Starting phenix.real_space_refine on Wed Sep 17 11:49:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z65_39792/09_2025/8z65_39792.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z65_39792/09_2025/8z65_39792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z65_39792/09_2025/8z65_39792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z65_39792/09_2025/8z65_39792.map" model { file = "/net/cci-nas-00/data/ceres_data/8z65_39792/09_2025/8z65_39792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z65_39792/09_2025/8z65_39792.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 52 5.16 5 C 5415 2.51 5 N 1481 2.21 5 O 1546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s 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: 8494 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1860 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2447 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 7, 'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "G" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 321 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "S" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1695 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2171 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'ARG:plan': 7, 'ASP:plan': 8, 'PHE:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 6, 'ASN:plan1': 3, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 149 Time building chain proxies: 2.40, per 1000 atoms: 0.28 Number of scatterers: 8494 At special positions: 0 Unit cell: (87.74, 121.36, 126.28, 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 52 16.00 O 1546 8.00 N 1481 7.00 C 5415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 554.5 milliseconds Enol-peptide restraints added in 1.4 microseconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 37.5% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 6 through 39 removed outlier: 3.506A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.561A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.554A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.542A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 14 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.891A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.091A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 48 removed outlier: 3.832A pdb=" N PHE R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 52 through 78 removed outlier: 3.565A pdb=" N ASN R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 120 removed outlier: 4.550A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 129 Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 151 through 155 Processing helix chain 'R' and resid 177 through 190 removed outlier: 3.616A pdb=" N PHE R 190 " --> pdb=" O VAL R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 210 removed outlier: 4.299A pdb=" N GLY R 210 " --> pdb=" O ARG R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 252 Proline residue: R 239 - end of helix removed outlier: 3.672A pdb=" N ILE R 250 " --> pdb=" O SER R 246 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR R 251 " --> pdb=" O ARG R 247 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU R 252 " --> pdb=" O SER R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 263 Processing helix chain 'R' and resid 264 through 276 Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 304 removed outlier: 3.647A pdb=" N ASN R 303 " --> pdb=" O LYS R 299 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 223 removed outlier: 4.634A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLY A 47 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 253 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.320A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.752A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.657A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.534A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.906A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.434A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.259A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.439A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.439A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 147 through 148 removed outlier: 6.152A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1299 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: 1.56 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1355 1.30 - 1.43: 2433 1.43 - 1.56: 4831 1.56 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 8691 Sorted by residual: bond pdb=" C GLU A 27 " pdb=" O GLU A 27 " ideal model delta sigma weight residual 1.237 1.167 0.069 1.17e-02 7.31e+03 3.52e+01 bond pdb=" CZ ARG A 15 " pdb=" NH2 ARG A 15 " ideal model delta sigma weight residual 1.330 1.256 0.074 1.30e-02 5.92e+03 3.22e+01 bond pdb=" CA ASP A 9 " pdb=" CB ASP A 9 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.56e-02 4.11e+03 3.08e+01 bond pdb=" CA ASP A 9 " pdb=" C ASP A 9 " ideal model delta sigma weight residual 1.523 1.458 0.066 1.30e-02 5.92e+03 2.54e+01 bond pdb=" CA HIS R 269 " pdb=" C HIS R 269 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.29e-02 6.01e+03 2.01e+01 ... (remaining 8686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 11602 2.39 - 4.78: 215 4.78 - 7.17: 28 7.17 - 9.55: 7 9.55 - 11.94: 3 Bond angle restraints: 11855 Sorted by residual: angle pdb=" N ARG R 162 " pdb=" CA ARG R 162 " pdb=" C ARG R 162 " ideal model delta sigma weight residual 112.54 123.31 -10.77 1.22e+00 6.72e-01 7.79e+01 angle pdb=" C HIS R 165 " pdb=" CA HIS R 165 " pdb=" CB HIS R 165 " ideal model delta sigma weight residual 110.62 99.99 10.63 1.51e+00 4.39e-01 4.96e+01 angle pdb=" N ASP R 161 " pdb=" CA ASP R 161 " pdb=" C ASP R 161 " ideal model delta sigma weight residual 109.24 118.49 -9.25 1.51e+00 4.39e-01 3.76e+01 angle pdb=" N TRP R 256 " pdb=" CA TRP R 256 " pdb=" C TRP R 256 " ideal model delta sigma weight residual 111.07 104.69 6.38 1.07e+00 8.73e-01 3.55e+01 angle pdb=" N VAL R 186 " pdb=" CA VAL R 186 " pdb=" C VAL R 186 " ideal model delta sigma weight residual 110.62 117.01 -6.39 1.14e+00 7.69e-01 3.15e+01 ... (remaining 11850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 4564 16.72 - 33.44: 393 33.44 - 50.16: 75 50.16 - 66.88: 13 66.88 - 83.59: 8 Dihedral angle restraints: 5053 sinusoidal: 1717 harmonic: 3336 Sorted by residual: dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 152.16 27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" C GLN A 29 " pdb=" N GLN A 29 " pdb=" CA GLN A 29 " pdb=" CB GLN A 29 " ideal model delta harmonic sigma weight residual -122.60 -135.48 12.88 0 2.50e+00 1.60e-01 2.65e+01 dihedral pdb=" C LYS A 17 " pdb=" N LYS A 17 " pdb=" CA LYS A 17 " pdb=" CB LYS A 17 " ideal model delta harmonic sigma weight residual -122.60 -135.10 12.50 0 2.50e+00 1.60e-01 2.50e+01 ... (remaining 5050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1325 0.116 - 0.232: 32 0.232 - 0.348: 5 0.348 - 0.465: 1 0.465 - 0.581: 3 Chirality restraints: 1366 Sorted by residual: chirality pdb=" CA HIS R 269 " pdb=" N HIS R 269 " pdb=" C HIS R 269 " pdb=" CB HIS R 269 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" CA GLN A 29 " pdb=" N GLN A 29 " pdb=" C GLN A 29 " pdb=" CB GLN A 29 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" CA LYS A 17 " pdb=" N LYS A 17 " pdb=" C LYS A 17 " pdb=" CB LYS A 17 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.70e+00 ... (remaining 1363 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.022 2.00e-02 2.50e+03 1.67e-02 5.57e+00 pdb=" CG TYR B 59 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO S 75 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 260 " -0.011 2.00e-02 2.50e+03 1.40e-02 3.44e+00 pdb=" CG PHE R 260 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE R 260 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE R 260 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE R 260 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 260 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE R 260 " -0.000 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 75 2.60 - 3.17: 7267 3.17 - 3.75: 13156 3.75 - 4.32: 18392 4.32 - 4.90: 30999 Nonbonded interactions: 69889 Sorted by model distance: nonbonded pdb=" OG SER R 112 " pdb=" OG SER R 200 " model vdw 2.023 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.063 3.040 nonbonded pdb=" NZ LYS A 243 " pdb=" OD2 ASP B 228 " model vdw 2.159 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.189 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.202 3.040 ... (remaining 69884 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.960 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.480 Find NCS groups from input model: 0.050 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:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.008 0.087 8693 Z= 0.429 Angle : 0.818 11.942 11859 Z= 0.482 Chirality : 0.060 0.581 1366 Planarity : 0.005 0.049 1513 Dihedral : 13.564 83.594 2895 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.24 % Allowed : 0.73 % Favored : 99.03 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 5.41 % 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: -0.38 (0.25), residues: 1131 helix: 0.69 (0.27), residues: 381 sheet: -0.07 (0.30), residues: 289 loop : -1.11 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 180 TYR 0.040 0.003 TYR B 59 PHE 0.032 0.002 PHE R 260 TRP 0.015 0.002 TRP A 244 HIS 0.018 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00800 ( 8691) covalent geometry : angle 0.81764 (11855) SS BOND : bond 0.00084 ( 2) SS BOND : angle 1.35901 ( 4) hydrogen bonds : bond 0.18118 ( 449) hydrogen bonds : angle 7.34065 ( 1299) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 221 LYS cc_start: 0.7680 (mppt) cc_final: 0.7444 (mppt) REVERT: A 258 VAL cc_start: 0.8657 (p) cc_final: 0.8311 (t) REVERT: A 347 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7653 (ttm-80) REVERT: B 258 ASP cc_start: 0.6702 (t70) cc_final: 0.6419 (t0) REVERT: S 116 THR cc_start: 0.8119 (t) cc_final: 0.7831 (p) REVERT: R 104 SER cc_start: 0.7867 (m) cc_final: 0.7663 (m) REVERT: R 141 VAL cc_start: 0.8343 (p) cc_final: 0.8008 (t) REVERT: R 174 MET cc_start: 0.7142 (tpp) cc_final: 0.6686 (mmm) REVERT: R 190 PHE cc_start: 0.7758 (t80) cc_final: 0.7494 (t80) outliers start: 2 outliers final: 2 residues processed: 230 average time/residue: 0.4878 time to fit residues: 120.5504 Evaluate side-chains 207 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain R residue 105 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 88 ASN S 39 GLN R 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.120657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.104286 restraints weight = 12914.136| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.82 r_work: 0.3206 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8693 Z= 0.214 Angle : 0.639 12.147 11859 Z= 0.338 Chirality : 0.045 0.157 1366 Planarity : 0.005 0.048 1513 Dihedral : 4.975 39.784 1241 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.27 % Allowed : 11.03 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.13 (0.25), residues: 1131 helix: 1.45 (0.27), residues: 371 sheet: 0.10 (0.31), residues: 278 loop : -0.98 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 202 TYR 0.029 0.002 TYR B 59 PHE 0.016 0.002 PHE B 151 TRP 0.019 0.002 TRP B 339 HIS 0.012 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 8691) covalent geometry : angle 0.63848 (11855) SS BOND : bond 0.00158 ( 2) SS BOND : angle 1.12910 ( 4) hydrogen bonds : bond 0.05069 ( 449) hydrogen bonds : angle 5.20550 ( 1299) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 56 ILE cc_start: 0.7770 (mt) cc_final: 0.7505 (tp) REVERT: A 221 LYS cc_start: 0.8182 (mppt) cc_final: 0.7793 (mppt) REVERT: A 299 GLU cc_start: 0.7352 (mt-10) cc_final: 0.7132 (mt-10) REVERT: A 347 ARG cc_start: 0.8307 (ttm-80) cc_final: 0.8089 (ttp-110) REVERT: A 368 ASP cc_start: 0.6997 (m-30) cc_final: 0.6597 (m-30) REVERT: B 136 SER cc_start: 0.8458 (t) cc_final: 0.8243 (m) REVERT: B 156 GLN cc_start: 0.8586 (mt0) cc_final: 0.8310 (mt0) REVERT: B 170 ASP cc_start: 0.7987 (t0) cc_final: 0.7705 (t70) REVERT: B 228 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8079 (p0) REVERT: B 258 ASP cc_start: 0.7350 (t70) cc_final: 0.6835 (t0) REVERT: B 304 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7923 (mmm-85) REVERT: B 323 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7592 (p0) REVERT: S 115 THR cc_start: 0.8336 (p) cc_final: 0.8061 (m) REVERT: S 245 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8028 (mm) REVERT: R 95 PHE cc_start: 0.7212 (t80) cc_final: 0.6727 (t80) REVERT: R 174 MET cc_start: 0.7126 (tpp) cc_final: 0.6764 (mmm) REVERT: R 280 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8296 (m) outliers start: 27 outliers final: 11 residues processed: 230 average time/residue: 0.4392 time to fit residues: 109.6400 Evaluate side-chains 220 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 276 SER Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 18 optimal weight: 0.5980 chunk 83 optimal weight: 0.0170 chunk 64 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 0.0970 chunk 108 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 230 ASN B 237 ASN S 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107781 restraints weight = 12699.187| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.75 r_work: 0.3257 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8693 Z= 0.118 Angle : 0.547 10.579 11859 Z= 0.288 Chirality : 0.042 0.166 1366 Planarity : 0.004 0.050 1513 Dihedral : 4.466 43.630 1239 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.03 % Allowed : 16.85 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.45 (0.26), residues: 1131 helix: 1.75 (0.27), residues: 378 sheet: 0.19 (0.31), residues: 271 loop : -0.78 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 124 TYR 0.013 0.001 TYR R 66 PHE 0.015 0.001 PHE A 222 TRP 0.018 0.002 TRP B 339 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8691) covalent geometry : angle 0.54701 (11855) SS BOND : bond 0.00244 ( 2) SS BOND : angle 0.69917 ( 4) hydrogen bonds : bond 0.03999 ( 449) hydrogen bonds : angle 4.63459 ( 1299) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8380 (t) cc_final: 0.8017 (t) REVERT: A 56 ILE cc_start: 0.7668 (mt) cc_final: 0.7461 (tp) REVERT: A 221 LYS cc_start: 0.8075 (mppt) cc_final: 0.7653 (mppt) REVERT: A 299 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7122 (mt-10) REVERT: A 347 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.8006 (ttp-110) REVERT: A 368 ASP cc_start: 0.6953 (m-30) cc_final: 0.6551 (m-30) REVERT: A 380 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.7265 (ttp80) REVERT: B 165 THR cc_start: 0.7236 (m) cc_final: 0.6995 (p) REVERT: B 170 ASP cc_start: 0.7879 (t0) cc_final: 0.7598 (t70) REVERT: B 228 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7978 (OUTLIER) REVERT: B 258 ASP cc_start: 0.7333 (t70) cc_final: 0.6857 (t0) REVERT: S 7 SER cc_start: 0.8353 (OUTLIER) cc_final: 0.8016 (m) REVERT: S 219 LEU cc_start: 0.8784 (tp) cc_final: 0.8546 (mm) REVERT: S 227 TYR cc_start: 0.8261 (m-80) cc_final: 0.7988 (m-80) REVERT: S 245 LEU cc_start: 0.8235 (mt) cc_final: 0.8029 (mm) REVERT: R 174 MET cc_start: 0.7149 (tpp) cc_final: 0.6923 (mmm) outliers start: 25 outliers final: 10 residues processed: 214 average time/residue: 0.4827 time to fit residues: 111.2349 Evaluate side-chains 218 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.104634 restraints weight = 13011.246| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.86 r_work: 0.3204 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8693 Z= 0.187 Angle : 0.586 9.656 11859 Z= 0.309 Chirality : 0.043 0.138 1366 Planarity : 0.005 0.054 1513 Dihedral : 4.636 46.408 1239 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.48 % Allowed : 17.09 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.38 (0.25), residues: 1131 helix: 1.73 (0.27), residues: 373 sheet: 0.09 (0.30), residues: 277 loop : -0.80 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 124 TYR 0.016 0.002 TYR A 37 PHE 0.018 0.002 PHE R 93 TRP 0.016 0.002 TRP B 339 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 8691) covalent geometry : angle 0.58632 (11855) SS BOND : bond 0.00229 ( 2) SS BOND : angle 0.97114 ( 4) hydrogen bonds : bond 0.04433 ( 449) hydrogen bonds : angle 4.73003 ( 1299) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8503 (t) cc_final: 0.8184 (t) REVERT: A 56 ILE cc_start: 0.7731 (mt) cc_final: 0.7473 (tp) REVERT: A 258 VAL cc_start: 0.8720 (p) cc_final: 0.8470 (t) REVERT: A 299 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7171 (mt-10) REVERT: A 347 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7937 (ttp-110) REVERT: A 368 ASP cc_start: 0.7029 (m-30) cc_final: 0.6603 (m-30) REVERT: A 380 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7287 (ttp80) REVERT: B 157 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8138 (tp) REVERT: B 190 LEU cc_start: 0.8345 (tp) cc_final: 0.8113 (tt) REVERT: B 228 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7971 (p0) REVERT: B 258 ASP cc_start: 0.7416 (t70) cc_final: 0.6911 (t0) REVERT: S 7 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.8001 (m) REVERT: S 219 LEU cc_start: 0.8830 (tp) cc_final: 0.8604 (mm) REVERT: S 245 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8080 (mm) outliers start: 37 outliers final: 25 residues processed: 226 average time/residue: 0.4496 time to fit residues: 109.9663 Evaluate side-chains 228 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 193 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 245 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 276 SER Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 0.9980 chunk 77 optimal weight: 0.0870 chunk 79 optimal weight: 0.0170 chunk 97 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.122966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106794 restraints weight = 12910.143| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.77 r_work: 0.3240 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8693 Z= 0.128 Angle : 0.550 12.675 11859 Z= 0.287 Chirality : 0.042 0.138 1366 Planarity : 0.004 0.052 1513 Dihedral : 4.445 46.526 1239 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.39 % Allowed : 19.27 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.54 (0.26), residues: 1131 helix: 1.82 (0.27), residues: 383 sheet: 0.03 (0.31), residues: 286 loop : -0.63 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 124 TYR 0.015 0.001 TYR B 59 PHE 0.014 0.001 PHE A 222 TRP 0.015 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8691) covalent geometry : angle 0.55004 (11855) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.68053 ( 4) hydrogen bonds : bond 0.03861 ( 449) hydrogen bonds : angle 4.52791 ( 1299) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8426 (t) cc_final: 0.8100 (t) REVERT: A 53 LYS cc_start: 0.8012 (pttt) cc_final: 0.7792 (pttt) REVERT: A 56 ILE cc_start: 0.7673 (mt) cc_final: 0.7438 (tp) REVERT: A 299 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7132 (mt-10) REVERT: A 347 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.8010 (ttp-110) REVERT: A 368 ASP cc_start: 0.6953 (m-30) cc_final: 0.6533 (m-30) REVERT: A 380 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7268 (ttp80) REVERT: B 170 ASP cc_start: 0.7882 (t0) cc_final: 0.7598 (t70) REVERT: B 175 GLN cc_start: 0.7706 (mm110) cc_final: 0.7494 (mm110) REVERT: B 228 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7952 (p0) REVERT: B 258 ASP cc_start: 0.7420 (t70) cc_final: 0.6930 (t0) REVERT: B 304 ARG cc_start: 0.7975 (mmm-85) cc_final: 0.7690 (mmm-85) REVERT: B 340 ASN cc_start: 0.7476 (t0) cc_final: 0.7098 (t0) REVERT: S 7 SER cc_start: 0.8337 (OUTLIER) cc_final: 0.8025 (m) REVERT: S 115 THR cc_start: 0.8319 (p) cc_final: 0.8096 (m) REVERT: S 219 LEU cc_start: 0.8781 (tp) cc_final: 0.8566 (mm) REVERT: R 174 MET cc_start: 0.6927 (OUTLIER) cc_final: 0.6581 (mmm) REVERT: R 242 VAL cc_start: 0.8285 (t) cc_final: 0.8016 (p) outliers start: 28 outliers final: 17 residues processed: 220 average time/residue: 0.4674 time to fit residues: 111.3207 Evaluate side-chains 227 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 0.0570 chunk 66 optimal weight: 0.3980 chunk 97 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 0.0020 chunk 108 optimal weight: 0.0370 chunk 50 optimal weight: 0.8980 overall best weight: 0.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.124800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107914 restraints weight = 12724.213| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.89 r_work: 0.3255 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8693 Z= 0.109 Angle : 0.535 11.215 11859 Z= 0.277 Chirality : 0.041 0.132 1366 Planarity : 0.004 0.052 1513 Dihedral : 4.296 47.763 1239 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.79 % Allowed : 20.61 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.66 (0.26), residues: 1131 helix: 2.01 (0.27), residues: 383 sheet: 0.11 (0.31), residues: 286 loop : -0.66 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 124 TYR 0.012 0.001 TYR A 37 PHE 0.014 0.001 PHE A 222 TRP 0.024 0.002 TRP R 142 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8691) covalent geometry : angle 0.53508 (11855) SS BOND : bond 0.00277 ( 2) SS BOND : angle 0.65606 ( 4) hydrogen bonds : bond 0.03583 ( 449) hydrogen bonds : angle 4.36510 ( 1299) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8374 (t) cc_final: 0.8048 (t) REVERT: A 221 LYS cc_start: 0.7984 (mppt) cc_final: 0.7516 (mppt) REVERT: A 299 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7166 (mt-10) REVERT: A 347 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7988 (ttp-110) REVERT: A 368 ASP cc_start: 0.7009 (m-30) cc_final: 0.6562 (m-30) REVERT: A 391 TYR cc_start: 0.8527 (m-80) cc_final: 0.8241 (m-80) REVERT: B 110 ASN cc_start: 0.8382 (m110) cc_final: 0.8012 (m-40) REVERT: B 155 ASN cc_start: 0.7946 (t0) cc_final: 0.7627 (t0) REVERT: B 170 ASP cc_start: 0.7836 (t0) cc_final: 0.7479 (t70) REVERT: B 175 GLN cc_start: 0.7738 (mm110) cc_final: 0.7499 (mm110) REVERT: B 228 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7952 (p0) REVERT: B 258 ASP cc_start: 0.7447 (t70) cc_final: 0.6952 (t0) REVERT: B 340 ASN cc_start: 0.7367 (t0) cc_final: 0.7024 (t0) REVERT: S 115 THR cc_start: 0.8295 (p) cc_final: 0.8027 (m) REVERT: S 219 LEU cc_start: 0.8732 (tp) cc_final: 0.8511 (mm) REVERT: R 174 MET cc_start: 0.6956 (mmm) cc_final: 0.6649 (mmm) REVERT: R 242 VAL cc_start: 0.8308 (t) cc_final: 0.8037 (p) outliers start: 23 outliers final: 15 residues processed: 215 average time/residue: 0.4799 time to fit residues: 111.3210 Evaluate side-chains 219 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 186 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 110 optimal weight: 0.0570 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 24 optimal weight: 0.0000 chunk 21 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.106414 restraints weight = 12833.786| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.77 r_work: 0.3235 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8693 Z= 0.154 Angle : 0.572 10.564 11859 Z= 0.296 Chirality : 0.043 0.135 1366 Planarity : 0.004 0.051 1513 Dihedral : 4.461 47.992 1239 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.88 % Allowed : 21.21 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.69 (0.26), residues: 1131 helix: 1.94 (0.26), residues: 384 sheet: 0.19 (0.30), residues: 285 loop : -0.60 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 124 TYR 0.016 0.002 TYR A 37 PHE 0.015 0.002 PHE A 222 TRP 0.025 0.002 TRP R 142 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8691) covalent geometry : angle 0.57165 (11855) SS BOND : bond 0.00299 ( 2) SS BOND : angle 1.11346 ( 4) hydrogen bonds : bond 0.04013 ( 449) hydrogen bonds : angle 4.48562 ( 1299) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8466 (t) cc_final: 0.8146 (t) REVERT: A 56 ILE cc_start: 0.7702 (mt) cc_final: 0.7462 (tp) REVERT: A 221 LYS cc_start: 0.8022 (mppt) cc_final: 0.7553 (mppt) REVERT: A 299 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7171 (mt-10) REVERT: A 347 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7993 (ttp-110) REVERT: A 368 ASP cc_start: 0.6959 (m-30) cc_final: 0.6549 (m-30) REVERT: A 380 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7335 (ttp80) REVERT: B 155 ASN cc_start: 0.7959 (t0) cc_final: 0.7522 (t0) REVERT: B 165 THR cc_start: 0.7131 (OUTLIER) cc_final: 0.6903 (p) REVERT: B 170 ASP cc_start: 0.7890 (t0) cc_final: 0.7689 (t0) REVERT: B 175 GLN cc_start: 0.7713 (mm110) cc_final: 0.7462 (mm110) REVERT: B 228 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7915 (p0) REVERT: B 258 ASP cc_start: 0.7426 (t70) cc_final: 0.6938 (t0) REVERT: B 340 ASN cc_start: 0.7351 (t0) cc_final: 0.7002 (t0) REVERT: S 7 SER cc_start: 0.8297 (OUTLIER) cc_final: 0.8059 (m) REVERT: S 219 LEU cc_start: 0.8796 (tp) cc_final: 0.8570 (mm) REVERT: R 174 MET cc_start: 0.7001 (mmm) cc_final: 0.6651 (mmm) REVERT: R 186 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7733 (t) REVERT: R 242 VAL cc_start: 0.8286 (t) cc_final: 0.8011 (p) REVERT: R 271 SER cc_start: 0.7596 (p) cc_final: 0.7368 (m) REVERT: R 285 LEU cc_start: 0.8117 (mt) cc_final: 0.7888 (mp) outliers start: 32 outliers final: 19 residues processed: 221 average time/residue: 0.4648 time to fit residues: 110.9406 Evaluate side-chains 230 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 276 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 47 optimal weight: 0.0470 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 93 optimal weight: 0.0970 chunk 61 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.123041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106873 restraints weight = 12793.009| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.78 r_work: 0.3245 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8693 Z= 0.135 Angle : 0.556 9.770 11859 Z= 0.287 Chirality : 0.042 0.166 1366 Planarity : 0.004 0.044 1513 Dihedral : 4.410 48.927 1239 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.27 % Allowed : 21.58 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.76 (0.26), residues: 1131 helix: 2.03 (0.27), residues: 384 sheet: 0.15 (0.30), residues: 291 loop : -0.53 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 124 TYR 0.015 0.001 TYR A 37 PHE 0.014 0.001 PHE A 222 TRP 0.032 0.002 TRP R 142 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8691) covalent geometry : angle 0.55636 (11855) SS BOND : bond 0.00283 ( 2) SS BOND : angle 0.75813 ( 4) hydrogen bonds : bond 0.03844 ( 449) hydrogen bonds : angle 4.45575 ( 1299) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8442 (t) cc_final: 0.8137 (t) REVERT: A 56 ILE cc_start: 0.7689 (mt) cc_final: 0.7446 (tp) REVERT: A 221 LYS cc_start: 0.8002 (mppt) cc_final: 0.7516 (mppt) REVERT: A 299 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7153 (mt-10) REVERT: A 347 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.7992 (ttp-110) REVERT: A 368 ASP cc_start: 0.6972 (m-30) cc_final: 0.6512 (m-30) REVERT: B 155 ASN cc_start: 0.7957 (t0) cc_final: 0.7412 (t0) REVERT: B 165 THR cc_start: 0.7110 (OUTLIER) cc_final: 0.6882 (p) REVERT: B 170 ASP cc_start: 0.7856 (t0) cc_final: 0.7607 (t0) REVERT: B 175 GLN cc_start: 0.7696 (mm110) cc_final: 0.7429 (mm110) REVERT: B 186 ASP cc_start: 0.7584 (m-30) cc_final: 0.7227 (m-30) REVERT: B 228 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7916 (p0) REVERT: B 258 ASP cc_start: 0.7428 (t70) cc_final: 0.6954 (t0) REVERT: B 304 ARG cc_start: 0.8010 (mmm-85) cc_final: 0.7789 (mmm-85) REVERT: B 340 ASN cc_start: 0.7386 (t0) cc_final: 0.7018 (t0) REVERT: S 7 SER cc_start: 0.8377 (p) cc_final: 0.8168 (m) REVERT: S 219 LEU cc_start: 0.8797 (tp) cc_final: 0.8572 (mm) REVERT: R 174 MET cc_start: 0.6947 (mmm) cc_final: 0.6601 (mmm) REVERT: R 186 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7743 (t) REVERT: R 242 VAL cc_start: 0.8296 (t) cc_final: 0.8022 (p) REVERT: R 271 SER cc_start: 0.7557 (p) cc_final: 0.7334 (m) REVERT: R 285 LEU cc_start: 0.8045 (mt) cc_final: 0.7828 (mp) outliers start: 27 outliers final: 18 residues processed: 216 average time/residue: 0.4673 time to fit residues: 109.1304 Evaluate side-chains 223 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 276 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 88 optimal weight: 0.7980 chunk 81 optimal weight: 0.1980 chunk 94 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 0.0050 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105956 restraints weight = 12764.744| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.86 r_work: 0.3221 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8693 Z= 0.156 Angle : 0.584 9.580 11859 Z= 0.300 Chirality : 0.043 0.152 1366 Planarity : 0.004 0.045 1513 Dihedral : 4.503 48.965 1239 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.27 % Allowed : 21.82 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.73 (0.26), residues: 1131 helix: 1.99 (0.26), residues: 384 sheet: 0.20 (0.30), residues: 290 loop : -0.59 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 124 TYR 0.016 0.002 TYR A 37 PHE 0.015 0.002 PHE A 222 TRP 0.042 0.002 TRP R 142 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8691) covalent geometry : angle 0.58435 (11855) SS BOND : bond 0.00248 ( 2) SS BOND : angle 0.87219 ( 4) hydrogen bonds : bond 0.04045 ( 449) hydrogen bonds : angle 4.50882 ( 1299) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8468 (t) cc_final: 0.8160 (t) REVERT: A 56 ILE cc_start: 0.7679 (mt) cc_final: 0.7422 (tp) REVERT: A 299 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7207 (mt-10) REVERT: A 347 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.8012 (ttp-110) REVERT: A 368 ASP cc_start: 0.6997 (m-30) cc_final: 0.6533 (m-30) REVERT: B 155 ASN cc_start: 0.7975 (t0) cc_final: 0.7394 (t0) REVERT: B 165 THR cc_start: 0.7192 (OUTLIER) cc_final: 0.6951 (p) REVERT: B 170 ASP cc_start: 0.7889 (t0) cc_final: 0.7591 (t0) REVERT: B 175 GLN cc_start: 0.7739 (mm110) cc_final: 0.7467 (mm110) REVERT: B 228 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7963 (p0) REVERT: B 258 ASP cc_start: 0.7429 (t70) cc_final: 0.6917 (t0) REVERT: B 340 ASN cc_start: 0.7476 (t0) cc_final: 0.7099 (t0) REVERT: S 7 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8165 (m) REVERT: S 219 LEU cc_start: 0.8832 (tp) cc_final: 0.8600 (mm) REVERT: R 142 TRP cc_start: 0.8358 (m100) cc_final: 0.8027 (m100) REVERT: R 174 MET cc_start: 0.7000 (mmm) cc_final: 0.6660 (mmm) REVERT: R 186 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7722 (t) REVERT: R 242 VAL cc_start: 0.8309 (t) cc_final: 0.8028 (p) REVERT: R 271 SER cc_start: 0.7688 (p) cc_final: 0.7474 (m) REVERT: R 285 LEU cc_start: 0.8089 (mt) cc_final: 0.7885 (mp) outliers start: 27 outliers final: 20 residues processed: 217 average time/residue: 0.4684 time to fit residues: 109.8380 Evaluate side-chains 230 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 276 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 chunk 74 optimal weight: 0.0060 chunk 98 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.2980 chunk 8 optimal weight: 0.0370 overall best weight: 0.1874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.109892 restraints weight = 12832.879| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.79 r_work: 0.3283 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8693 Z= 0.104 Angle : 0.538 9.092 11859 Z= 0.277 Chirality : 0.042 0.150 1366 Planarity : 0.004 0.045 1513 Dihedral : 4.251 48.548 1239 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.55 % Allowed : 22.79 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.82 (0.26), residues: 1131 helix: 2.13 (0.27), residues: 385 sheet: 0.17 (0.30), residues: 296 loop : -0.54 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 124 TYR 0.014 0.001 TYR A 391 PHE 0.013 0.001 PHE A 222 TRP 0.033 0.002 TRP R 142 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8691) covalent geometry : angle 0.53838 (11855) SS BOND : bond 0.00350 ( 2) SS BOND : angle 0.57386 ( 4) hydrogen bonds : bond 0.03497 ( 449) hydrogen bonds : angle 4.34888 ( 1299) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8358 (t) cc_final: 0.8019 (t) REVERT: A 343 ASP cc_start: 0.7123 (m-30) cc_final: 0.6630 (m-30) REVERT: A 347 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7968 (ttp-110) REVERT: A 368 ASP cc_start: 0.6956 (m-30) cc_final: 0.6534 (m-30) REVERT: A 391 TYR cc_start: 0.8529 (m-80) cc_final: 0.8226 (m-80) REVERT: B 110 ASN cc_start: 0.8307 (m110) cc_final: 0.7963 (m-40) REVERT: B 155 ASN cc_start: 0.7862 (t0) cc_final: 0.7352 (t0) REVERT: B 170 ASP cc_start: 0.7766 (t0) cc_final: 0.7510 (t0) REVERT: B 175 GLN cc_start: 0.7713 (mm110) cc_final: 0.7478 (mm110) REVERT: B 186 ASP cc_start: 0.7515 (m-30) cc_final: 0.7273 (m-30) REVERT: B 258 ASP cc_start: 0.7389 (t70) cc_final: 0.6999 (t0) REVERT: B 304 ARG cc_start: 0.7987 (mmm-85) cc_final: 0.7615 (mmm-85) REVERT: B 340 ASN cc_start: 0.7332 (t0) cc_final: 0.6965 (t0) REVERT: S 219 LEU cc_start: 0.8773 (tp) cc_final: 0.8565 (mm) REVERT: R 142 TRP cc_start: 0.8234 (m100) cc_final: 0.7997 (m100) REVERT: R 174 MET cc_start: 0.6994 (mmm) cc_final: 0.6674 (mmm) REVERT: R 186 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7757 (t) REVERT: R 242 VAL cc_start: 0.8293 (t) cc_final: 0.8036 (p) REVERT: R 271 SER cc_start: 0.7595 (p) cc_final: 0.7375 (m) REVERT: R 285 LEU cc_start: 0.7821 (mt) cc_final: 0.7616 (mp) outliers start: 21 outliers final: 12 residues processed: 214 average time/residue: 0.4861 time to fit residues: 111.9752 Evaluate side-chains 219 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 186 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 73 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 0.0050 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 125 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106354 restraints weight = 12805.798| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.88 r_work: 0.3237 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8693 Z= 0.154 Angle : 0.584 9.960 11859 Z= 0.300 Chirality : 0.043 0.161 1366 Planarity : 0.004 0.045 1513 Dihedral : 4.429 48.899 1239 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.67 % Allowed : 23.03 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.81 (0.26), residues: 1131 helix: 2.05 (0.27), residues: 384 sheet: 0.26 (0.30), residues: 287 loop : -0.53 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 124 TYR 0.016 0.002 TYR A 37 PHE 0.015 0.002 PHE A 222 TRP 0.033 0.002 TRP R 142 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8691) covalent geometry : angle 0.58351 (11855) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.79292 ( 4) hydrogen bonds : bond 0.04014 ( 449) hydrogen bonds : angle 4.48057 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3551.37 seconds wall clock time: 61 minutes 26.42 seconds (3686.42 seconds total)