 0.8479 (tpp-160) cc_final: 0.8252 (tpp80) REVERT: B 365 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7176 (tm-30) REVERT: B 397 SER cc_start: 0.8604 (m) cc_final: 0.8017 (p) REVERT: B 412 ASP cc_start: 0.7719 (p0) cc_final: 0.7476 (p0) outliers start: 36 outliers final: 28 residues processed: 380 average time/residue: 0.2343 time to fit residues: 117.6093 Evaluate side-chains 400 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 371 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 383 ASP Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 130 MET Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 386 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 103 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 63 optimal weight: 0.0170 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.125061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109828 restraints weight = 14379.235| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.70 r_work: 0.3312 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9503 Z= 0.210 Angle : 0.592 13.306 12907 Z= 0.304 Chirality : 0.048 0.186 1500 Planarity : 0.005 0.038 1640 Dihedral : 4.589 21.414 1270 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 3.14 % Allowed : 18.55 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.26), residues: 1176 helix: 0.75 (0.34), residues: 242 sheet: 0.37 (0.27), residues: 389 loop : -1.30 (0.29), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 427 HIS 0.008 0.001 HIS B 128 PHE 0.042 0.002 PHE C 220 TYR 0.010 0.001 TYR C 280 ARG 0.005 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 382 time to evaluate : 0.950 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: A 105 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7746 (mmmt) REVERT: A 107 VAL cc_start: 0.8324 (t) cc_final: 0.7984 (m) REVERT: A 109 VAL cc_start: 0.9068 (t) cc_final: 0.8740 (m) REVERT: A 111 LYS cc_start: 0.8965 (ttpp) cc_final: 0.8712 (ttpp) REVERT: A 120 GLN cc_start: 0.8733 (tt0) cc_final: 0.7985 (tm-30) REVERT: A 122 PHE cc_start: 0.8740 (t80) cc_final: 0.8445 (t80) REVERT: A 123 LYS cc_start: 0.8677 (mtmm) cc_final: 0.8446 (mtmm) REVERT: A 124 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8151 (mt-10) REVERT: A 128 HIS cc_start: 0.8767 (t70) cc_final: 0.8521 (t70) REVERT: A 131 GLU cc_start: 0.8046 (tt0) cc_final: 0.7724 (tt0) REVERT: A 134 MET cc_start: 0.7721 (mmm) cc_final: 0.6906 (tpt) REVERT: A 159 LYS cc_start: 0.8589 (mptt) cc_final: 0.8224 (mptt) REVERT: A 202 MET cc_start: 0.8708 (ptt) cc_final: 0.8447 (ptm) REVERT: A 213 THR cc_start: 0.7833 (p) cc_final: 0.7577 (p) REVERT: A 218 GLU cc_start: 0.7994 (pp20) cc_final: 0.7539 (pp20) REVERT: A 219 ASN cc_start: 0.8346 (t0) cc_final: 0.7993 (t0) REVERT: A 228 ILE cc_start: 0.8916 (mt) cc_final: 0.8660 (tp) REVERT: A 245 VAL cc_start: 0.8522 (t) cc_final: 0.8193 (p) REVERT: A 356 ARG cc_start: 0.8460 (ttm170) cc_final: 0.8209 (tpp80) REVERT: A 365 GLU cc_start: 0.7512 (tm-30) cc_final: 0.6736 (tm-30) REVERT: A 391 ARG cc_start: 0.8289 (ptp-110) cc_final: 0.7752 (ptp-110) REVERT: A 397 SER cc_start: 0.8600 (m) cc_final: 0.7947 (p) REVERT: A 423 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: D 103 SER cc_start: 0.8832 (t) cc_final: 0.8587 (t) REVERT: D 105 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7534 (mmmt) REVERT: D 109 VAL cc_start: 0.9031 (t) cc_final: 0.8752 (m) REVERT: D 122 PHE cc_start: 0.8796 (t80) cc_final: 0.8538 (t80) REVERT: D 123 LYS cc_start: 0.8643 (mmtm) cc_final: 0.7968 (mmmm) REVERT: D 124 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8041 (mt-10) REVERT: D 130 MET cc_start: 0.7944 (tpp) cc_final: 0.7636 (tpp) REVERT: D 134 MET cc_start: 0.7750 (ttt) cc_final: 0.7345 (ttt) REVERT: D 154 PHE cc_start: 0.7729 (t80) cc_final: 0.6895 (t80) REVERT: D 158 LYS cc_start: 0.8862 (mtpt) cc_final: 0.8309 (mtpt) REVERT: D 193 LEU cc_start: 0.8283 (mm) cc_final: 0.8024 (mm) REVERT: D 211 PHE cc_start: 0.8417 (m-80) cc_final: 0.8173 (m-80) REVERT: D 218 GLU cc_start: 0.7760 (pp20) cc_final: 0.7273 (pp20) REVERT: D 221 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8211 (mm-40) REVERT: D 245 VAL cc_start: 0.8380 (t) cc_final: 0.8032 (p) REVERT: D 278 MET cc_start: 0.7747 (mmm) cc_final: 0.7409 (mmm) REVERT: D 285 GLU cc_start: 0.7973 (pm20) cc_final: 0.7644 (pm20) REVERT: D 335 MET cc_start: 0.8483 (mmm) cc_final: 0.7626 (mmm) REVERT: D 397 SER cc_start: 0.8626 (m) cc_final: 0.7989 (p) REVERT: D 425 LEU cc_start: 0.8534 (mt) cc_final: 0.8288 (mp) REVERT: C 109 VAL cc_start: 0.9004 (t) cc_final: 0.8702 (m) REVERT: C 111 LYS cc_start: 0.8889 (ttpp) cc_final: 0.8609 (ttpp) REVERT: C 118 LEU cc_start: 0.8766 (mt) cc_final: 0.8555 (mt) REVERT: C 120 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8223 (tm-30) REVERT: C 122 PHE cc_start: 0.8694 (t80) cc_final: 0.8441 (t80) REVERT: C 123 LYS cc_start: 0.8711 (mmtm) cc_final: 0.8388 (mmtm) REVERT: C 144 GLU cc_start: 0.7547 (pt0) cc_final: 0.7266 (pt0) REVERT: C 154 PHE cc_start: 0.7640 (t80) cc_final: 0.6762 (t80) REVERT: C 158 LYS cc_start: 0.9021 (mtpt) cc_final: 0.7942 (mtpt) REVERT: C 159 LYS cc_start: 0.8493 (mmmt) cc_final: 0.7918 (mmmt) REVERT: C 174 GLN cc_start: 0.8072 (mt0) cc_final: 0.7796 (mt0) REVERT: C 176 ASP cc_start: 0.8000 (m-30) cc_final: 0.7688 (m-30) REVERT: C 218 GLU cc_start: 0.7944 (pp20) cc_final: 0.7499 (pp20) REVERT: C 226 GLN cc_start: 0.8418 (tt0) cc_final: 0.8182 (tt0) REVERT: C 228 ILE cc_start: 0.8947 (mt) cc_final: 0.8630 (tp) REVERT: C 243 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.7683 (ptm160) REVERT: C 281 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7788 (mm-40) REVERT: C 285 GLU cc_start: 0.7884 (pm20) cc_final: 0.7490 (pm20) REVERT: C 346 THR cc_start: 0.8512 (m) cc_final: 0.8030 (p) REVERT: C 352 SER cc_start: 0.8607 (t) cc_final: 0.8372 (t) REVERT: C 365 GLU cc_start: 0.7548 (tm-30) cc_final: 0.6954 (tm-30) REVERT: C 397 SER cc_start: 0.8644 (m) cc_final: 0.7795 (p) REVERT: B 105 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7358 (mmmt) REVERT: B 113 MET cc_start: 0.7763 (ttm) cc_final: 0.7523 (ttm) REVERT: B 120 GLN cc_start: 0.8639 (tt0) cc_final: 0.8013 (tt0) REVERT: B 124 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7874 (mt-10) REVERT: B 125 LEU cc_start: 0.8918 (tp) cc_final: 0.8680 (tt) REVERT: B 132 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7928 (mt-10) REVERT: B 154 PHE cc_start: 0.7792 (t80) cc_final: 0.7067 (t80) REVERT: B 158 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8486 (mtpt) REVERT: B 218 GLU cc_start: 0.7921 (pp20) cc_final: 0.7419 (pp20) REVERT: B 228 ILE cc_start: 0.9129 (mm) cc_final: 0.8897 (tp) REVERT: B 239 ARG cc_start: 0.8614 (mtm180) cc_final: 0.8300 (mtp180) REVERT: B 285 GLU cc_start: 0.7996 (pm20) cc_final: 0.7644 (pm20) REVERT: B 335 MET cc_start: 0.8565 (mpp) cc_final: 0.8283 (mmm) REVERT: B 356 ARG cc_start: 0.8441 (tpp-160) cc_final: 0.8208 (tpp80) REVERT: B 397 SER cc_start: 0.8587 (m) cc_final: 0.8032 (p) REVERT: B 412 ASP cc_start: 0.7646 (p0) cc_final: 0.7422 (p0) REVERT: B 416 ASP cc_start: 0.8171 (t0) cc_final: 0.7890 (t0) outliers start: 33 outliers final: 24 residues processed: 391 average time/residue: 0.2467 time to fit residues: 125.9626 Evaluate side-chains 403 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 378 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 386 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 102 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.125613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110273 restraints weight = 14439.585| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.71 r_work: 0.3312 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9503 Z= 0.221 Angle : 0.591 9.716 12907 Z= 0.305 Chirality : 0.048 0.196 1500 Planarity : 0.005 0.038 1640 Dihedral : 4.543 20.775 1270 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 3.04 % Allowed : 19.89 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1176 helix: 0.77 (0.34), residues: 246 sheet: 0.40 (0.27), residues: 383 loop : -1.18 (0.29), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 100 HIS 0.005 0.001 HIS B 128 PHE 0.041 0.002 PHE C 220 TYR 0.007 0.001 TYR D 280 ARG 0.005 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 377 time to evaluate : 1.043 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: A 105 LYS cc_start: 0.8230 (mmmt) cc_final: 0.7821 (mmmt) REVERT: A 107 VAL cc_start: 0.8314 (t) cc_final: 0.7969 (m) REVERT: A 109 VAL cc_start: 0.9068 (t) cc_final: 0.8749 (m) REVERT: A 111 LYS cc_start: 0.8942 (ttpp) cc_final: 0.8679 (ttpp) REVERT: A 120 GLN cc_start: 0.8731 (tt0) cc_final: 0.8388 (tm-30) REVERT: A 122 PHE cc_start: 0.8754 (t80) cc_final: 0.8461 (t80) REVERT: A 123 LYS cc_start: 0.8652 (mtmm) cc_final: 0.8416 (mtmm) REVERT: A 124 GLU cc_start: 0.8680 (mt-10) cc_final: 0.8369 (mt-10) REVERT: A 128 HIS cc_start: 0.8624 (t70) cc_final: 0.8349 (t-170) REVERT: A 131 GLU cc_start: 0.8029 (tt0) cc_final: 0.7721 (tt0) REVERT: A 134 MET cc_start: 0.7690 (mmm) cc_final: 0.7478 (tpt) REVERT: A 159 LYS cc_start: 0.8584 (mptt) cc_final: 0.8212 (mptt) REVERT: A 202 MET cc_start: 0.8691 (ptt) cc_final: 0.8426 (ptm) REVERT: A 213 THR cc_start: 0.7859 (p) cc_final: 0.7618 (p) REVERT: A 218 GLU cc_start: 0.7951 (pp20) cc_final: 0.7452 (pp20) REVERT: A 219 ASN cc_start: 0.8283 (t0) cc_final: 0.7912 (t0) REVERT: A 228 ILE cc_start: 0.8906 (mt) cc_final: 0.8651 (tp) REVERT: A 245 VAL cc_start: 0.8493 (t) cc_final: 0.8180 (p) REVERT: A 346 THR cc_start: 0.8749 (m) cc_final: 0.8226 (p) REVERT: A 356 ARG cc_start: 0.8454 (ttm170) cc_final: 0.8189 (tpp80) REVERT: A 365 GLU cc_start: 0.7526 (tm-30) cc_final: 0.6734 (tm-30) REVERT: A 391 ARG cc_start: 0.8306 (ptp-110) cc_final: 0.7735 (ptp-110) REVERT: A 397 SER cc_start: 0.8596 (m) cc_final: 0.7940 (p) REVERT: A 423 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8316 (tt0) REVERT: D 103 SER cc_start: 0.8858 (t) cc_final: 0.8622 (t) REVERT: D 105 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7659 (mmmt) REVERT: D 109 VAL cc_start: 0.9025 (t) cc_final: 0.8753 (m) REVERT: D 122 PHE cc_start: 0.8799 (t80) cc_final: 0.8570 (t80) REVERT: D 123 LYS cc_start: 0.8628 (mmtm) cc_final: 0.8004 (mmmm) REVERT: D 124 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8023 (mt-10) REVERT: D 130 MET cc_start: 0.7928 (tpp) cc_final: 0.7626 (tpp) REVERT: D 134 MET cc_start: 0.7758 (ttt) cc_final: 0.7310 (ttt) REVERT: D 154 PHE cc_start: 0.7688 (t80) cc_final: 0.6959 (t80) REVERT: D 158 LYS cc_start: 0.8873 (mtpt) cc_final: 0.8313 (mtpt) REVERT: D 211 PHE cc_start: 0.8465 (m-80) cc_final: 0.8195 (m-80) REVERT: D 218 GLU cc_start: 0.7785 (pp20) cc_final: 0.7281 (pp20) REVERT: D 221 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8288 (mm-40) REVERT: D 245 VAL cc_start: 0.8379 (t) cc_final: 0.8030 (p) REVERT: D 278 MET cc_start: 0.7733 (mmm) cc_final: 0.7397 (mmm) REVERT: D 285 GLU cc_start: 0.7966 (pm20) cc_final: 0.7645 (pm20) REVERT: D 397 SER cc_start: 0.8640 (m) cc_final: 0.7997 (p) REVERT: D 425 LEU cc_start: 0.8560 (mt) cc_final: 0.8311 (mp) REVERT: C 109 VAL cc_start: 0.9007 (t) cc_final: 0.8694 (m) REVERT: C 111 LYS cc_start: 0.8897 (ttpp) cc_final: 0.8593 (ttpp) REVERT: C 120 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8196 (tm-30) REVERT: C 122 PHE cc_start: 0.8706 (t80) cc_final: 0.8442 (t80) REVERT: C 123 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8308 (mmtm) REVERT: C 134 MET cc_start: 0.7728 (tpt) cc_final: 0.7237 (tpt) REVERT: C 154 PHE cc_start: 0.7622 (t80) cc_final: 0.6753 (t80) REVERT: C 158 LYS cc_start: 0.9023 (mtpt) cc_final: 0.7945 (mtpt) REVERT: C 159 LYS cc_start: 0.8510 (mmmt) cc_final: 0.7907 (mmmt) REVERT: C 174 GLN cc_start: 0.8081 (mt0) cc_final: 0.7819 (mt0) REVERT: C 176 ASP cc_start: 0.8000 (m-30) cc_final: 0.7673 (m-30) REVERT: C 218 GLU cc_start: 0.7925 (pp20) cc_final: 0.7459 (pp20) REVERT: C 226 GLN cc_start: 0.8404 (tt0) cc_final: 0.8166 (tt0) REVERT: C 243 ARG cc_start: 0.8280 (ttp-170) cc_final: 0.7696 (ptm160) REVERT: C 245 VAL cc_start: 0.8549 (t) cc_final: 0.8132 (p) REVERT: C 281 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7782 (mm-40) REVERT: C 285 GLU cc_start: 0.7882 (pm20) cc_final: 0.7488 (pm20) REVERT: C 346 THR cc_start: 0.8530 (m) cc_final: 0.8054 (p) REVERT: C 352 SER cc_start: 0.8611 (t) cc_final: 0.8370 (t) REVERT: C 365 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6939 (tm-30) REVERT: C 397 SER cc_start: 0.8649 (m) cc_final: 0.7789 (p) REVERT: B 105 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7402 (mmmt) REVERT: B 113 MET cc_start: 0.7755 (ttm) cc_final: 0.7527 (ttm) REVERT: B 120 GLN cc_start: 0.8637 (tt0) cc_final: 0.8006 (tt0) REVERT: B 124 GLU cc_start: 0.8470 (mt-10) cc_final: 0.7914 (mt-10) REVERT: B 125 LEU cc_start: 0.8915 (tp) cc_final: 0.8691 (tt) REVERT: B 154 PHE cc_start: 0.7767 (t80) cc_final: 0.7117 (t80) REVERT: B 158 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8471 (mtpt) REVERT: B 195 GLN cc_start: 0.7901 (mm-40) cc_final: 0.7487 (mm-40) REVERT: B 204 PHE cc_start: 0.8599 (m-80) cc_final: 0.8231 (m-80) REVERT: B 228 ILE cc_start: 0.9106 (mm) cc_final: 0.8863 (tp) REVERT: B 239 ARG cc_start: 0.8614 (mtm180) cc_final: 0.8303 (mtp180) REVERT: B 285 GLU cc_start: 0.8007 (pm20) cc_final: 0.7662 (pm20) REVERT: B 311 VAL cc_start: 0.8593 (p) cc_final: 0.8261 (m) REVERT: B 335 MET cc_start: 0.8569 (mpp) cc_final: 0.8301 (mmm) REVERT: B 356 ARG cc_start: 0.8436 (tpp-160) cc_final: 0.8212 (tpp80) REVERT: B 397 SER cc_start: 0.8583 (m) cc_final: 0.8032 (p) REVERT: B 412 ASP cc_start: 0.7613 (p0) cc_final: 0.7383 (p0) REVERT: B 416 ASP cc_start: 0.8143 (t0) cc_final: 0.7864 (t0) outliers start: 32 outliers final: 23 residues processed: 386 average time/residue: 0.2579 time to fit residues: 130.2042 Evaluate side-chains 398 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 374 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 chunk 74 optimal weight: 0.4980 chunk 80 optimal weight: 0.0670 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 112 optimal weight: 0.0050 chunk 86 optimal weight: 0.7980 overall best weight: 0.2910 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 GLN A 392 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.112883 restraints weight = 14934.364| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.86 r_work: 0.3355 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9503 Z= 0.161 Angle : 0.585 9.636 12907 Z= 0.299 Chirality : 0.048 0.225 1500 Planarity : 0.005 0.043 1640 Dihedral : 4.435 19.967 1270 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 3.04 % Allowed : 20.84 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1176 helix: 0.68 (0.34), residues: 247 sheet: 0.55 (0.29), residues: 344 loop : -0.97 (0.28), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 100 HIS 0.004 0.001 HIS B 128 PHE 0.040 0.002 PHE C 220 TYR 0.009 0.001 TYR D 189 ARG 0.005 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 387 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7829 (mmmt) REVERT: A 107 VAL cc_start: 0.8276 (t) cc_final: 0.7901 (m) REVERT: A 109 VAL cc_start: 0.9074 (t) cc_final: 0.8755 (m) REVERT: A 111 LYS cc_start: 0.8951 (ttpp) cc_final: 0.8688 (ttpp) REVERT: A 120 GLN cc_start: 0.8664 (tt0) cc_final: 0.8318 (tm-30) REVERT: A 122 PHE cc_start: 0.8681 (t80) cc_final: 0.8360 (t80) REVERT: A 123 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8216 (mtmm) REVERT: A 124 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8345 (mt-10) REVERT: A 131 GLU cc_start: 0.7997 (tt0) cc_final: 0.7682 (tt0) REVERT: A 159 LYS cc_start: 0.8583 (mptt) cc_final: 0.8183 (mptt) REVERT: A 202 MET cc_start: 0.8702 (ptt) cc_final: 0.8440 (ptm) REVERT: A 204 PHE cc_start: 0.8665 (m-80) cc_final: 0.8268 (m-80) REVERT: A 213 THR cc_start: 0.7746 (p) cc_final: 0.7490 (p) REVERT: A 228 ILE cc_start: 0.8845 (mt) cc_final: 0.8585 (tp) REVERT: A 245 VAL cc_start: 0.8488 (t) cc_final: 0.8140 (p) REVERT: A 311 VAL cc_start: 0.8382 (p) cc_final: 0.8029 (m) REVERT: A 346 THR cc_start: 0.8697 (m) cc_final: 0.8127 (p) REVERT: A 356 ARG cc_start: 0.8455 (ttm170) cc_final: 0.8186 (tpp80) REVERT: A 365 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6721 (tm-30) REVERT: A 391 ARG cc_start: 0.8300 (ptp-110) cc_final: 0.7726 (ptp-110) REVERT: A 397 SER cc_start: 0.8575 (m) cc_final: 0.7935 (p) REVERT: D 103 SER cc_start: 0.8835 (t) cc_final: 0.8572 (t) REVERT: D 105 LYS cc_start: 0.8266 (mmmt) cc_final: 0.7658 (mmmt) REVERT: D 109 VAL cc_start: 0.9013 (t) cc_final: 0.8747 (m) REVERT: D 122 PHE cc_start: 0.8735 (t80) cc_final: 0.8495 (t80) REVERT: D 123 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8023 (mmmm) REVERT: D 124 GLU cc_start: 0.8558 (mt-10) cc_final: 0.7998 (mt-10) REVERT: D 130 MET cc_start: 0.8014 (tpp) cc_final: 0.7682 (tpp) REVERT: D 134 MET cc_start: 0.7559 (ttt) cc_final: 0.7088 (ttt) REVERT: D 154 PHE cc_start: 0.7655 (t80) cc_final: 0.6884 (t80) REVERT: D 158 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8184 (mtpt) REVERT: D 193 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7626 (mm) REVERT: D 211 PHE cc_start: 0.8388 (m-80) cc_final: 0.8090 (m-80) REVERT: D 218 GLU cc_start: 0.7730 (pp20) cc_final: 0.7200 (pp20) REVERT: D 221 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8227 (mm-40) REVERT: D 245 VAL cc_start: 0.8389 (t) cc_final: 0.8009 (p) REVERT: D 278 MET cc_start: 0.7733 (mmm) cc_final: 0.7298 (mmm) REVERT: D 285 GLU cc_start: 0.8024 (pm20) cc_final: 0.7673 (pm20) REVERT: D 289 ASP cc_start: 0.8008 (p0) cc_final: 0.7763 (p0) REVERT: D 335 MET cc_start: 0.8439 (mmm) cc_final: 0.7815 (mmm) REVERT: D 385 ARG cc_start: 0.7546 (ttm170) cc_final: 0.7171 (ttm170) REVERT: D 397 SER cc_start: 0.8613 (m) cc_final: 0.7987 (p) REVERT: C 109 VAL cc_start: 0.9015 (t) cc_final: 0.8699 (m) REVERT: C 111 LYS cc_start: 0.8891 (ttpp) cc_final: 0.8560 (ttpp) REVERT: C 120 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8236 (tm-30) REVERT: C 122 PHE cc_start: 0.8612 (t80) cc_final: 0.8378 (t80) REVERT: C 123 LYS cc_start: 0.8654 (mmtm) cc_final: 0.8350 (mmtm) REVERT: C 134 MET cc_start: 0.7675 (tpt) cc_final: 0.7114 (tpt) REVERT: C 154 PHE cc_start: 0.7643 (t80) cc_final: 0.6739 (t80) REVERT: C 158 LYS cc_start: 0.9020 (mtpt) cc_final: 0.7904 (mtpt) REVERT: C 159 LYS cc_start: 0.8486 (mmmt) cc_final: 0.7841 (mmmt) REVERT: C 174 GLN cc_start: 0.8134 (mt0) cc_final: 0.7886 (mt0) REVERT: C 176 ASP cc_start: 0.7935 (m-30) cc_final: 0.7638 (m-30) REVERT: C 204 PHE cc_start: 0.8622 (m-80) cc_final: 0.8313 (m-80) REVERT: C 218 GLU cc_start: 0.7793 (pp20) cc_final: 0.7282 (pp20) REVERT: C 228 ILE cc_start: 0.8922 (mt) cc_final: 0.8603 (tp) REVERT: C 243 ARG cc_start: 0.8300 (ttp-170) cc_final: 0.7743 (ptm160) REVERT: C 245 VAL cc_start: 0.8510 (t) cc_final: 0.8089 (p) REVERT: C 281 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7758 (mm-40) REVERT: C 285 GLU cc_start: 0.7944 (pm20) cc_final: 0.7530 (pm20) REVERT: C 335 MET cc_start: 0.8376 (mmm) cc_final: 0.7864 (mtp) REVERT: C 352 SER cc_start: 0.8610 (t) cc_final: 0.8357 (t) REVERT: C 356 ARG cc_start: 0.8597 (ttm-80) cc_final: 0.8382 (ttm170) REVERT: C 365 GLU cc_start: 0.7442 (tm-30) cc_final: 0.6837 (tm-30) REVERT: C 397 SER cc_start: 0.8642 (m) cc_final: 0.7792 (p) REVERT: B 105 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7341 (mmmt) REVERT: B 113 MET cc_start: 0.7848 (ttm) cc_final: 0.7622 (ttm) REVERT: B 134 MET cc_start: 0.7411 (tpp) cc_final: 0.6968 (tpt) REVERT: B 154 PHE cc_start: 0.7739 (t80) cc_final: 0.7055 (t80) REVERT: B 158 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8429 (mtpt) REVERT: B 195 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7399 (mm-40) REVERT: B 204 PHE cc_start: 0.8412 (m-80) cc_final: 0.7983 (m-80) REVERT: B 221 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8212 (mm-40) REVERT: B 228 ILE cc_start: 0.9064 (mm) cc_final: 0.8791 (tp) REVERT: B 285 GLU cc_start: 0.8055 (pm20) cc_final: 0.7684 (pm20) REVERT: B 311 VAL cc_start: 0.8510 (p) cc_final: 0.8176 (m) REVERT: B 335 MET cc_start: 0.8559 (mpp) cc_final: 0.8265 (mmm) REVERT: B 356 ARG cc_start: 0.8436 (tpp-160) cc_final: 0.8203 (tpp80) REVERT: B 397 SER cc_start: 0.8583 (m) cc_final: 0.8026 (p) REVERT: B 412 ASP cc_start: 0.7549 (p0) cc_final: 0.7297 (p0) REVERT: B 416 ASP cc_start: 0.8231 (t0) cc_final: 0.7934 (t0) outliers start: 32 outliers final: 22 residues processed: 396 average time/residue: 0.2709 time to fit residues: 138.3783 Evaluate side-chains 403 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 380 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 18 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.126759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.111413 restraints weight = 14776.694| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.80 r_work: 0.3335 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9503 Z= 0.216 Angle : 0.606 10.674 12907 Z= 0.310 Chirality : 0.048 0.220 1500 Planarity : 0.005 0.038 1640 Dihedral : 4.446 19.726 1270 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 3.04 % Allowed : 21.79 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.26), residues: 1176 helix: 0.77 (0.34), residues: 246 sheet: 0.60 (0.28), residues: 352 loop : -1.15 (0.28), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 100 HIS 0.008 0.001 HIS A 128 PHE 0.044 0.002 PHE C 220 TYR 0.007 0.001 TYR D 189 ARG 0.007 0.000 ARG C 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 387 time to evaluate : 1.046 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: A 105 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7801 (mmmt) REVERT: A 107 VAL cc_start: 0.8325 (t) cc_final: 0.7885 (m) REVERT: A 109 VAL cc_start: 0.9087 (t) cc_final: 0.8757 (m) REVERT: A 111 LYS cc_start: 0.8930 (ttpp) cc_final: 0.8675 (ttpp) REVERT: A 120 GLN cc_start: 0.8705 (tt0) cc_final: 0.8381 (tm-30) REVERT: A 122 PHE cc_start: 0.8757 (t80) cc_final: 0.8476 (t80) REVERT: A 124 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8403 (mt-10) REVERT: A 131 GLU cc_start: 0.8043 (tt0) cc_final: 0.7716 (tt0) REVERT: A 132 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7935 (mt-10) REVERT: A 134 MET cc_start: 0.7577 (tpt) cc_final: 0.7096 (tpt) REVERT: A 159 LYS cc_start: 0.8545 (mptt) cc_final: 0.8120 (mptt) REVERT: A 202 MET cc_start: 0.8719 (ptt) cc_final: 0.8467 (ptm) REVERT: A 204 PHE cc_start: 0.8692 (m-80) cc_final: 0.8270 (m-80) REVERT: A 213 THR cc_start: 0.7817 (p) cc_final: 0.7562 (p) REVERT: A 228 ILE cc_start: 0.8850 (mt) cc_final: 0.8608 (tp) REVERT: A 245 VAL cc_start: 0.8480 (t) cc_final: 0.8060 (m) REVERT: A 311 VAL cc_start: 0.8413 (p) cc_final: 0.8056 (m) REVERT: A 346 THR cc_start: 0.8681 (m) cc_final: 0.8149 (p) REVERT: A 356 ARG cc_start: 0.8466 (ttm170) cc_final: 0.8182 (tpp80) REVERT: A 365 GLU cc_start: 0.7501 (tm-30) cc_final: 0.6698 (tm-30) REVERT: A 391 ARG cc_start: 0.8312 (ptp-110) cc_final: 0.7718 (ptp-110) REVERT: A 397 SER cc_start: 0.8597 (m) cc_final: 0.7942 (p) REVERT: D 103 SER cc_start: 0.8845 (t) cc_final: 0.8611 (t) REVERT: D 105 LYS cc_start: 0.8260 (mmmt) cc_final: 0.7670 (mmmt) REVERT: D 109 VAL cc_start: 0.9018 (t) cc_final: 0.8753 (m) REVERT: D 122 PHE cc_start: 0.8757 (t80) cc_final: 0.8523 (t80) REVERT: D 123 LYS cc_start: 0.8608 (mmtm) cc_final: 0.8011 (mmmm) REVERT: D 124 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8049 (mt-10) REVERT: D 130 MET cc_start: 0.8099 (tpp) cc_final: 0.7763 (tpp) REVERT: D 134 MET cc_start: 0.7614 (ttt) cc_final: 0.7196 (ttt) REVERT: D 154 PHE cc_start: 0.7665 (t80) cc_final: 0.6894 (t80) REVERT: D 158 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8239 (mtpt) REVERT: D 193 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7826 (mm) REVERT: D 211 PHE cc_start: 0.8384 (m-80) cc_final: 0.8129 (m-80) REVERT: D 218 GLU cc_start: 0.7746 (pp20) cc_final: 0.7230 (pp20) REVERT: D 221 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8285 (mm-40) REVERT: D 245 VAL cc_start: 0.8390 (t) cc_final: 0.8014 (p) REVERT: D 285 GLU cc_start: 0.8005 (pm20) cc_final: 0.7682 (pm20) REVERT: D 309 THR cc_start: 0.8405 (t) cc_final: 0.8062 (m) REVERT: D 335 MET cc_start: 0.8426 (mmm) cc_final: 0.7768 (mmm) REVERT: D 385 ARG cc_start: 0.7595 (ttm170) cc_final: 0.7191 (ttm170) REVERT: D 391 ARG cc_start: 0.8346 (ptp90) cc_final: 0.7903 (ptp-110) REVERT: D 397 SER cc_start: 0.8624 (m) cc_final: 0.7971 (p) REVERT: C 109 VAL cc_start: 0.9006 (t) cc_final: 0.8682 (m) REVERT: C 111 LYS cc_start: 0.8888 (ttpp) cc_final: 0.8584 (ttpp) REVERT: C 120 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8211 (tm-30) REVERT: C 122 PHE cc_start: 0.8665 (t80) cc_final: 0.8405 (t80) REVERT: C 123 LYS cc_start: 0.8652 (mmtm) cc_final: 0.8339 (mmtm) REVERT: C 154 PHE cc_start: 0.7668 (t80) cc_final: 0.6756 (t80) REVERT: C 158 LYS cc_start: 0.9022 (mtpt) cc_final: 0.7910 (mtpt) REVERT: C 159 LYS cc_start: 0.8478 (mmmt) cc_final: 0.7841 (mmmt) REVERT: C 174 GLN cc_start: 0.8123 (mt0) cc_final: 0.7754 (mp10) REVERT: C 176 ASP cc_start: 0.7974 (m-30) cc_final: 0.7649 (m-30) REVERT: C 204 PHE cc_start: 0.8638 (m-80) cc_final: 0.8302 (m-80) REVERT: C 218 GLU cc_start: 0.7807 (pp20) cc_final: 0.7295 (pp20) REVERT: C 228 ILE cc_start: 0.8918 (mt) cc_final: 0.8600 (tp) REVERT: C 243 ARG cc_start: 0.8322 (ttp-170) cc_final: 0.7757 (ptm160) REVERT: C 281 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7784 (mm-40) REVERT: C 285 GLU cc_start: 0.7981 (pm20) cc_final: 0.7566 (pm20) REVERT: C 352 SER cc_start: 0.8623 (t) cc_final: 0.8372 (t) REVERT: C 356 ARG cc_start: 0.8594 (ttm-80) cc_final: 0.8373 (ttm170) REVERT: C 365 GLU cc_start: 0.7438 (tm-30) cc_final: 0.6840 (tm-30) REVERT: C 397 SER cc_start: 0.8649 (m) cc_final: 0.7784 (p) REVERT: B 105 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7294 (mmmt) REVERT: B 113 MET cc_start: 0.7833 (ttm) cc_final: 0.7544 (ttm) REVERT: B 120 GLN cc_start: 0.8540 (tt0) cc_final: 0.8282 (tm-30) REVERT: B 154 PHE cc_start: 0.7733 (t80) cc_final: 0.7073 (t80) REVERT: B 158 LYS cc_start: 0.8963 (mtpt) cc_final: 0.8451 (mtpt) REVERT: B 195 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7410 (mm-40) REVERT: B 204 PHE cc_start: 0.8540 (m-80) cc_final: 0.8217 (m-80) REVERT: B 228 ILE cc_start: 0.9060 (mm) cc_final: 0.8816 (tp) REVERT: B 239 ARG cc_start: 0.8633 (mtm180) cc_final: 0.8315 (mtp180) REVERT: B 285 GLU cc_start: 0.8073 (pm20) cc_final: 0.7706 (pm20) REVERT: B 335 MET cc_start: 0.8534 (mpp) cc_final: 0.8269 (mmm) REVERT: B 346 THR cc_start: 0.8536 (m) cc_final: 0.8001 (p) REVERT: B 356 ARG cc_start: 0.8443 (tpp-160) cc_final: 0.8199 (tpp80) REVERT: B 367 LYS cc_start: 0.8344 (ttmm) cc_final: 0.8050 (ttmm) REVERT: B 397 SER cc_start: 0.8591 (m) cc_final: 0.7969 (p) REVERT: B 412 ASP cc_start: 0.7540 (p0) cc_final: 0.7290 (p0) REVERT: B 416 ASP cc_start: 0.8208 (t0) cc_final: 0.7918 (t0) outliers start: 32 outliers final: 25 residues processed: 397 average time/residue: 0.2697 time to fit residues: 138.1078 Evaluate side-chains 408 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 382 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 228 ILE Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 391 ARG Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 93 optimal weight: 0.7980 chunk 116 optimal weight: 0.0770 chunk 12 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.126646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.111270 restraints weight = 15012.283| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.85 r_work: 0.3335 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9503 Z= 0.212 Angle : 0.617 10.246 12907 Z= 0.314 Chirality : 0.048 0.192 1500 Planarity : 0.005 0.040 1640 Dihedral : 4.485 19.544 1270 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 2.85 % Allowed : 22.93 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.26), residues: 1176 helix: 0.75 (0.35), residues: 246 sheet: 0.47 (0.27), residues: 372 loop : -1.17 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 100 HIS 0.008 0.001 HIS A 128 PHE 0.042 0.002 PHE C 220 TYR 0.007 0.001 TYR C 280 ARG 0.009 0.000 ARG A 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 381 time to evaluate : 0.981 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: A 105 LYS cc_start: 0.8221 (mmmt) cc_final: 0.7775 (mmmt) REVERT: A 107 VAL cc_start: 0.8308 (t) cc_final: 0.7864 (m) REVERT: A 109 VAL cc_start: 0.9084 (t) cc_final: 0.8789 (m) REVERT: A 111 LYS cc_start: 0.8945 (ttpp) cc_final: 0.8674 (ttpp) REVERT: A 120 GLN cc_start: 0.8728 (tt0) cc_final: 0.8398 (tm-30) REVERT: A 122 PHE cc_start: 0.8752 (t80) cc_final: 0.8382 (t80) REVERT: A 124 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8412 (mt-10) REVERT: A 128 HIS cc_start: 0.8686 (t-170) cc_final: 0.8319 (t70) REVERT: A 131 GLU cc_start: 0.8039 (tt0) cc_final: 0.7699 (tt0) REVERT: A 132 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 134 MET cc_start: 0.7629 (tpt) cc_final: 0.7233 (tpt) REVERT: A 159 LYS cc_start: 0.8522 (mptt) cc_final: 0.8032 (mptt) REVERT: A 202 MET cc_start: 0.8714 (ptt) cc_final: 0.8457 (ptm) REVERT: A 204 PHE cc_start: 0.8682 (m-80) cc_final: 0.8246 (m-80) REVERT: A 213 THR cc_start: 0.7842 (p) cc_final: 0.7599 (p) REVERT: A 218 GLU cc_start: 0.7662 (pp20) cc_final: 0.7168 (pp20) REVERT: A 228 ILE cc_start: 0.8814 (mt) cc_final: 0.8570 (tp) REVERT: A 245 VAL cc_start: 0.8466 (t) cc_final: 0.8044 (m) REVERT: A 311 VAL cc_start: 0.8392 (p) cc_final: 0.8029 (m) REVERT: A 346 THR cc_start: 0.8648 (m) cc_final: 0.8121 (p) REVERT: A 356 ARG cc_start: 0.8485 (ttm170) cc_final: 0.8194 (tpp80) REVERT: A 365 GLU cc_start: 0.7488 (tm-30) cc_final: 0.6698 (tm-30) REVERT: A 391 ARG cc_start: 0.8323 (ptp-110) cc_final: 0.7740 (ptp-110) REVERT: A 397 SER cc_start: 0.8567 (m) cc_final: 0.7915 (p) REVERT: D 103 SER cc_start: 0.8844 (t) cc_final: 0.8616 (t) REVERT: D 105 LYS cc_start: 0.8257 (mmmt) cc_final: 0.7656 (mmmt) REVERT: D 109 VAL cc_start: 0.9017 (t) cc_final: 0.8759 (m) REVERT: D 122 PHE cc_start: 0.8759 (t80) cc_final: 0.8536 (t80) REVERT: D 123 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8000 (mmmm) REVERT: D 124 GLU cc_start: 0.8547 (mt-10) cc_final: 0.7985 (mt-10) REVERT: D 130 MET cc_start: 0.8130 (tpp) cc_final: 0.7824 (tpp) REVERT: D 134 MET cc_start: 0.7663 (ttt) cc_final: 0.7264 (ttt) REVERT: D 154 PHE cc_start: 0.7684 (t80) cc_final: 0.6953 (t80) REVERT: D 158 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8249 (mtpt) REVERT: D 193 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7820 (mm) REVERT: D 211 PHE cc_start: 0.8449 (m-80) cc_final: 0.8222 (m-80) REVERT: D 215 PHE cc_start: 0.8066 (m-80) cc_final: 0.7757 (m-80) REVERT: D 218 GLU cc_start: 0.7786 (pp20) cc_final: 0.7265 (pp20) REVERT: D 221 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8273 (mm-40) REVERT: D 245 VAL cc_start: 0.8386 (t) cc_final: 0.8003 (p) REVERT: D 278 MET cc_start: 0.7651 (mmm) cc_final: 0.7293 (mmm) REVERT: D 285 GLU cc_start: 0.8020 (pm20) cc_final: 0.7670 (pm20) REVERT: D 335 MET cc_start: 0.8410 (mmm) cc_final: 0.7810 (mmm) REVERT: D 385 ARG cc_start: 0.7605 (ttm170) cc_final: 0.7233 (ttm170) REVERT: D 391 ARG cc_start: 0.8358 (ptp90) cc_final: 0.7916 (ptp-110) REVERT: D 397 SER cc_start: 0.8615 (m) cc_final: 0.7956 (p) REVERT: C 109 VAL cc_start: 0.9001 (t) cc_final: 0.8684 (m) REVERT: C 111 LYS cc_start: 0.8910 (ttpp) cc_final: 0.8602 (ttpp) REVERT: C 120 GLN cc_start: 0.8575 (tm-30) cc_final: 0.8214 (tm-30) REVERT: C 122 PHE cc_start: 0.8642 (t80) cc_final: 0.8392 (t80) REVERT: C 123 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8337 (mmtm) REVERT: C 154 PHE cc_start: 0.7669 (t80) cc_final: 0.6751 (t80) REVERT: C 158 LYS cc_start: 0.9024 (mtpt) cc_final: 0.7891 (mtpt) REVERT: C 159 LYS cc_start: 0.8476 (mmmt) cc_final: 0.7825 (mmmt) REVERT: C 174 GLN cc_start: 0.8139 (mt0) cc_final: 0.7752 (mp10) REVERT: C 176 ASP cc_start: 0.7985 (m-30) cc_final: 0.7670 (m-30) REVERT: C 204 PHE cc_start: 0.8637 (m-80) cc_final: 0.8303 (m-80) REVERT: C 218 GLU cc_start: 0.7783 (pp20) cc_final: 0.7254 (pp20) REVERT: C 228 ILE cc_start: 0.8907 (mt) cc_final: 0.8589 (tp) REVERT: C 243 ARG cc_start: 0.8300 (ttp-170) cc_final: 0.7757 (ptm160) REVERT: C 245 VAL cc_start: 0.8513 (t) cc_final: 0.8085 (p) REVERT: C 281 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7769 (mm-40) REVERT: C 285 GLU cc_start: 0.7975 (pm20) cc_final: 0.7542 (pm20) REVERT: C 335 MET cc_start: 0.8481 (mmm) cc_final: 0.7845 (mtm) REVERT: C 346 THR cc_start: 0.8515 (m) cc_final: 0.8014 (p) REVERT: C 352 SER cc_start: 0.8621 (t) cc_final: 0.8372 (t) REVERT: C 356 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.8387 (ttm170) REVERT: C 365 GLU cc_start: 0.7445 (tm-30) cc_final: 0.6844 (tm-30) REVERT: C 391 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8121 (ptp90) REVERT: C 397 SER cc_start: 0.8646 (m) cc_final: 0.7757 (p) REVERT: B 105 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7216 (mmmt) REVERT: B 120 GLN cc_start: 0.8508 (tt0) cc_final: 0.8245 (tm-30) REVERT: B 154 PHE cc_start: 0.7745 (t80) cc_final: 0.7095 (t80) REVERT: B 158 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8449 (mtpt) REVERT: B 195 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7364 (mm-40) REVERT: B 204 PHE cc_start: 0.8491 (m-80) cc_final: 0.8077 (m-80) REVERT: B 228 ILE cc_start: 0.9028 (mm) cc_final: 0.8801 (tp) REVERT: B 285 GLU cc_start: 0.8078 (pm20) cc_final: 0.7676 (pm20) REVERT: B 311 VAL cc_start: 0.8528 (p) cc_final: 0.8195 (m) REVERT: B 335 MET cc_start: 0.8513 (mpp) cc_final: 0.8270 (mmm) REVERT: B 346 THR cc_start: 0.8547 (m) cc_final: 0.8026 (p) REVERT: B 356 ARG cc_start: 0.8446 (tpp-160) cc_final: 0.8195 (tpp80) REVERT: B 367 LYS cc_start: 0.8349 (ttmm) cc_final: 0.8056 (ttmm) REVERT: B 397 SER cc_start: 0.8611 (m) cc_final: 0.7962 (p) REVERT: B 412 ASP cc_start: 0.7511 (p0) cc_final: 0.7261 (p0) REVERT: B 416 ASP cc_start: 0.8186 (t0) cc_final: 0.7892 (t0) outliers start: 30 outliers final: 26 residues processed: 390 average time/residue: 0.2617 time to fit residues: 132.5297 Evaluate side-chains 408 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 380 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 282 VAL Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 391 ARG Chi-restraints excluded: chain C residue 409 CYS Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 217 PHE Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 40 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 74 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 93 optimal weight: 0.2980 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS ** C 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111960 restraints weight = 14756.035| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.86 r_work: 0.3334 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9503 Z= 0.198 Angle : 0.615 11.139 12907 Z= 0.311 Chirality : 0.048 0.188 1500 Planarity : 0.005 0.039 1640 Dihedral : 4.453 19.262 1270 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 2.85 % Allowed : 22.84 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.26), residues: 1176 helix: 0.86 (0.35), residues: 238 sheet: 0.56 (0.28), residues: 341 loop : -1.04 (0.27), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 100 HIS 0.008 0.001 HIS A 128 PHE 0.039 0.002 PHE C 220 TYR 0.007 0.001 TYR C 280 ARG 0.007 0.000 ARG C 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4579.14 seconds wall clock time: 81 minutes 36.45 seconds (4896.45 seconds total)