Starting phenix.real_space_refine on Wed Sep 17 15:16:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cr3_45831/09_2025/9cr3_45831.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cr3_45831/09_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_45831/09_2025/9cr3_45831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cr3_45831/09_2025/9cr3_45831.map" model { file = "/net/cci-nas-00/data/ceres_data/9cr3_45831/09_2025/9cr3_45831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cr3_45831/09_2025/9cr3_45831.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.35, per 1000 atoms: 0.25 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: 0.94 Conformation dependent library (CDL) restraints added in 313.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.37 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: 1.62 Time building geometry restraints manager: 1.18 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: 2.310 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.550 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.620 ------------------------------------------------------------------------------- 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= 0.138 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.000 ARG C 387 TYR 0.010 0.001 TYR D 280 PHE 0.031 0.002 PHE A 220 TRP 0.012 0.001 TRP C 427 HIS 0.002 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9503) covalent geometry : angle 0.62042 (12907) hydrogen bonds : bond 0.13222 ( 358) hydrogen bonds : angle 6.00491 ( 948) *********************** 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 : 0.362 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: 0.0963 time to fit residues: 49.9587 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 : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.124866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109406 restraints weight = 14688.193| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.88 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: 0.7970 moved from start: 0.1149 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= 0.187 Angle : 0.588 7.853 12907 Z= 0.307 Chirality : 0.049 0.208 1500 Planarity : 0.005 0.039 1640 Dihedral : 4.730 21.749 1270 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 1.52 % Allowed : 10.09 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.26), residues: 1176 helix: 0.40 (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 ARG 0.004 0.000 ARG D 391 TYR 0.012 0.001 TYR B 137 PHE 0.033 0.002 PHE D 220 TRP 0.010 0.001 TRP C 427 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9503) covalent geometry : angle 0.58792 (12907) hydrogen bonds : bond 0.03732 ( 358) hydrogen bonds : angle 5.41188 ( 948) *********************** 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 387 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 371 time to evaluate : 0.361 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: 0.8125 (mmmt) cc_final: 0.7814 (mmmt) REVERT: A 107 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.7992 (m) REVERT: A 111 LYS cc_start: 0.9007 (ttpp) cc_final: 0.8749 (ttpp) REVERT: A 120 GLN cc_start: 0.8694 (tt0) cc_final: 0.7954 (tm-30) REVERT: A 122 PHE cc_start: 0.8744 (t80) cc_final: 0.8517 (t80) REVERT: A 123 LYS cc_start: 0.8729 (mtmm) cc_final: 0.8484 (mtmm) REVERT: A 124 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8109 (mt-10) REVERT: A 130 MET cc_start: 0.7996 (tpp) cc_final: 0.7790 (tpp) REVERT: A 131 GLU cc_start: 0.8279 (tt0) cc_final: 0.7936 (tt0) REVERT: A 159 LYS cc_start: 0.8610 (mptt) cc_final: 0.8285 (mptt) REVERT: A 202 MET cc_start: 0.8719 (ptt) cc_final: 0.8464 (ptm) REVERT: A 204 PHE cc_start: 0.8686 (m-80) cc_final: 0.8406 (m-80) REVERT: A 219 ASN cc_start: 0.8523 (t0) cc_final: 0.8062 (t0) REVERT: A 228 ILE cc_start: 0.9011 (mt) cc_final: 0.8777 (tp) REVERT: A 245 VAL cc_start: 0.8534 (t) cc_final: 0.8281 (p) REVERT: A 365 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6895 (tm-30) REVERT: A 375 ARG cc_start: 0.8186 (mpp-170) cc_final: 0.7984 (mpp-170) REVERT: A 392 HIS cc_start: 0.8459 (m90) cc_final: 0.8231 (m90) REVERT: A 397 SER cc_start: 0.8637 (m) cc_final: 0.7936 (p) REVERT: D 98 LEU cc_start: 0.8395 (tp) cc_final: 0.8018 (mt) REVERT: D 103 SER cc_start: 0.8810 (t) cc_final: 0.8542 (t) REVERT: D 105 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7833 (mmmt) REVERT: D 109 VAL cc_start: 0.9013 (t) cc_final: 0.8733 (m) REVERT: D 120 GLN cc_start: 0.8751 (tt0) cc_final: 0.8062 (tm-30) REVERT: D 122 PHE cc_start: 0.8842 (t80) cc_final: 0.8531 (t80) REVERT: D 123 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8039 (mmmm) REVERT: D 124 GLU cc_start: 0.8567 (mt-10) cc_final: 0.7956 (mt-10) REVERT: D 130 MET cc_start: 0.8119 (tpp) cc_final: 0.7795 (tpp) REVERT: D 134 MET cc_start: 0.7672 (ttt) cc_final: 0.7374 (ttt) REVERT: D 154 PHE cc_start: 0.7963 (t80) cc_final: 0.7041 (t80) REVERT: D 158 LYS cc_start: 0.8858 (mtpt) cc_final: 0.8356 (mtpt) REVERT: D 176 ASP cc_start: 0.8241 (m-30) cc_final: 0.7908 (m-30) REVERT: D 193 LEU cc_start: 0.8469 (mm) cc_final: 0.8264 (mm) REVERT: D 211 PHE cc_start: 0.8397 (m-80) cc_final: 0.8084 (m-80) REVERT: D 215 PHE cc_start: 0.8449 (m-80) cc_final: 0.7822 (m-80) REVERT: D 218 GLU cc_start: 0.8031 (pp20) cc_final: 0.7740 (pp20) REVERT: D 219 ASN cc_start: 0.8521 (t0) cc_final: 0.8085 (t0) REVERT: D 221 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8321 (mm-40) REVERT: D 245 VAL cc_start: 0.8299 (t) cc_final: 0.7970 (p) REVERT: D 278 MET cc_start: 0.7970 (mmm) cc_final: 0.7713 (mmm) REVERT: D 285 GLU cc_start: 0.8052 (pm20) cc_final: 0.7444 (pm20) REVERT: D 335 MET cc_start: 0.8494 (mmm) cc_final: 0.7603 (mmm) REVERT: D 397 SER cc_start: 0.8633 (m) cc_final: 0.7970 (p) REVERT: D 425 LEU cc_start: 0.8473 (mt) cc_final: 0.8245 (mp) REVERT: C 105 LYS cc_start: 0.8239 (mmpt) cc_final: 0.7904 (mmpt) REVERT: C 106 SER cc_start: 0.7807 (p) cc_final: 0.7518 (p) REVERT: C 109 VAL cc_start: 0.9010 (t) cc_final: 0.8685 (m) REVERT: C 112 LYS cc_start: 0.8365 (ttmt) cc_final: 0.8097 (ttmt) REVERT: C 122 PHE cc_start: 0.8729 (t80) cc_final: 0.8503 (t80) REVERT: C 123 LYS cc_start: 0.8748 (mmtm) cc_final: 0.8458 (mmtm) REVERT: C 134 MET cc_start: 0.7788 (ttt) cc_final: 0.7562 (ttt) REVERT: C 154 PHE cc_start: 0.7628 (t80) cc_final: 0.6939 (t80) REVERT: C 158 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8060 (mtpt) REVERT: C 159 LYS cc_start: 0.8559 (mmmt) cc_final: 0.8053 (mmmt) REVERT: C 174 GLN cc_start: 0.8074 (mt0) cc_final: 0.7798 (mt0) REVERT: C 176 ASP cc_start: 0.8066 (m-30) cc_final: 0.7670 (m-30) REVERT: C 204 PHE cc_start: 0.8686 (m-80) cc_final: 0.8354 (m-80) REVERT: C 218 GLU cc_start: 0.8110 (pp20) cc_final: 0.7800 (pp20) REVERT: C 226 GLN cc_start: 0.8388 (tt0) cc_final: 0.8134 (tt0) REVERT: C 243 ARG cc_start: 0.8205 (ttp-170) cc_final: 0.7735 (ptm160) REVERT: C 245 VAL cc_start: 0.8476 (t) cc_final: 0.8083 (m) REVERT: C 278 MET cc_start: 0.7573 (mmm) cc_final: 0.7191 (mmm) REVERT: C 281 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7931 (mm-40) REVERT: C 285 GLU cc_start: 0.7942 (pm20) cc_final: 0.7533 (pm20) REVERT: C 319 SER cc_start: 0.8742 (p) cc_final: 0.8320 (t) REVERT: C 324 SER cc_start: 0.8449 (m) cc_final: 0.8240 (p) REVERT: C 335 MET cc_start: 0.8743 (mpp) cc_final: 0.8422 (mmm) REVERT: C 346 THR cc_start: 0.8602 (m) cc_final: 0.8133 (p) REVERT: C 352 SER cc_start: 0.8569 (t) cc_final: 0.8324 (t) REVERT: C 365 GLU cc_start: 0.7454 (tm-30) cc_final: 0.6892 (tm-30) REVERT: C 397 SER cc_start: 0.8689 (m) cc_final: 0.7741 (p) REVERT: B 98 LEU cc_start: 0.8217 (tp) cc_final: 0.7723 (mt) REVERT: B 105 LYS cc_start: 0.7829 (mmmt) cc_final: 0.7302 (mmmt) REVERT: B 111 LYS cc_start: 0.8918 (ttpp) cc_final: 0.8555 (ttpp) REVERT: B 113 MET cc_start: 0.7828 (ttm) cc_final: 0.7479 (ttm) REVERT: B 124 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 125 LEU cc_start: 0.8967 (tp) cc_final: 0.8763 (tt) REVERT: B 154 PHE cc_start: 0.7888 (t80) cc_final: 0.7109 (t80) REVERT: B 158 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8479 (mtpt) REVERT: B 202 MET cc_start: 0.8590 (ptt) cc_final: 0.8260 (ptm) REVERT: B 204 PHE cc_start: 0.8602 (m-80) cc_final: 0.8250 (m-80) REVERT: B 218 GLU cc_start: 0.8098 (pp20) cc_final: 0.7816 (pp20) REVERT: B 226 GLN cc_start: 0.8578 (tt0) cc_final: 0.8291 (tt0) REVERT: B 239 ARG cc_start: 0.8627 (mtm180) cc_final: 0.8341 (mtp180) REVERT: B 279 GLN cc_start: 0.8498 (tt0) cc_final: 0.8243 (tp40) REVERT: B 285 GLU cc_start: 0.7982 (pm20) cc_final: 0.7578 (pm20) REVERT: B 294 SER cc_start: 0.8197 (m) cc_final: 0.7694 (p) REVERT: B 335 MET cc_start: 0.8581 (mpp) cc_final: 0.8310 (mmm) REVERT: B 367 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8019 (ttmm) REVERT: B 397 SER cc_start: 0.8606 (m) cc_final: 0.7880 (p) outliers start: 16 outliers final: 6 residues processed: 374 average time/residue: 0.1088 time to fit residues: 54.6581 Evaluate side-chains 381 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 374 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 77 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 chunk 17 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.124979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.109233 restraints weight = 14434.949| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.74 r_work: 0.3299 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9503 Z= 0.176 Angle : 0.583 8.268 12907 Z= 0.307 Chirality : 0.048 0.167 1500 Planarity : 0.005 0.038 1640 Dihedral : 4.718 22.885 1270 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 2.09 % Allowed : 14.27 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.26), residues: 1176 helix: 0.36 (0.34), residues: 250 sheet: 0.44 (0.27), residues: 383 loop : -1.34 (0.29), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 391 TYR 0.009 0.001 TYR C 280 PHE 0.037 0.002 PHE D 220 TRP 0.009 0.001 TRP C 427 HIS 0.010 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9503) covalent geometry : angle 0.58299 (12907) hydrogen bonds : bond 0.03690 ( 358) hydrogen bonds : angle 5.32250 ( 948) *********************** 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 394 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 372 time to evaluate : 0.367 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: 0.8032 (mmmt) cc_final: 0.7648 (mmmt) REVERT: A 107 VAL cc_start: 0.8534 (t) cc_final: 0.8044 (m) REVERT: A 111 LYS cc_start: 0.8989 (ttpp) cc_final: 0.8731 (ttpp) REVERT: A 120 GLN cc_start: 0.8694 (tt0) cc_final: 0.7964 (tm-30) REVERT: A 122 PHE cc_start: 0.8707 (t80) cc_final: 0.8448 (t80) REVERT: A 123 LYS cc_start: 0.8690 (mtmm) cc_final: 0.8466 (mtmm) REVERT: A 124 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8145 (mt-10) REVERT: A 131 GLU cc_start: 0.8180 (tt0) cc_final: 0.7878 (tt0) REVERT: A 159 LYS cc_start: 0.8547 (mptt) cc_final: 0.8203 (mptt) REVERT: A 202 MET cc_start: 0.8726 (ptt) cc_final: 0.8482 (ptm) REVERT: A 204 PHE cc_start: 0.8718 (m-80) cc_final: 0.8366 (m-80) REVERT: A 213 THR cc_start: 0.7808 (p) cc_final: 0.7553 (p) REVERT: A 219 ASN cc_start: 0.8446 (t0) cc_final: 0.8002 (t0) REVERT: A 228 ILE cc_start: 0.8948 (mt) cc_final: 0.8725 (tp) REVERT: A 245 VAL cc_start: 0.8564 (t) cc_final: 0.8193 (m) REVERT: A 365 GLU cc_start: 0.7467 (tm-30) cc_final: 0.6710 (tm-30) REVERT: A 392 HIS cc_start: 0.8440 (m90) cc_final: 0.8237 (m90) REVERT: A 397 SER cc_start: 0.8654 (m) cc_final: 0.7971 (p) REVERT: A 423 GLN cc_start: 0.8561 (tp40) cc_final: 0.8323 (tt0) REVERT: D 98 LEU cc_start: 0.8431 (tp) cc_final: 0.8082 (mt) REVERT: D 103 SER cc_start: 0.8833 (t) cc_final: 0.8581 (t) REVERT: D 105 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7735 (mmmt) REVERT: D 109 VAL cc_start: 0.9036 (t) cc_final: 0.8747 (m) REVERT: D 120 GLN cc_start: 0.8800 (tt0) cc_final: 0.8336 (tt0) REVERT: D 122 PHE cc_start: 0.8815 (t80) cc_final: 0.8477 (t80) REVERT: D 123 LYS cc_start: 0.8663 (mmtm) cc_final: 0.8003 (mmmm) REVERT: D 124 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8004 (mt-10) REVERT: D 130 MET cc_start: 0.8056 (tpp) cc_final: 0.7815 (tpp) REVERT: D 134 MET cc_start: 0.7731 (ttt) cc_final: 0.7411 (ttt) REVERT: D 154 PHE cc_start: 0.7801 (t80) cc_final: 0.6923 (t80) REVERT: D 158 LYS cc_start: 0.8864 (mtpt) cc_final: 0.8340 (mtpt) REVERT: D 176 ASP cc_start: 0.8180 (m-30) cc_final: 0.7874 (m-30) REVERT: D 211 PHE cc_start: 0.8408 (m-80) cc_final: 0.8041 (m-80) REVERT: D 215 PHE cc_start: 0.8556 (m-80) cc_final: 0.7997 (m-80) REVERT: D 218 GLU cc_start: 0.7887 (pp20) cc_final: 0.7531 (pp20) REVERT: D 221 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8295 (mm-40) REVERT: D 245 VAL cc_start: 0.8359 (t) cc_final: 0.7973 (p) REVERT: D 278 MET cc_start: 0.7841 (mmm) cc_final: 0.7581 (mmm) REVERT: D 285 GLU cc_start: 0.7998 (pm20) cc_final: 0.7540 (pm20) REVERT: D 395 SER cc_start: 0.8569 (t) cc_final: 0.8282 (p) REVERT: D 397 SER cc_start: 0.8677 (m) cc_final: 0.7984 (p) REVERT: D 425 LEU cc_start: 0.8558 (mt) cc_final: 0.8323 (mp) REVERT: C 106 SER cc_start: 0.7850 (p) cc_final: 0.7614 (p) REVERT: C 109 VAL cc_start: 0.9006 (t) cc_final: 0.8701 (m) REVERT: C 112 LYS cc_start: 0.8327 (ttmt) cc_final: 0.8045 (ttmt) REVERT: C 122 PHE cc_start: 0.8741 (t80) cc_final: 0.8512 (t80) REVERT: C 123 LYS cc_start: 0.8747 (mmtm) cc_final: 0.8442 (mmtm) REVERT: C 154 PHE cc_start: 0.7606 (t80) cc_final: 0.6887 (t80) REVERT: C 158 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8040 (mtpt) REVERT: C 159 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8035 (mmmt) REVERT: C 174 GLN cc_start: 0.8077 (mt0) cc_final: 0.7822 (mt0) REVERT: C 176 ASP cc_start: 0.8055 (m-30) cc_final: 0.7683 (m-30) REVERT: C 218 GLU cc_start: 0.8024 (pp20) cc_final: 0.7704 (pp20) REVERT: C 226 GLN cc_start: 0.8390 (tt0) cc_final: 0.8150 (tt0) REVERT: C 243 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7756 (ptm160) REVERT: C 245 VAL cc_start: 0.8518 (t) cc_final: 0.8100 (m) REVERT: C 278 MET cc_start: 0.7439 (mmm) cc_final: 0.7179 (mmm) REVERT: C 281 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7824 (mm-40) REVERT: C 285 GLU cc_start: 0.7867 (pm20) cc_final: 0.7498 (pm20) REVERT: C 319 SER cc_start: 0.8709 (p) cc_final: 0.8302 (t) REVERT: C 324 SER cc_start: 0.8441 (m) cc_final: 0.8240 (p) REVERT: C 335 MET cc_start: 0.8726 (mpp) cc_final: 0.8450 (mmm) REVERT: C 346 THR cc_start: 0.8552 (m) cc_final: 0.8122 (p) REVERT: C 352 SER cc_start: 0.8561 (t) cc_final: 0.8320 (t) REVERT: C 356 ARG cc_start: 0.8612 (ttm-80) cc_final: 0.8293 (ttm170) REVERT: C 365 GLU cc_start: 0.7487 (tm-30) cc_final: 0.6912 (tm-30) REVERT: C 397 SER cc_start: 0.8683 (m) cc_final: 0.7834 (p) REVERT: B 105 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7195 (mmmt) REVERT: B 111 LYS cc_start: 0.8856 (ttpp) cc_final: 0.8490 (ttpp) REVERT: B 113 MET cc_start: 0.7784 (ttm) cc_final: 0.7413 (ttm) REVERT: B 124 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7852 (mt-10) REVERT: B 125 LEU cc_start: 0.8962 (tp) cc_final: 0.8739 (tt) REVERT: B 154 PHE cc_start: 0.7861 (t80) cc_final: 0.7028 (t80) REVERT: B 158 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8465 (mtpt) REVERT: B 202 MET cc_start: 0.8622 (ptt) cc_final: 0.8374 (ptm) REVERT: B 204 PHE cc_start: 0.8637 (m-80) cc_final: 0.8346 (m-80) REVERT: B 218 GLU cc_start: 0.8041 (pp20) cc_final: 0.7735 (pp20) REVERT: B 226 GLN cc_start: 0.8625 (tt0) cc_final: 0.8358 (tt0) REVERT: B 228 ILE cc_start: 0.9160 (mm) cc_final: 0.8952 (tp) REVERT: B 239 ARG cc_start: 0.8622 (mtm180) cc_final: 0.8342 (mtp180) REVERT: B 278 MET cc_start: 0.7814 (mmm) cc_final: 0.7402 (mmm) REVERT: B 279 GLN cc_start: 0.8508 (tt0) cc_final: 0.8303 (tp40) REVERT: B 285 GLU cc_start: 0.7956 (pm20) cc_final: 0.7619 (pm20) REVERT: B 311 VAL cc_start: 0.8587 (p) cc_final: 0.8254 (m) REVERT: B 335 MET cc_start: 0.8557 (mpp) cc_final: 0.8323 (mmm) REVERT: B 365 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7164 (tm-30) REVERT: B 397 SER cc_start: 0.8620 (m) cc_final: 0.8011 (p) outliers start: 22 outliers final: 16 residues processed: 376 average time/residue: 0.1075 time to fit residues: 54.3643 Evaluate side-chains 381 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 365 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 310 THR 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 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 Chi-restraints excluded: chain B residue 386 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 95 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 0.3980 chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 0.0000 chunk 103 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.126631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111159 restraints weight = 14354.130| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.73 r_work: 0.3328 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1728 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= 0.121 Angle : 0.571 10.067 12907 Z= 0.293 Chirality : 0.047 0.162 1500 Planarity : 0.005 0.035 1640 Dihedral : 4.565 21.652 1270 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 2.57 % Allowed : 16.65 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.26), residues: 1176 helix: 0.62 (0.34), residues: 248 sheet: 0.47 (0.27), residues: 380 loop : -1.16 (0.30), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 391 TYR 0.008 0.001 TYR C 280 PHE 0.037 0.002 PHE D 220 TRP 0.009 0.001 TRP C 427 HIS 0.002 0.000 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9503) covalent geometry : angle 0.57104 (12907) hydrogen bonds : bond 0.03333 ( 358) hydrogen bonds : angle 5.14335 ( 948) *********************** 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 393 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 366 time to evaluate : 0.360 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 98 LEU cc_start: 0.8263 (tp) cc_final: 0.7530 (mt) REVERT: A 105 LYS cc_start: 0.8019 (mmmt) cc_final: 0.7186 (mmmt) REVERT: A 111 LYS cc_start: 0.8957 (ttpp) cc_final: 0.8699 (ttpp) REVERT: A 120 GLN cc_start: 0.8716 (tt0) cc_final: 0.7970 (tm-30) REVERT: A 122 PHE cc_start: 0.8713 (t80) cc_final: 0.8442 (t80) REVERT: A 123 LYS cc_start: 0.8653 (mtmm) cc_final: 0.8420 (mtmm) REVERT: A 124 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8148 (mt-10) REVERT: A 131 GLU cc_start: 0.8135 (tt0) cc_final: 0.7846 (tt0) REVERT: A 159 LYS cc_start: 0.8566 (mptt) cc_final: 0.8205 (mptt) REVERT: A 202 MET cc_start: 0.8735 (ptt) cc_final: 0.8514 (ptm) REVERT: A 204 PHE cc_start: 0.8674 (m-80) cc_final: 0.8382 (m-80) REVERT: A 218 GLU cc_start: 0.8033 (pp20) cc_final: 0.7575 (pp20) REVERT: A 219 ASN cc_start: 0.8403 (t0) cc_final: 0.8035 (t0) REVERT: A 228 ILE cc_start: 0.8867 (mt) cc_final: 0.8618 (tp) REVERT: A 245 VAL cc_start: 0.8550 (t) cc_final: 0.8284 (p) REVERT: A 365 GLU cc_start: 0.7476 (tm-30) cc_final: 0.6720 (tm-30) REVERT: A 392 HIS cc_start: 0.8399 (m90) cc_final: 0.8193 (m90) REVERT: A 397 SER cc_start: 0.8590 (m) cc_final: 0.7939 (p) REVERT: A 423 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: D 98 LEU cc_start: 0.8388 (tp) cc_final: 0.8077 (mt) REVERT: D 103 SER cc_start: 0.8824 (t) cc_final: 0.8594 (t) REVERT: D 105 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7607 (mmmt) REVERT: D 109 VAL cc_start: 0.9021 (t) cc_final: 0.8760 (m) REVERT: D 122 PHE cc_start: 0.8776 (t80) cc_final: 0.8429 (t80) REVERT: D 123 LYS cc_start: 0.8627 (mmtm) cc_final: 0.7994 (mmmm) REVERT: D 124 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8018 (mt-10) REVERT: D 130 MET cc_start: 0.8030 (tpp) cc_final: 0.7710 (tpp) REVERT: D 134 MET cc_start: 0.7669 (ttt) cc_final: 0.7327 (ttt) REVERT: D 154 PHE cc_start: 0.7738 (t80) cc_final: 0.6911 (t80) REVERT: D 158 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8291 (mtpt) REVERT: D 176 ASP cc_start: 0.8130 (m-30) cc_final: 0.7836 (m-30) REVERT: D 211 PHE cc_start: 0.8371 (m-80) cc_final: 0.8033 (m-80) REVERT: D 213 THR cc_start: 0.7986 (p) cc_final: 0.7707 (p) REVERT: D 215 PHE cc_start: 0.8468 (m-80) cc_final: 0.7926 (m-80) REVERT: D 218 GLU cc_start: 0.7758 (pp20) cc_final: 0.7295 (pp20) REVERT: D 221 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8231 (mm-40) REVERT: D 245 VAL cc_start: 0.8377 (t) cc_final: 0.7986 (p) REVERT: D 278 MET cc_start: 0.7778 (mmm) cc_final: 0.7446 (mmm) REVERT: D 285 GLU cc_start: 0.8001 (pm20) cc_final: 0.7580 (pm20) REVERT: D 335 MET cc_start: 0.8490 (mmm) cc_final: 0.7691 (mmm) REVERT: D 395 SER cc_start: 0.8608 (t) cc_final: 0.8318 (p) REVERT: D 397 SER cc_start: 0.8643 (m) cc_final: 0.7974 (p) REVERT: D 425 LEU cc_start: 0.8462 (mt) cc_final: 0.8259 (mp) REVERT: C 105 LYS cc_start: 0.8016 (mmpt) cc_final: 0.7765 (mmtt) REVERT: C 109 VAL cc_start: 0.9025 (t) cc_final: 0.8695 (m) REVERT: C 111 LYS cc_start: 0.8901 (ttpp) cc_final: 0.8653 (ttpp) REVERT: C 112 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8027 (ttmt) REVERT: C 120 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8209 (tm-30) REVERT: C 122 PHE cc_start: 0.8696 (t80) cc_final: 0.8462 (t80) REVERT: C 123 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8406 (mmtm) REVERT: C 154 PHE cc_start: 0.7572 (t80) cc_final: 0.6798 (t80) REVERT: C 158 LYS cc_start: 0.9007 (mtpt) cc_final: 0.7979 (mtpt) REVERT: C 159 LYS cc_start: 0.8480 (mmmt) cc_final: 0.7944 (mmmt) REVERT: C 174 GLN cc_start: 0.8078 (mt0) cc_final: 0.7846 (mt0) REVERT: C 176 ASP cc_start: 0.8023 (m-30) cc_final: 0.7676 (m-30) REVERT: C 204 PHE cc_start: 0.8669 (m-80) cc_final: 0.8332 (m-80) REVERT: C 218 GLU cc_start: 0.8018 (pp20) cc_final: 0.7641 (pp20) REVERT: C 226 GLN cc_start: 0.8387 (tt0) cc_final: 0.8141 (tt0) REVERT: C 228 ILE cc_start: 0.8998 (mt) cc_final: 0.8683 (tp) REVERT: C 243 ARG cc_start: 0.8249 (ttp-170) cc_final: 0.7766 (ptm160) REVERT: C 281 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7796 (mm-40) REVERT: C 285 GLU cc_start: 0.7886 (pm20) cc_final: 0.7513 (pm20) REVERT: C 335 MET cc_start: 0.8723 (mpp) cc_final: 0.8449 (mmm) REVERT: C 352 SER cc_start: 0.8554 (t) cc_final: 0.8304 (t) REVERT: C 365 GLU cc_start: 0.7464 (tm-30) cc_final: 0.6880 (tm-30) REVERT: C 397 SER cc_start: 0.8654 (m) cc_final: 0.7835 (p) REVERT: B 98 LEU cc_start: 0.8266 (tp) cc_final: 0.7786 (mt) REVERT: B 105 LYS cc_start: 0.7817 (mmmt) cc_final: 0.7222 (mmmt) REVERT: B 113 MET cc_start: 0.7709 (ttm) cc_final: 0.7481 (ttm) REVERT: B 125 LEU cc_start: 0.8948 (tp) cc_final: 0.8735 (tt) REVERT: B 154 PHE cc_start: 0.7740 (t80) cc_final: 0.6956 (t80) REVERT: B 158 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8461 (mtpt) REVERT: B 202 MET cc_start: 0.8596 (ptt) cc_final: 0.8387 (ptm) REVERT: B 226 GLN cc_start: 0.8603 (tt0) cc_final: 0.8373 (tt0) REVERT: B 228 ILE cc_start: 0.9119 (mm) cc_final: 0.8893 (tp) REVERT: B 239 ARG cc_start: 0.8605 (mtm180) cc_final: 0.8306 (mtp180) REVERT: B 285 GLU cc_start: 0.7975 (pm20) cc_final: 0.7646 (pm20) REVERT: B 335 MET cc_start: 0.8558 (mpp) cc_final: 0.8262 (mmm) REVERT: B 356 ARG cc_start: 0.8440 (tpp-160) cc_final: 0.8200 (tpp80) REVERT: B 365 GLU cc_start: 0.7598 (tm-30) cc_final: 0.7148 (tm-30) REVERT: B 367 LYS cc_start: 0.8340 (ttmm) cc_final: 0.8018 (ttmm) REVERT: B 397 SER cc_start: 0.8581 (m) cc_final: 0.7932 (p) REVERT: B 412 ASP cc_start: 0.7720 (p0) cc_final: 0.7500 (p0) outliers start: 27 outliers final: 16 residues processed: 373 average time/residue: 0.1054 time to fit residues: 52.5759 Evaluate side-chains 370 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 353 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 282 VAL Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 364 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 101 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.0570 chunk 59 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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** ** B 128 HIS ** 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 = 0.3680 r_free = 0.3680 target = 0.125686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110379 restraints weight = 14487.976| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.74 r_work: 0.3318 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9503 Z= 0.140 Angle : 0.589 14.189 12907 Z= 0.301 Chirality : 0.048 0.176 1500 Planarity : 0.005 0.035 1640 Dihedral : 4.547 21.476 1270 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 3.52 % Allowed : 17.22 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.26), residues: 1176 helix: 0.76 (0.34), residues: 243 sheet: 0.48 (0.27), residues: 381 loop : -1.13 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 391 TYR 0.009 0.001 TYR C 280 PHE 0.035 0.002 PHE C 220 TRP 0.007 0.001 TRP C 427 HIS 0.010 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9503) covalent geometry : angle 0.58930 (12907) hydrogen bonds : bond 0.03436 ( 358) hydrogen bonds : angle 5.12847 ( 948) *********************** 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 407 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 370 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8279 (tp) cc_final: 0.7535 (mt) REVERT: A 105 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7756 (mmmt) REVERT: A 111 LYS cc_start: 0.8956 (ttpp) cc_final: 0.8708 (ttpp) REVERT: A 120 GLN cc_start: 0.8715 (tt0) cc_final: 0.7951 (tm-30) REVERT: A 122 PHE cc_start: 0.8723 (t80) cc_final: 0.8446 (t80) REVERT: A 123 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8415 (mtmm) REVERT: A 124 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8139 (mt-10) REVERT: A 131 GLU cc_start: 0.8109 (tt0) cc_final: 0.7777 (tt0) REVERT: A 134 MET cc_start: 0.7621 (tpp) cc_final: 0.7133 (tpt) REVERT: A 159 LYS cc_start: 0.8566 (mptt) cc_final: 0.8193 (mptt) REVERT: A 202 MET cc_start: 0.8725 (ptt) cc_final: 0.8481 (ptm) REVERT: A 204 PHE cc_start: 0.8701 (m-80) cc_final: 0.8347 (m-80) REVERT: A 213 THR cc_start: 0.7794 (p) cc_final: 0.7535 (p) REVERT: A 218 GLU cc_start: 0.8008 (pp20) cc_final: 0.7540 (pp20) REVERT: A 219 ASN cc_start: 0.8372 (t0) cc_final: 0.8009 (t0) REVERT: A 228 ILE cc_start: 0.8897 (mt) cc_final: 0.8658 (tp) REVERT: A 245 VAL cc_start: 0.8517 (t) cc_final: 0.8240 (p) REVERT: A 365 GLU cc_start: 0.7532 (tm-30) cc_final: 0.6742 (tm-30) REVERT: A 397 SER cc_start: 0.8586 (m) cc_final: 0.7923 (p) REVERT: A 423 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: D 98 LEU cc_start: 0.8406 (tp) cc_final: 0.8116 (mt) REVERT: D 103 SER cc_start: 0.8831 (t) cc_final: 0.8586 (t) REVERT: D 105 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7583 (mmmt) REVERT: D 109 VAL cc_start: 0.9018 (t) cc_final: 0.8762 (m) REVERT: D 122 PHE cc_start: 0.8776 (t80) cc_final: 0.8466 (t80) REVERT: D 123 LYS cc_start: 0.8645 (mmtm) cc_final: 0.7988 (mmmm) REVERT: D 124 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8044 (mt-10) REVERT: D 130 MET cc_start: 0.8026 (tpp) cc_final: 0.7707 (tpp) REVERT: D 134 MET cc_start: 0.7691 (ttt) cc_final: 0.7289 (ttt) REVERT: D 154 PHE cc_start: 0.7742 (t80) cc_final: 0.7053 (t80) REVERT: D 176 ASP cc_start: 0.8150 (m-30) cc_final: 0.7832 (m-30) REVERT: D 211 PHE cc_start: 0.8425 (m-80) cc_final: 0.8156 (m-80) REVERT: D 213 THR cc_start: 0.7971 (p) cc_final: 0.7670 (p) REVERT: D 218 GLU cc_start: 0.7713 (pp20) cc_final: 0.7224 (pp20) REVERT: D 221 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8239 (mm-40) REVERT: D 245 VAL cc_start: 0.8376 (t) cc_final: 0.7982 (p) REVERT: D 278 MET cc_start: 0.7776 (mmm) cc_final: 0.7444 (mmm) REVERT: D 285 GLU cc_start: 0.7991 (pm20) cc_final: 0.7620 (pm20) REVERT: D 335 MET cc_start: 0.8504 (mmm) cc_final: 0.7616 (mmm) REVERT: D 395 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8341 (p) REVERT: D 397 SER cc_start: 0.8621 (m) cc_final: 0.7950 (p) REVERT: D 425 LEU cc_start: 0.8521 (mt) cc_final: 0.8276 (mp) REVERT: C 109 VAL cc_start: 0.8998 (t) cc_final: 0.8676 (m) REVERT: C 111 LYS cc_start: 0.8906 (ttpp) cc_final: 0.8641 (ttpp) REVERT: C 112 LYS cc_start: 0.8313 (ttmt) cc_final: 0.8029 (ttmt) REVERT: C 118 LEU cc_start: 0.8739 (mt) cc_final: 0.8527 (mt) REVERT: C 120 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8195 (tm-30) REVERT: C 122 PHE cc_start: 0.8693 (t80) cc_final: 0.8449 (t80) REVERT: C 123 LYS cc_start: 0.8717 (mmtm) cc_final: 0.8410 (mmtm) REVERT: C 134 MET cc_start: 0.7751 (tpp) cc_final: 0.7491 (tpt) REVERT: C 154 PHE cc_start: 0.7600 (t80) cc_final: 0.6793 (t80) REVERT: C 158 LYS cc_start: 0.9022 (mtpt) cc_final: 0.7976 (mtpt) REVERT: C 159 LYS cc_start: 0.8500 (mmmt) cc_final: 0.7926 (mmmt) REVERT: C 174 GLN cc_start: 0.8091 (mt0) cc_final: 0.7723 (mp10) REVERT: C 176 ASP cc_start: 0.7982 (m-30) cc_final: 0.7665 (m-30) REVERT: C 204 PHE cc_start: 0.8665 (m-80) cc_final: 0.8292 (m-80) REVERT: C 218 GLU cc_start: 0.7995 (pp20) cc_final: 0.7590 (pp20) REVERT: C 226 GLN cc_start: 0.8378 (tt0) cc_final: 0.8128 (tt0) REVERT: C 228 ILE cc_start: 0.8986 (mt) cc_final: 0.8666 (tp) REVERT: C 243 ARG cc_start: 0.8259 (ttp-170) cc_final: 0.7741 (ptm160) REVERT: C 245 VAL cc_start: 0.8535 (t) cc_final: 0.8116 (p) REVERT: C 281 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7820 (mm-40) REVERT: C 285 GLU cc_start: 0.7920 (pm20) cc_final: 0.7532 (pm20) REVERT: C 335 MET cc_start: 0.8702 (mpp) cc_final: 0.8443 (mmm) REVERT: C 352 SER cc_start: 0.8571 (t) cc_final: 0.8323 (t) REVERT: C 365 GLU cc_start: 0.7471 (tm-30) cc_final: 0.6897 (tm-30) REVERT: C 397 SER cc_start: 0.8658 (m) cc_final: 0.7815 (p) REVERT: B 105 LYS cc_start: 0.7873 (mmmt) cc_final: 0.7320 (mmmt) REVERT: B 113 MET cc_start: 0.7718 (ttm) cc_final: 0.7474 (ttm) REVERT: B 125 LEU cc_start: 0.8954 (tp) cc_final: 0.8746 (tt) REVERT: B 154 PHE cc_start: 0.7769 (t80) cc_final: 0.7021 (t80) REVERT: B 158 LYS cc_start: 0.8979 (mtpt) cc_final: 0.8487 (mtpt) REVERT: B 202 MET cc_start: 0.8615 (ptt) cc_final: 0.8350 (ptm) REVERT: B 226 GLN cc_start: 0.8577 (tt0) cc_final: 0.8370 (tt0) REVERT: B 228 ILE cc_start: 0.9120 (mm) cc_final: 0.8892 (tp) REVERT: B 239 ARG cc_start: 0.8640 (mtm180) cc_final: 0.8339 (mtp180) REVERT: B 241 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8182 (ttmm) REVERT: B 278 MET cc_start: 0.7627 (mmm) cc_final: 0.7335 (mmm) REVERT: B 285 GLU cc_start: 0.8009 (pm20) cc_final: 0.7656 (pm20) REVERT: B 311 VAL cc_start: 0.8580 (p) cc_final: 0.8255 (m) REVERT: B 335 MET cc_start: 0.8567 (mpp) cc_final: 0.8277 (mmm) REVERT: B 356 ARG cc_start: 0.8438 (tpp-160) cc_final: 0.8185 (tpp80) REVERT: B 367 LYS cc_start: 0.8363 (ttmm) cc_final: 0.8065 (ttmm) REVERT: B 397 SER cc_start: 0.8578 (m) cc_final: 0.7929 (p) REVERT: B 412 ASP cc_start: 0.7668 (p0) cc_final: 0.7450 (p0) REVERT: B 416 ASP cc_start: 0.8223 (t0) cc_final: 0.7935 (t0) outliers start: 37 outliers final: 24 residues processed: 384 average time/residue: 0.1185 time to fit residues: 61.2482 Evaluate side-chains 394 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 368 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 386 LYS 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 395 SER 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.124933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.109339 restraints weight = 14407.929| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.72 r_work: 0.3296 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9503 Z= 0.189 Angle : 0.592 9.786 12907 Z= 0.307 Chirality : 0.048 0.187 1500 Planarity : 0.005 0.038 1640 Dihedral : 4.588 21.268 1270 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 3.33 % Allowed : 18.65 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.26), residues: 1176 helix: 0.79 (0.34), residues: 244 sheet: 0.46 (0.27), residues: 385 loop : -1.21 (0.29), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 385 TYR 0.008 0.001 TYR C 280 PHE 0.038 0.002 PHE D 220 TRP 0.006 0.001 TRP C 427 HIS 0.006 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9503) covalent geometry : angle 0.59236 (12907) hydrogen bonds : bond 0.03646 ( 358) hydrogen bonds : angle 5.12288 ( 948) *********************** 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 406 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 371 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7684 (mmmt) REVERT: A 111 LYS cc_start: 0.8952 (ttpp) cc_final: 0.8713 (ttpp) REVERT: A 120 GLN cc_start: 0.8714 (tt0) cc_final: 0.8352 (tm-30) REVERT: A 122 PHE cc_start: 0.8724 (t80) cc_final: 0.8458 (t80) REVERT: A 123 LYS cc_start: 0.8667 (mtmm) cc_final: 0.8445 (mtmm) REVERT: A 124 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8378 (mt-10) REVERT: A 130 MET cc_start: 0.7960 (tpp) cc_final: 0.7751 (mpp) REVERT: A 131 GLU cc_start: 0.8078 (tt0) cc_final: 0.7752 (tt0) REVERT: A 159 LYS cc_start: 0.8567 (mptt) cc_final: 0.8192 (mptt) REVERT: A 202 MET cc_start: 0.8721 (ptt) cc_final: 0.8463 (ptm) REVERT: A 213 THR cc_start: 0.7902 (p) cc_final: 0.7672 (p) REVERT: A 218 GLU cc_start: 0.8072 (pp20) cc_final: 0.7593 (pp20) REVERT: A 219 ASN cc_start: 0.8393 (t0) cc_final: 0.8029 (t0) REVERT: A 228 ILE cc_start: 0.8920 (mt) cc_final: 0.8676 (tp) REVERT: A 245 VAL cc_start: 0.8522 (t) cc_final: 0.8231 (p) REVERT: A 346 THR cc_start: 0.8719 (m) cc_final: 0.8228 (p) REVERT: A 365 GLU cc_start: 0.7512 (tm-30) cc_final: 0.6738 (tm-30) REVERT: A 397 SER cc_start: 0.8589 (m) cc_final: 0.7920 (p) REVERT: A 423 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: D 103 SER cc_start: 0.8842 (t) cc_final: 0.8597 (t) REVERT: D 105 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7574 (mmmt) REVERT: D 109 VAL cc_start: 0.9026 (t) cc_final: 0.8779 (m) REVERT: D 122 PHE cc_start: 0.8799 (t80) cc_final: 0.8532 (t80) REVERT: D 123 LYS cc_start: 0.8647 (mmtm) cc_final: 0.8018 (mmmm) REVERT: D 124 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8073 (mt-10) REVERT: D 130 MET cc_start: 0.7982 (tpp) cc_final: 0.7672 (tpp) REVERT: D 132 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7906 (mt-10) REVERT: D 134 MET cc_start: 0.7770 (ttt) cc_final: 0.7341 (ttt) REVERT: D 154 PHE cc_start: 0.7725 (t80) cc_final: 0.6945 (t80) REVERT: D 158 LYS cc_start: 0.8891 (mtpt) cc_final: 0.8340 (mtpt) REVERT: D 193 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8057 (mm) REVERT: D 211 PHE cc_start: 0.8466 (m-80) cc_final: 0.8141 (m-80) REVERT: D 218 GLU cc_start: 0.7775 (pp20) cc_final: 0.7274 (pp20) REVERT: D 221 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8320 (mm-40) REVERT: D 245 VAL cc_start: 0.8387 (t) cc_final: 0.8003 (p) REVERT: D 278 MET cc_start: 0.7790 (mmm) cc_final: 0.7470 (mmm) REVERT: D 285 GLU cc_start: 0.7980 (pm20) cc_final: 0.7651 (pm20) REVERT: D 289 ASP cc_start: 0.7996 (p0) cc_final: 0.7730 (p0) REVERT: D 395 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.8390 (p) REVERT: D 397 SER cc_start: 0.8663 (m) cc_final: 0.7971 (p) REVERT: D 425 LEU cc_start: 0.8575 (mt) cc_final: 0.8333 (mp) REVERT: C 109 VAL cc_start: 0.8993 (t) cc_final: 0.8691 (m) REVERT: C 111 LYS cc_start: 0.8905 (ttpp) cc_final: 0.8597 (ttpp) REVERT: C 122 PHE cc_start: 0.8737 (t80) cc_final: 0.8515 (t80) REVERT: C 123 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8327 (mmtm) REVERT: C 154 PHE cc_start: 0.7620 (t80) cc_final: 0.6736 (t80) REVERT: C 158 LYS cc_start: 0.9033 (mtpt) cc_final: 0.7979 (mtpt) REVERT: C 159 LYS cc_start: 0.8513 (mmmt) cc_final: 0.7937 (mmmt) REVERT: C 174 GLN cc_start: 0.8076 (mt0) cc_final: 0.7799 (mt0) REVERT: C 176 ASP cc_start: 0.8004 (m-30) cc_final: 0.7661 (m-30) REVERT: C 198 VAL cc_start: 0.8591 (t) cc_final: 0.8307 (p) REVERT: C 218 GLU cc_start: 0.7994 (pp20) cc_final: 0.7566 (pp20) REVERT: C 226 GLN cc_start: 0.8390 (tt0) cc_final: 0.8163 (tt0) REVERT: C 228 ILE cc_start: 0.8974 (mt) cc_final: 0.8632 (tp) REVERT: C 243 ARG cc_start: 0.8258 (ttp-170) cc_final: 0.7724 (ptm160) REVERT: C 245 VAL cc_start: 0.8540 (t) cc_final: 0.8126 (p) REVERT: C 281 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7801 (mm-40) REVERT: C 285 GLU cc_start: 0.7904 (pm20) cc_final: 0.7521 (pm20) REVERT: C 346 THR cc_start: 0.8535 (m) cc_final: 0.8096 (p) REVERT: C 352 SER cc_start: 0.8614 (t) cc_final: 0.8380 (t) REVERT: C 365 GLU cc_start: 0.7492 (tm-30) cc_final: 0.6724 (tm-30) REVERT: C 397 SER cc_start: 0.8662 (m) cc_final: 0.7803 (p) REVERT: B 105 LYS cc_start: 0.7941 (mmmt) cc_final: 0.7365 (mmmt) REVERT: B 113 MET cc_start: 0.7747 (ttm) cc_final: 0.7502 (ttm) REVERT: B 124 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7965 (mt-10) REVERT: B 125 LEU cc_start: 0.8914 (tp) cc_final: 0.8673 (tt) REVERT: B 128 HIS cc_start: 0.8643 (t-170) cc_final: 0.8315 (t70) REVERT: B 132 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8064 (mt-10) REVERT: B 136 VAL cc_start: 0.8771 (t) cc_final: 0.8559 (p) REVERT: B 154 PHE cc_start: 0.7808 (t80) cc_final: 0.7139 (t80) REVERT: B 158 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8508 (mtpt) REVERT: B 195 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7501 (mm-40) REVERT: B 202 MET cc_start: 0.8645 (ptt) cc_final: 0.8366 (ptm) REVERT: B 228 ILE cc_start: 0.9091 (mm) cc_final: 0.8853 (tp) REVERT: B 278 MET cc_start: 0.7683 (mmm) cc_final: 0.7474 (mmm) REVERT: B 285 GLU cc_start: 0.8009 (pm20) cc_final: 0.7661 (pm20) REVERT: B 335 MET cc_start: 0.8569 (mpp) cc_final: 0.8308 (mmm) REVERT: B 397 SER cc_start: 0.8610 (m) cc_final: 0.8021 (p) REVERT: B 412 ASP cc_start: 0.7650 (p0) cc_final: 0.7393 (p0) REVERT: B 416 ASP cc_start: 0.8195 (t0) cc_final: 0.7915 (t0) outliers start: 35 outliers final: 26 residues processed: 383 average time/residue: 0.1192 time to fit residues: 61.2763 Evaluate side-chains 397 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 368 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 278 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 423 GLN 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 D residue 395 SER 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 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 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 56 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 35 optimal weight: 0.0470 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 87 optimal weight: 0.0470 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.126944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111697 restraints weight = 15052.045| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.87 r_work: 0.3337 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9503 Z= 0.113 Angle : 0.588 13.994 12907 Z= 0.298 Chirality : 0.047 0.201 1500 Planarity : 0.005 0.037 1640 Dihedral : 4.476 20.497 1270 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 3.24 % Allowed : 19.22 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.26), residues: 1176 helix: 0.79 (0.34), residues: 242 sheet: 0.53 (0.27), residues: 378 loop : -1.24 (0.29), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.009 0.001 TYR D 189 PHE 0.039 0.002 PHE C 220 TRP 0.009 0.001 TRP A 100 HIS 0.004 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9503) covalent geometry : angle 0.58822 (12907) hydrogen bonds : bond 0.03277 ( 358) hydrogen bonds : angle 5.03527 ( 948) *********************** 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 413 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 379 time to evaluate : 0.371 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: 0.8191 (mmmt) cc_final: 0.7820 (mmmt) REVERT: A 111 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8677 (ttpp) REVERT: A 120 GLN cc_start: 0.8679 (tt0) cc_final: 0.8326 (tm-30) REVERT: A 122 PHE cc_start: 0.8701 (t80) cc_final: 0.8390 (t80) REVERT: A 123 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8231 (mtmm) REVERT: A 124 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8342 (mt-10) REVERT: A 128 HIS cc_start: 0.8693 (t70) cc_final: 0.8479 (t70) REVERT: A 130 MET cc_start: 0.8088 (tpp) cc_final: 0.7886 (mpp) REVERT: A 131 GLU cc_start: 0.8033 (tt0) cc_final: 0.7716 (tt0) REVERT: A 134 MET cc_start: 0.7607 (tpp) cc_final: 0.7089 (tpt) REVERT: A 159 LYS cc_start: 0.8575 (mptt) cc_final: 0.8188 (mptt) REVERT: A 202 MET cc_start: 0.8712 (ptt) cc_final: 0.8453 (ptm) REVERT: A 204 PHE cc_start: 0.8678 (m-80) cc_final: 0.8294 (m-80) REVERT: A 213 THR cc_start: 0.7800 (p) cc_final: 0.7540 (p) REVERT: A 218 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7422 (pp20) REVERT: A 219 ASN cc_start: 0.8274 (t0) cc_final: 0.7889 (t0) REVERT: A 228 ILE cc_start: 0.8886 (mt) cc_final: 0.8636 (tp) REVERT: A 245 VAL cc_start: 0.8503 (t) cc_final: 0.8149 (p) REVERT: A 346 THR cc_start: 0.8657 (m) cc_final: 0.8131 (p) REVERT: A 356 ARG cc_start: 0.8433 (ttm170) cc_final: 0.8161 (tpp80) REVERT: A 365 GLU cc_start: 0.7519 (tm-30) cc_final: 0.6715 (tm-30) REVERT: A 391 ARG cc_start: 0.8280 (ptp-110) cc_final: 0.7703 (ptp-110) REVERT: A 397 SER cc_start: 0.8572 (m) cc_final: 0.7933 (p) REVERT: A 423 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8354 (tt0) REVERT: D 103 SER cc_start: 0.8825 (t) cc_final: 0.8559 (t) REVERT: D 105 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7542 (mmmt) REVERT: D 109 VAL cc_start: 0.9023 (t) cc_final: 0.8786 (m) REVERT: D 122 PHE cc_start: 0.8752 (t80) cc_final: 0.8495 (t80) REVERT: D 123 LYS cc_start: 0.8604 (mmtm) cc_final: 0.8010 (mmmm) REVERT: D 124 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8020 (mt-10) REVERT: D 130 MET cc_start: 0.8073 (tpp) cc_final: 0.7727 (tpp) REVERT: D 134 MET cc_start: 0.7671 (ttt) cc_final: 0.7220 (ttt) REVERT: D 154 PHE cc_start: 0.7697 (t80) cc_final: 0.6981 (t80) REVERT: D 158 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8328 (mtpt) REVERT: D 193 LEU cc_start: 0.8247 (mm) cc_final: 0.8032 (mm) REVERT: D 211 PHE cc_start: 0.8411 (m-80) cc_final: 0.8105 (m-80) REVERT: D 215 PHE cc_start: 0.8494 (m-80) cc_final: 0.7890 (m-80) REVERT: D 218 GLU cc_start: 0.7729 (pp20) cc_final: 0.7202 (pp20) REVERT: D 221 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8253 (mm-40) REVERT: D 245 VAL cc_start: 0.8356 (t) cc_final: 0.7946 (p) REVERT: D 278 MET cc_start: 0.7764 (mmm) cc_final: 0.7411 (mmm) REVERT: D 285 GLU cc_start: 0.8008 (pm20) cc_final: 0.7639 (pm20) REVERT: D 335 MET cc_start: 0.8460 (mmm) cc_final: 0.7736 (mmm) REVERT: D 395 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.8373 (p) REVERT: D 397 SER cc_start: 0.8616 (m) cc_final: 0.7939 (p) REVERT: C 109 VAL cc_start: 0.9006 (t) cc_final: 0.8689 (m) REVERT: C 111 LYS cc_start: 0.8891 (ttpp) cc_final: 0.8601 (ttpp) REVERT: C 120 GLN cc_start: 0.8639 (tm-30) cc_final: 0.8283 (tm-30) REVERT: C 122 PHE cc_start: 0.8658 (t80) cc_final: 0.8406 (t80) REVERT: C 123 LYS cc_start: 0.8688 (mmtm) cc_final: 0.8368 (mmtm) REVERT: C 134 MET cc_start: 0.7693 (tpp) cc_final: 0.7367 (tpt) REVERT: C 154 PHE cc_start: 0.7664 (t80) cc_final: 0.6745 (t80) REVERT: C 158 LYS cc_start: 0.9033 (mtpt) cc_final: 0.7922 (mtpt) REVERT: C 159 LYS cc_start: 0.8521 (mmmt) cc_final: 0.7894 (mmmt) REVERT: C 174 GLN cc_start: 0.8103 (mt0) cc_final: 0.7723 (mp10) REVERT: C 176 ASP cc_start: 0.7931 (m-30) cc_final: 0.7621 (m-30) REVERT: C 204 PHE cc_start: 0.8629 (m-80) cc_final: 0.8242 (m-80) REVERT: C 218 GLU cc_start: 0.7916 (pp20) cc_final: 0.7456 (pp20) REVERT: C 226 GLN cc_start: 0.8439 (tt0) cc_final: 0.8185 (tt0) REVERT: C 228 ILE cc_start: 0.8927 (mt) cc_final: 0.8617 (tp) REVERT: C 243 ARG cc_start: 0.8291 (ttp-170) cc_final: 0.7735 (ptm160) REVERT: C 245 VAL cc_start: 0.8508 (t) cc_final: 0.8087 (p) REVERT: C 281 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7800 (mm-40) REVERT: C 285 GLU cc_start: 0.7976 (pm20) cc_final: 0.7543 (pm20) REVERT: C 352 SER cc_start: 0.8609 (t) cc_final: 0.8355 (t) REVERT: C 356 ARG cc_start: 0.8586 (ttm-80) cc_final: 0.8383 (ttm170) REVERT: C 365 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6651 (tm-30) REVERT: C 397 SER cc_start: 0.8647 (m) cc_final: 0.7795 (p) REVERT: B 105 LYS cc_start: 0.7903 (mmmt) cc_final: 0.7323 (mmmt) REVERT: B 113 MET cc_start: 0.7793 (ttm) cc_final: 0.7532 (ttm) REVERT: B 128 HIS cc_start: 0.8527 (t-170) cc_final: 0.8248 (t70) REVERT: B 132 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8016 (mt-10) REVERT: B 136 VAL cc_start: 0.8710 (t) cc_final: 0.8401 (m) REVERT: B 154 PHE cc_start: 0.7787 (t80) cc_final: 0.7106 (t80) REVERT: B 158 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8478 (mtpt) REVERT: B 195 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7451 (mm-40) REVERT: B 204 PHE cc_start: 0.8530 (m-80) cc_final: 0.8174 (m-80) REVERT: B 228 ILE cc_start: 0.9037 (mm) cc_final: 0.8813 (tp) REVERT: B 239 ARG cc_start: 0.8617 (mtm180) cc_final: 0.8298 (mtp180) REVERT: B 285 GLU cc_start: 0.8082 (pm20) cc_final: 0.7690 (pm20) REVERT: B 335 MET cc_start: 0.8589 (mpp) cc_final: 0.8289 (mmm) REVERT: B 367 LYS cc_start: 0.8332 (ttmm) cc_final: 0.8027 (ttmm) REVERT: B 397 SER cc_start: 0.8593 (m) cc_final: 0.7948 (p) REVERT: B 412 ASP cc_start: 0.7556 (p0) cc_final: 0.7316 (p0) REVERT: B 416 ASP cc_start: 0.8276 (t0) cc_final: 0.7972 (t0) outliers start: 34 outliers final: 23 residues processed: 389 average time/residue: 0.1243 time to fit residues: 63.8380 Evaluate side-chains 400 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 374 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 278 MET Chi-restraints excluded: chain A residue 282 VAL 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 364 VAL Chi-restraints excluded: chain D residue 395 SER 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 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 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 0 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.0060 chunk 77 optimal weight: 0.0980 overall best weight: 0.5200 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.127093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.111846 restraints weight = 14827.256| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.80 r_work: 0.3338 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2280 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= 0.125 Angle : 0.588 10.276 12907 Z= 0.299 Chirality : 0.048 0.213 1500 Planarity : 0.005 0.037 1640 Dihedral : 4.435 19.979 1270 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 3.62 % Allowed : 19.89 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.26), residues: 1176 helix: 0.73 (0.34), residues: 242 sheet: 0.52 (0.27), residues: 379 loop : -1.10 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 375 TYR 0.007 0.001 TYR B 280 PHE 0.043 0.002 PHE C 220 TRP 0.009 0.001 TRP A 100 HIS 0.004 0.001 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9503) covalent geometry : angle 0.58763 (12907) hydrogen bonds : bond 0.03307 ( 358) hydrogen bonds : angle 5.00973 ( 948) *********************** 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 427 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 389 time to evaluate : 0.405 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: 0.8199 (mmmt) cc_final: 0.7679 (mmmt) REVERT: A 111 LYS cc_start: 0.8926 (ttpp) cc_final: 0.8669 (ttpp) REVERT: A 120 GLN cc_start: 0.8690 (tt0) cc_final: 0.7970 (tm-30) REVERT: A 122 PHE cc_start: 0.8715 (t80) cc_final: 0.8426 (t80) REVERT: A 124 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8138 (mt-10) REVERT: A 130 MET cc_start: 0.8051 (tpp) cc_final: 0.7845 (mpp) REVERT: A 131 GLU cc_start: 0.8008 (tt0) cc_final: 0.7722 (tt0) REVERT: A 159 LYS cc_start: 0.8525 (mptt) cc_final: 0.8109 (mptt) REVERT: A 202 MET cc_start: 0.8724 (ptt) cc_final: 0.8477 (ptm) REVERT: A 204 PHE cc_start: 0.8684 (m-80) cc_final: 0.8300 (m-80) REVERT: A 213 THR cc_start: 0.7801 (p) cc_final: 0.7548 (p) REVERT: A 218 GLU cc_start: 0.7844 (pp20) cc_final: 0.7285 (pp20) REVERT: A 219 ASN cc_start: 0.8164 (t0) cc_final: 0.7800 (t0) REVERT: A 228 ILE cc_start: 0.8867 (mt) cc_final: 0.8620 (tp) REVERT: A 245 VAL cc_start: 0.8495 (t) cc_final: 0.8147 (p) REVERT: A 311 VAL cc_start: 0.8398 (p) cc_final: 0.8051 (m) REVERT: A 346 THR cc_start: 0.8648 (m) cc_final: 0.8141 (p) REVERT: A 356 ARG cc_start: 0.8471 (ttm170) cc_final: 0.8197 (tpp80) REVERT: A 365 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6724 (tm-30) REVERT: A 391 ARG cc_start: 0.8303 (ptp-110) cc_final: 0.7722 (ptp-110) REVERT: A 397 SER cc_start: 0.8584 (m) cc_final: 0.7937 (p) REVERT: A 423 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8356 (tt0) REVERT: D 103 SER cc_start: 0.8825 (t) cc_final: 0.8566 (t) REVERT: D 105 LYS cc_start: 0.8173 (mmmt) cc_final: 0.7531 (mmmt) REVERT: D 109 VAL cc_start: 0.9029 (t) cc_final: 0.8796 (m) REVERT: D 122 PHE cc_start: 0.8758 (t80) cc_final: 0.8515 (t80) REVERT: D 123 LYS cc_start: 0.8610 (mmtm) cc_final: 0.8030 (mmmm) REVERT: D 124 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8013 (mt-10) REVERT: D 130 MET cc_start: 0.8049 (tpp) cc_final: 0.7715 (tpp) REVERT: D 134 MET cc_start: 0.7634 (ttt) cc_final: 0.7222 (ttt) REVERT: D 154 PHE cc_start: 0.7649 (t80) cc_final: 0.6902 (t80) REVERT: D 158 LYS cc_start: 0.8873 (mtpt) cc_final: 0.8238 (mtpt) REVERT: D 193 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8058 (mm) REVERT: D 215 PHE cc_start: 0.8508 (m-80) cc_final: 0.7955 (m-80) REVERT: D 221 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8233 (mm-40) REVERT: D 245 VAL cc_start: 0.8390 (t) cc_final: 0.7967 (p) REVERT: D 278 MET cc_start: 0.7755 (mmm) cc_final: 0.7402 (mmm) REVERT: D 285 GLU cc_start: 0.7999 (pm20) cc_final: 0.7670 (pm20) REVERT: D 335 MET cc_start: 0.8453 (mmm) cc_final: 0.7734 (mmm) REVERT: D 385 ARG cc_start: 0.7584 (ttm170) cc_final: 0.7207 (ttm170) REVERT: D 391 ARG cc_start: 0.8302 (ptp90) cc_final: 0.8070 (ptp90) REVERT: D 395 SER cc_start: 0.8625 (OUTLIER) cc_final: 0.8384 (p) REVERT: D 397 SER cc_start: 0.8626 (m) cc_final: 0.7954 (p) REVERT: C 109 VAL cc_start: 0.8997 (t) cc_final: 0.8673 (m) REVERT: C 111 LYS cc_start: 0.8893 (ttpp) cc_final: 0.8610 (ttpp) REVERT: C 120 GLN cc_start: 0.8641 (tm-30) cc_final: 0.8285 (tm-30) REVERT: C 122 PHE cc_start: 0.8629 (t80) cc_final: 0.8375 (t80) REVERT: C 123 LYS cc_start: 0.8683 (mmtm) cc_final: 0.8373 (mmtm) REVERT: C 134 MET cc_start: 0.7715 (tpp) cc_final: 0.7439 (tpt) REVERT: C 154 PHE cc_start: 0.7649 (t80) cc_final: 0.6733 (t80) REVERT: C 158 LYS cc_start: 0.9030 (mtpt) cc_final: 0.7921 (mtpt) REVERT: C 159 LYS cc_start: 0.8499 (mmmt) cc_final: 0.7860 (mmmt) REVERT: C 174 GLN cc_start: 0.8107 (mt0) cc_final: 0.7738 (mp10) REVERT: C 176 ASP cc_start: 0.7939 (m-30) cc_final: 0.7641 (m-30) REVERT: C 204 PHE cc_start: 0.8646 (m-80) cc_final: 0.8262 (m-80) REVERT: C 218 GLU cc_start: 0.7852 (pp20) cc_final: 0.7383 (pp20) REVERT: C 226 GLN cc_start: 0.8379 (tt0) cc_final: 0.8132 (tt0) REVERT: C 243 ARG cc_start: 0.8272 (ttp-170) cc_final: 0.7745 (ptm160) REVERT: C 245 VAL cc_start: 0.8525 (t) cc_final: 0.8108 (p) REVERT: C 281 GLN cc_start: 0.8048 (mm-40) cc_final: 0.7782 (mm-40) REVERT: C 285 GLU cc_start: 0.7965 (pm20) cc_final: 0.7553 (pm20) REVERT: C 352 SER cc_start: 0.8622 (t) cc_final: 0.8375 (t) REVERT: C 356 ARG cc_start: 0.8591 (ttm-80) cc_final: 0.8388 (ttm170) REVERT: C 365 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6640 (tm-30) REVERT: C 397 SER cc_start: 0.8650 (m) cc_final: 0.7812 (p) REVERT: B 105 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7337 (mmmt) REVERT: B 113 MET cc_start: 0.7824 (ttm) cc_final: 0.7594 (ttm) REVERT: B 128 HIS cc_start: 0.8494 (t-170) cc_final: 0.8286 (t70) REVERT: B 132 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7999 (mt-10) REVERT: B 136 VAL cc_start: 0.8683 (t) cc_final: 0.8418 (m) REVERT: B 154 PHE cc_start: 0.7757 (t80) cc_final: 0.7095 (t80) REVERT: B 158 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8494 (mtpt) REVERT: B 195 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7423 (mm-40) REVERT: B 202 MET cc_start: 0.8623 (ptt) cc_final: 0.8386 (ptm) REVERT: B 204 PHE cc_start: 0.8531 (m-80) cc_final: 0.8297 (m-80) REVERT: B 228 ILE cc_start: 0.9032 (mm) cc_final: 0.8809 (tp) REVERT: B 239 ARG cc_start: 0.8628 (mtm180) cc_final: 0.8314 (mtp180) REVERT: B 285 GLU cc_start: 0.8058 (pm20) cc_final: 0.7685 (pm20) REVERT: B 335 MET cc_start: 0.8550 (mpp) cc_final: 0.8268 (mmm) REVERT: B 367 LYS cc_start: 0.8339 (ttmm) cc_final: 0.8039 (ttmm) REVERT: B 397 SER cc_start: 0.8587 (m) cc_final: 0.7969 (p) REVERT: B 412 ASP cc_start: 0.7535 (p0) cc_final: 0.7307 (p0) REVERT: B 416 ASP cc_start: 0.8241 (t0) cc_final: 0.7947 (t0) outliers start: 38 outliers final: 27 residues processed: 401 average time/residue: 0.1314 time to fit residues: 68.4724 Evaluate side-chains 410 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 380 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 A residue 278 MET Chi-restraints excluded: chain A residue 282 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 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 395 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 85 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.126000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110702 restraints weight = 14827.464| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.79 r_work: 0.3328 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9503 Z= 0.163 Angle : 0.610 9.636 12907 Z= 0.313 Chirality : 0.048 0.202 1500 Planarity : 0.005 0.038 1640 Dihedral : 4.507 20.051 1270 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 2.95 % Allowed : 21.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.26), residues: 1176 helix: 0.74 (0.34), residues: 244 sheet: 0.51 (0.27), residues: 383 loop : -1.20 (0.29), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 375 TYR 0.007 0.001 TYR D 280 PHE 0.043 0.003 PHE C 220 TRP 0.009 0.001 TRP A 100 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 9503) covalent geometry : angle 0.60962 (12907) hydrogen bonds : bond 0.03533 ( 358) hydrogen bonds : angle 5.07419 ( 948) *********************** 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 415 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 384 time to evaluate : 0.382 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: 0.8238 (mmmt) cc_final: 0.7734 (mmmt) REVERT: A 111 LYS cc_start: 0.8920 (ttpp) cc_final: 0.8664 (ttpp) REVERT: A 120 GLN cc_start: 0.8723 (tt0) cc_final: 0.8038 (tm-30) REVERT: A 122 PHE cc_start: 0.8749 (t80) cc_final: 0.8430 (t80) REVERT: A 124 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8203 (mt-10) REVERT: A 131 GLU cc_start: 0.8060 (tt0) cc_final: 0.7780 (tt0) REVERT: A 132 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8057 (mt-10) REVERT: A 159 LYS cc_start: 0.8502 (mptt) cc_final: 0.8053 (mptt) REVERT: A 202 MET cc_start: 0.8739 (ptt) cc_final: 0.8494 (ptm) REVERT: A 204 PHE cc_start: 0.8704 (m-80) cc_final: 0.8270 (m-80) REVERT: A 213 THR cc_start: 0.7853 (p) cc_final: 0.7629 (p) REVERT: A 218 GLU cc_start: 0.7850 (pp20) cc_final: 0.7277 (pp20) REVERT: A 228 ILE cc_start: 0.8862 (mt) cc_final: 0.8610 (tp) REVERT: A 245 VAL cc_start: 0.8507 (t) cc_final: 0.8176 (p) REVERT: A 311 VAL cc_start: 0.8421 (p) cc_final: 0.8059 (m) REVERT: A 346 THR cc_start: 0.8630 (m) cc_final: 0.8125 (p) REVERT: A 356 ARG cc_start: 0.8465 (ttm170) cc_final: 0.8187 (tpp80) REVERT: A 365 GLU cc_start: 0.7502 (tm-30) cc_final: 0.6727 (tm-30) REVERT: A 391 ARG cc_start: 0.8323 (ptp-110) cc_final: 0.7740 (ptp-110) REVERT: A 397 SER cc_start: 0.8589 (m) cc_final: 0.7939 (p) REVERT: A 423 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8335 (tt0) REVERT: D 103 SER cc_start: 0.8836 (t) cc_final: 0.8573 (t) REVERT: D 105 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7545 (mmmt) REVERT: D 109 VAL cc_start: 0.9022 (t) cc_final: 0.8780 (m) REVERT: D 122 PHE cc_start: 0.8777 (t80) cc_final: 0.8548 (t80) REVERT: D 123 LYS cc_start: 0.8614 (mmtm) cc_final: 0.7968 (mmmm) REVERT: D 124 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8036 (mt-10) REVERT: D 130 MET cc_start: 0.8155 (tpp) cc_final: 0.7841 (tpp) REVERT: D 134 MET cc_start: 0.7633 (ttt) cc_final: 0.7253 (ttt) REVERT: D 154 PHE cc_start: 0.7671 (t80) cc_final: 0.6861 (t80) REVERT: D 158 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8256 (mtpt) REVERT: D 193 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8064 (mm) REVERT: D 218 GLU cc_start: 0.7723 (pp20) cc_final: 0.7203 (pp20) REVERT: D 221 GLN cc_start: 0.8593 (mm-40) cc_final: 0.8284 (mm-40) REVERT: D 245 VAL cc_start: 0.8395 (t) cc_final: 0.7975 (p) REVERT: D 278 MET cc_start: 0.7764 (mmm) cc_final: 0.7422 (mmm) REVERT: D 285 GLU cc_start: 0.8007 (pm20) cc_final: 0.7678 (pm20) REVERT: D 335 MET cc_start: 0.8451 (mmm) cc_final: 0.7745 (mmm) REVERT: D 385 ARG cc_start: 0.7629 (ttm170) cc_final: 0.7237 (ttm170) REVERT: D 391 ARG cc_start: 0.8336 (ptp90) cc_final: 0.8092 (ptp90) REVERT: D 395 SER cc_start: 0.8639 (OUTLIER) cc_final: 0.8419 (p) REVERT: D 397 SER cc_start: 0.8636 (m) cc_final: 0.7950 (p) REVERT: C 109 VAL cc_start: 0.8992 (t) cc_final: 0.8667 (m) REVERT: C 111 LYS cc_start: 0.8895 (ttpp) cc_final: 0.8608 (ttpp) REVERT: C 122 PHE cc_start: 0.8662 (t80) cc_final: 0.8399 (t80) REVERT: C 123 LYS cc_start: 0.8624 (mmtm) cc_final: 0.8288 (mmtm) REVERT: C 134 MET cc_start: 0.7772 (tpp) cc_final: 0.7310 (tpt) REVERT: C 144 GLU cc_start: 0.7478 (pt0) cc_final: 0.7222 (pt0) REVERT: C 154 PHE cc_start: 0.7635 (t80) cc_final: 0.6742 (t80) REVERT: C 158 LYS cc_start: 0.9039 (mtpt) cc_final: 0.7943 (mtpt) REVERT: C 159 LYS cc_start: 0.8503 (mmmt) cc_final: 0.7872 (mmmt) REVERT: C 174 GLN cc_start: 0.8093 (mt0) cc_final: 0.7825 (mt0) REVERT: C 176 ASP cc_start: 0.7962 (m-30) cc_final: 0.7641 (m-30) REVERT: C 204 PHE cc_start: 0.8654 (m-80) cc_final: 0.8249 (m-80) REVERT: C 218 GLU cc_start: 0.7819 (pp20) cc_final: 0.7327 (pp20) REVERT: C 228 ILE cc_start: 0.8926 (mt) cc_final: 0.8600 (tp) REVERT: C 243 ARG cc_start: 0.8294 (ttp-170) cc_final: 0.7739 (ptm160) REVERT: C 245 VAL cc_start: 0.8550 (t) cc_final: 0.8132 (p) REVERT: C 281 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7811 (mm-40) REVERT: C 285 GLU cc_start: 0.7972 (pm20) cc_final: 0.7557 (pm20) REVERT: C 335 MET cc_start: 0.8464 (mmm) cc_final: 0.8238 (mtt) REVERT: C 346 THR cc_start: 0.8514 (m) cc_final: 0.8022 (p) REVERT: C 352 SER cc_start: 0.8622 (t) cc_final: 0.8376 (t) REVERT: C 356 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8357 (ttm170) REVERT: C 365 GLU cc_start: 0.7440 (tm-30) cc_final: 0.6690 (tm-30) REVERT: C 397 SER cc_start: 0.8655 (m) cc_final: 0.7795 (p) REVERT: B 105 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7379 (mmmt) REVERT: B 128 HIS cc_start: 0.8513 (t-170) cc_final: 0.8308 (t70) REVERT: B 132 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7976 (mt-10) REVERT: B 136 VAL cc_start: 0.8622 (t) cc_final: 0.8389 (m) REVERT: B 154 PHE cc_start: 0.7774 (t80) cc_final: 0.7129 (t80) REVERT: B 158 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8488 (mtpt) REVERT: B 195 GLN cc_start: 0.7853 (mm-40) cc_final: 0.7432 (mm-40) REVERT: B 202 MET cc_start: 0.8593 (ptt) cc_final: 0.8374 (ptm) REVERT: B 204 PHE cc_start: 0.8539 (m-80) cc_final: 0.8311 (m-80) REVERT: B 228 ILE cc_start: 0.9030 (mm) cc_final: 0.8813 (tp) REVERT: B 239 ARG cc_start: 0.8619 (mtm180) cc_final: 0.8306 (mtp180) REVERT: B 285 GLU cc_start: 0.8078 (pm20) cc_final: 0.7697 (pm20) REVERT: B 311 VAL cc_start: 0.8558 (p) cc_final: 0.8231 (m) REVERT: B 335 MET cc_start: 0.8547 (mpp) cc_final: 0.8281 (mmm) REVERT: B 367 LYS cc_start: 0.8353 (ttmm) cc_final: 0.8058 (ttmm) REVERT: B 397 SER cc_start: 0.8593 (m) cc_final: 0.7948 (p) REVERT: B 412 ASP cc_start: 0.7534 (p0) cc_final: 0.7298 (p0) REVERT: B 416 ASP cc_start: 0.8243 (t0) cc_final: 0.7953 (t0) outliers start: 31 outliers final: 25 residues processed: 395 average time/residue: 0.1332 time to fit residues: 68.2440 Evaluate side-chains 410 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 382 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 278 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 423 GLN 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 395 SER Chi-restraints excluded: chain D residue 425 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 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 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 107 optimal weight: 1.9990 chunk 104 optimal weight: 0.0870 chunk 24 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.126647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.111290 restraints weight = 14836.336| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.82 r_work: 0.3337 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9503 Z= 0.143 Angle : 0.605 9.906 12907 Z= 0.310 Chirality : 0.048 0.240 1500 Planarity : 0.005 0.037 1640 Dihedral : 4.516 19.716 1270 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 2.95 % Allowed : 22.36 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.26), residues: 1176 helix: 0.84 (0.35), residues: 238 sheet: 0.62 (0.29), residues: 338 loop : -1.04 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 375 TYR 0.007 0.001 TYR D 280 PHE 0.048 0.002 PHE C 220 TRP 0.010 0.001 TRP A 100 HIS 0.007 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9503) covalent geometry : angle 0.60533 (12907) hydrogen bonds : bond 0.03450 ( 358) hydrogen bonds : angle 5.05453 ( 948) ********************** 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 415 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 384 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8272 (mmmt) cc_final: 0.7698 (mmmt) REVERT: A 111 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8649 (ttpp) REVERT: A 120 GLN cc_start: 0.8707 (tt0) cc_final: 0.8050 (tm-30) REVERT: A 122 PHE cc_start: 0.8759 (t80) cc_final: 0.8456 (t80) REVERT: A 123 LYS cc_start: 0.8862 (mttm) cc_final: 0.8469 (mttm) REVERT: A 124 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8286 (mt-10) REVERT: A 134 MET cc_start: 0.7762 (tpp) cc_final: 0.7122 (tpp) REVERT: A 202 MET cc_start: 0.8733 (ptt) cc_final: 0.8454 (ptm) REVERT: A 213 THR cc_start: 0.7847 (p) cc_final: 0.7625 (p) REVERT: A 218 GLU cc_start: 0.7729 (pp20) cc_final: 0.7149 (pp20) REVERT: A 228 ILE cc_start: 0.8822 (mt) cc_final: 0.8556 (tp) REVERT: A 245 VAL cc_start: 0.8479 (t) cc_final: 0.8132 (p) REVERT: A 311 VAL cc_start: 0.8408 (p) cc_final: 0.8032 (m) REVERT: A 346 THR cc_start: 0.8619 (m) cc_final: 0.8113 (p) REVERT: A 356 ARG cc_start: 0.8463 (ttm170) cc_final: 0.8189 (tpp80) REVERT: A 365 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6704 (tm-30) REVERT: A 391 ARG cc_start: 0.8323 (ptp-110) cc_final: 0.7747 (ptp-110) REVERT: A 397 SER cc_start: 0.8579 (m) cc_final: 0.7923 (p) REVERT: A 423 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: D 103 SER cc_start: 0.8845 (t) cc_final: 0.8611 (t) REVERT: D 105 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7528 (mmmt) REVERT: D 109 VAL cc_start: 0.9013 (t) cc_final: 0.8770 (m) REVERT: D 118 LEU cc_start: 0.8773 (mt) cc_final: 0.8559 (mt) REVERT: D 122 PHE cc_start: 0.8765 (t80) cc_final: 0.8560 (t80) REVERT: D 123 LYS cc_start: 0.8593 (mmtm) cc_final: 0.7956 (mmmm) REVERT: D 124 GLU cc_start: 0.8561 (mt-10) cc_final: 0.7985 (mt-10) REVERT: D 130 MET cc_start: 0.8186 (tpp) cc_final: 0.7865 (tpp) REVERT: D 134 MET cc_start: 0.7613 (ttt) cc_final: 0.7248 (ttt) REVERT: D 154 PHE cc_start: 0.7663 (t80) cc_final: 0.6887 (t80) REVERT: D 158 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8249 (mtpt) REVERT: D 193 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8039 (mm) REVERT: D 218 GLU cc_start: 0.7754 (pp20) cc_final: 0.7218 (pp20) REVERT: D 221 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8282 (mm-40) REVERT: D 245 VAL cc_start: 0.8389 (t) cc_final: 0.7964 (p) REVERT: D 278 MET cc_start: 0.7748 (mmm) cc_final: 0.7342 (mmm) REVERT: D 285 GLU cc_start: 0.8011 (pm20) cc_final: 0.7669 (pm20) REVERT: D 335 MET cc_start: 0.8443 (mmm) cc_final: 0.7695 (mmm) REVERT: D 385 ARG cc_start: 0.7609 (ttm170) cc_final: 0.7217 (ttm170) REVERT: D 391 ARG cc_start: 0.8324 (ptp90) cc_final: 0.8086 (ptp90) REVERT: D 395 SER cc_start: 0.8639 (OUTLIER) cc_final: 0.8422 (p) REVERT: D 397 SER cc_start: 0.8622 (m) cc_final: 0.7937 (p) REVERT: C 109 VAL cc_start: 0.8989 (t) cc_final: 0.8668 (m) REVERT: C 111 LYS cc_start: 0.8910 (ttpp) cc_final: 0.8616 (ttpp) REVERT: C 122 PHE cc_start: 0.8641 (t80) cc_final: 0.8385 (t80) REVERT: C 123 LYS cc_start: 0.8660 (mmtm) cc_final: 0.8360 (mmtm) REVERT: C 134 MET cc_start: 0.7799 (tpp) cc_final: 0.7362 (tpt) REVERT: C 154 PHE cc_start: 0.7666 (t80) cc_final: 0.6757 (t80) REVERT: C 158 LYS cc_start: 0.9031 (mtpt) cc_final: 0.7920 (mtpt) REVERT: C 159 LYS cc_start: 0.8477 (mmmt) cc_final: 0.7832 (mmmt) REVERT: C 174 GLN cc_start: 0.8096 (mt0) cc_final: 0.7833 (mt0) REVERT: C 176 ASP cc_start: 0.7969 (m-30) cc_final: 0.7648 (m-30) REVERT: C 204 PHE cc_start: 0.8637 (m-80) cc_final: 0.8229 (m-80) REVERT: C 218 GLU cc_start: 0.7840 (pp20) cc_final: 0.7320 (pp20) REVERT: C 228 ILE cc_start: 0.8911 (mt) cc_final: 0.8592 (tp) REVERT: C 243 ARG cc_start: 0.8303 (ttp-170) cc_final: 0.7746 (ptm160) REVERT: C 245 VAL cc_start: 0.8532 (t) cc_final: 0.8118 (p) REVERT: C 285 GLU cc_start: 0.7979 (pm20) cc_final: 0.7557 (pm20) REVERT: C 346 THR cc_start: 0.8505 (m) cc_final: 0.8009 (p) REVERT: C 352 SER cc_start: 0.8610 (t) cc_final: 0.8355 (t) REVERT: C 356 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8369 (ttm170) REVERT: C 365 GLU cc_start: 0.7434 (tm-30) cc_final: 0.6684 (tm-30) REVERT: C 397 SER cc_start: 0.8646 (m) cc_final: 0.7807 (p) REVERT: B 105 LYS cc_start: 0.7954 (mmmt) cc_final: 0.7359 (mmmt) REVERT: B 113 MET cc_start: 0.7735 (ttm) cc_final: 0.7470 (ttm) REVERT: B 120 GLN cc_start: 0.8524 (tt0) cc_final: 0.8263 (tm-30) REVERT: B 154 PHE cc_start: 0.7780 (t80) cc_final: 0.7123 (t80) REVERT: B 158 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8474 (mtpt) REVERT: B 195 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7438 (mm-40) REVERT: B 202 MET cc_start: 0.8608 (ptt) cc_final: 0.8367 (ptm) REVERT: B 204 PHE cc_start: 0.8505 (m-80) cc_final: 0.8267 (m-80) REVERT: B 228 ILE cc_start: 0.9003 (mm) cc_final: 0.8794 (tp) REVERT: B 278 MET cc_start: 0.7556 (mmm) cc_final: 0.7353 (mmm) REVERT: B 285 GLU cc_start: 0.8051 (pm20) cc_final: 0.7670 (pm20) REVERT: B 335 MET cc_start: 0.8540 (mpp) cc_final: 0.8283 (mmm) REVERT: B 367 LYS cc_start: 0.8328 (ttmm) cc_final: 0.8025 (ttmm) REVERT: B 397 SER cc_start: 0.8577 (m) cc_final: 0.7947 (p) REVERT: B 412 ASP cc_start: 0.7501 (p0) cc_final: 0.7250 (p0) REVERT: B 416 ASP cc_start: 0.8216 (t0) cc_final: 0.7922 (t0) outliers start: 31 outliers final: 26 residues processed: 395 average time/residue: 0.1326 time to fit residues: 68.0287 Evaluate side-chains 411 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 382 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 A residue 278 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 423 GLN 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 395 SER 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 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 33 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 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 ** 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 = 0.3692 r_free = 0.3692 target = 0.126348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.110965 restraints weight = 14787.469| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.82 r_work: 0.3328 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9503 Z= 0.148 Angle : 0.604 9.669 12907 Z= 0.310 Chirality : 0.048 0.191 1500 Planarity : 0.005 0.037 1640 Dihedral : 4.530 22.282 1270 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 3.14 % Allowed : 22.26 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.26), residues: 1176 helix: 0.77 (0.35), residues: 246 sheet: 0.68 (0.29), residues: 337 loop : -1.02 (0.28), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 375 TYR 0.008 0.001 TYR C 280 PHE 0.046 0.002 PHE C 220 TRP 0.009 0.001 TRP A 100 HIS 0.007 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9503) covalent geometry : angle 0.60367 (12907) hydrogen bonds : bond 0.03459 ( 358) hydrogen bonds : angle 5.02012 ( 948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2288.19 seconds wall clock time: 40 minutes 8.04 seconds (2408.04 seconds total)