Starting phenix.real_space_refine on Thu Jul 2 14:27:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vav_64906/07_2026/9vav_64906.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vav_64906/07_2026/9vav_64906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vav_64906/07_2026/9vav_64906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vav_64906/07_2026/9vav_64906.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vav_64906/07_2026/9vav_64906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vav_64906/07_2026/9vav_64906.map" } resolution = 2.99 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= 0.000 sd= 0.001 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 5667 2.51 5 N 1519 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8912 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2330 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1768 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 4, 'TRANS': 218} Chain breaks: 1 Chain: "B" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1763 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 1.63, per 1000 atoms: 0.18 Number of scatterers: 8912 At special positions: 0 Unit cell: (121.9, 116.6, 116.6, 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 1666 8.00 N 1519 7.00 C 5667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.06 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.11 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: 0.54 Conformation dependent library (CDL) restraints added in 332.8 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 38.2% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'R' and resid 59 through 90 Processing helix chain 'R' and resid 96 through 127 Proline residue: R 121 - end of helix removed outlier: 3.638A pdb=" N TYR R 125 " --> pdb=" O PRO R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 172 removed outlier: 3.527A pdb=" N ARG R 142 " --> pdb=" O ASP R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 178 removed outlier: 3.609A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 201 Processing helix chain 'R' and resid 202 through 207 Processing helix chain 'R' and resid 229 through 245 Processing helix chain 'R' and resid 245 through 273 removed outlier: 3.530A pdb=" N VAL R 250 " --> pdb=" O ILE R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 327 removed outlier: 4.424A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 363 removed outlier: 3.521A pdb=" N HIS R 343 " --> pdb=" O TYR R 339 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET R 347 " --> pdb=" O HIS R 343 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.527A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.230A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 231 No H-bonds generated for 'chain 'A' and resid 229 through 231' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.703A pdb=" N ILE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.575A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.879A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 210 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.213A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 227 removed outlier: 6.763A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.526A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.857A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.536A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.597A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.459A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.597A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.721A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.640A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1302 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: 1.38 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1792 1.33 - 1.46: 2910 1.46 - 1.59: 4309 1.59 - 1.72: 0 1.72 - 1.85: 88 Bond restraints: 9099 Sorted by residual: bond pdb=" CG HIS B 62 " pdb=" CD2 HIS B 62 " ideal model delta sigma weight residual 1.354 1.300 0.054 1.10e-02 8.26e+03 2.42e+01 bond pdb=" CA SER R 111 " pdb=" CB SER R 111 " ideal model delta sigma weight residual 1.529 1.457 0.072 1.58e-02 4.01e+03 2.08e+01 bond pdb=" CA SER A 264 " pdb=" CB SER A 264 " ideal model delta sigma weight residual 1.529 1.457 0.072 1.61e-02 3.86e+03 2.01e+01 bond pdb=" C PHE C 61 " pdb=" O PHE C 61 " ideal model delta sigma weight residual 1.231 1.318 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" CA SER R 253 " pdb=" CB SER R 253 " ideal model delta sigma weight residual 1.529 1.469 0.060 1.62e-02 3.81e+03 1.37e+01 ... (remaining 9094 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 9513 1.84 - 3.68: 2381 3.68 - 5.52: 374 5.52 - 7.36: 59 7.36 - 9.21: 11 Bond angle restraints: 12338 Sorted by residual: angle pdb=" N THR R 115 " pdb=" CA THR R 115 " pdb=" CB THR R 115 " ideal model delta sigma weight residual 110.12 119.33 -9.21 1.47e+00 4.63e-01 3.92e+01 angle pdb=" N PRO C 49 " pdb=" CA PRO C 49 " pdb=" C PRO C 49 " ideal model delta sigma weight residual 113.84 121.23 -7.39 1.30e+00 5.92e-01 3.23e+01 angle pdb=" N ILE A 332 " pdb=" CA ILE A 332 " pdb=" CB ILE A 332 " ideal model delta sigma weight residual 110.54 117.33 -6.79 1.36e+00 5.41e-01 2.49e+01 angle pdb=" C GLU A 14 " pdb=" CA GLU A 14 " pdb=" CB GLU A 14 " ideal model delta sigma weight residual 110.79 118.93 -8.14 1.66e+00 3.63e-01 2.40e+01 angle pdb=" N PRO B 194 " pdb=" CA PRO B 194 " pdb=" CB PRO B 194 " ideal model delta sigma weight residual 103.25 98.16 5.09 1.05e+00 9.07e-01 2.35e+01 ... (remaining 12333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 4956 17.80 - 35.60: 369 35.60 - 53.40: 49 53.40 - 71.20: 8 71.20 - 89.00: 3 Dihedral angle restraints: 5385 sinusoidal: 2062 harmonic: 3323 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual 93.00 -178.00 -89.00 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CA PHE B 278 " pdb=" C PHE B 278 " pdb=" N SER B 279 " pdb=" CA SER B 279 " ideal model delta harmonic sigma weight residual 180.00 155.16 24.84 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA ASN B 293 " pdb=" C ASN B 293 " pdb=" N CYS B 294 " pdb=" CA CYS B 294 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 5382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 897 0.078 - 0.156: 420 0.156 - 0.235: 76 0.235 - 0.313: 17 0.313 - 0.391: 2 Chirality restraints: 1412 Sorted by residual: chirality pdb=" CA ASN R 256 " pdb=" N ASN R 256 " pdb=" C ASN R 256 " pdb=" CB ASN R 256 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.82e+00 chirality pdb=" CA ARG B 48 " pdb=" N ARG B 48 " pdb=" C ARG B 48 " pdb=" CB ARG B 48 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1409 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 82 " -0.007 2.00e-02 2.50e+03 4.42e-02 4.89e+01 pdb=" CG TRP B 82 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP B 82 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TRP B 82 " -0.047 2.00e-02 2.50e+03 pdb=" NE1 TRP B 82 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP B 82 " -0.078 2.00e-02 2.50e+03 pdb=" CE3 TRP B 82 " -0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 82 " -0.037 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 82 " 0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP B 82 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 49 " -0.421 9.50e-02 1.11e+02 1.94e-01 4.88e+01 pdb=" NE ARG B 49 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG B 49 " 0.095 2.00e-02 2.50e+03 pdb=" NH1 ARG B 49 " -0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG B 49 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 309 " -0.027 2.00e-02 2.50e+03 5.34e-02 2.85e+01 pdb=" C ALA B 309 " 0.092 2.00e-02 2.50e+03 pdb=" O ALA B 309 " -0.034 2.00e-02 2.50e+03 pdb=" N GLY B 310 " -0.032 2.00e-02 2.50e+03 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 321 2.70 - 3.25: 9226 3.25 - 3.80: 14570 3.80 - 4.35: 20023 4.35 - 4.90: 32064 Nonbonded interactions: 76204 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR D 163 " model vdw 2.151 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.278 3.040 nonbonded pdb=" O TRP R 193 " pdb=" OG SER R 196 " model vdw 2.333 3.040 nonbonded pdb=" OE2 GLU A 187 " pdb=" NE ARG A 198 " model vdw 2.344 3.120 nonbonded pdb=" OG SER D 149 " pdb=" O LYS D 151 " model vdw 2.350 3.040 ... (remaining 76199 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: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.860 Find NCS groups from input model: 0.040 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 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 : 0.010 0.087 9101 Z= 0.668 Angle : 1.667 9.205 12342 Z= 1.126 Chirality : 0.089 0.391 1412 Planarity : 0.013 0.194 1559 Dihedral : 12.519 76.865 3237 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.75 % Allowed : 5.78 % Favored : 92.47 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.30 (0.22), residues: 1126 helix: -1.64 (0.22), residues: 397 sheet: -0.91 (0.29), residues: 290 loop : -1.62 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.006 ARG B 49 TYR 0.065 0.012 TYR D 102 PHE 0.049 0.011 PHE B 234 TRP 0.078 0.017 TRP B 82 HIS 0.025 0.005 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.01029 / 0.67 ( 9099) covalent geometry : angle 1.66664 / 1.13 (12338) SS BOND : bond 0.05947 / 2.88 ( 2) SS BOND : angle 2.62058 / 1.35 ( 4) hydrogen bonds : bond 0.19876 / 13.41 ( 461) hydrogen bonds : angle 7.96006 / 5.93 ( 1302) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 73 LEU cc_start: 0.9052 (mt) cc_final: 0.8807 (mp) REVERT: R 81 ASN cc_start: 0.8336 (m110) cc_final: 0.7841 (m110) REVERT: R 102 HIS cc_start: 0.8887 (m-70) cc_final: 0.8669 (m-70) REVERT: R 187 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8644 (tmtt) REVERT: A 284 LEU cc_start: 0.9135 (tp) cc_final: 0.8913 (tm) REVERT: A 305 GLN cc_start: 0.9446 (tt0) cc_final: 0.9226 (tt0) REVERT: B 254 ASP cc_start: 0.9145 (t70) cc_final: 0.8899 (t0) REVERT: D 135 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.7677 (m) REVERT: D 232 LYS cc_start: 0.8904 (tttt) cc_final: 0.8473 (ttpp) outliers start: 17 outliers final: 3 residues processed: 175 average time/residue: 0.6112 time to fit residues: 112.7306 Evaluate side-chains 110 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 81 ASN R 104 HIS R 172 HIS R 211 ASN R 343 HIS A 196 HIS A 205 GLN A 214 HIS ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN A 316 ASN B 13 GLN B 156 GLN B 239 ASN B 293 ASN B 340 ASN C 18 GLN D 3 GLN D 113 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.071264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.052910 restraints weight = 24120.706| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.19 r_work: 0.2632 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9101 Z= 0.206 Angle : 0.633 7.993 12342 Z= 0.342 Chirality : 0.044 0.181 1412 Planarity : 0.004 0.038 1559 Dihedral : 6.430 145.440 1243 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.68 % Allowed : 11.76 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.24), residues: 1126 helix: 1.47 (0.23), residues: 409 sheet: -0.17 (0.29), residues: 292 loop : -0.86 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 206 TYR 0.025 0.002 TYR A 303 PHE 0.017 0.002 PHE R 345 TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS R 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 ( 9099) covalent geometry : angle 0.63286 / 0.34 (12338) SS BOND : bond 0.00370 / 0.18 ( 2) SS BOND : angle 1.08589 / 0.53 ( 4) hydrogen bonds : bond 0.05451 / 3.58 ( 461) hydrogen bonds : angle 5.11862 / 3.78 ( 1302) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 102 HIS cc_start: 0.8193 (m-70) cc_final: 0.7975 (m-70) REVERT: R 187 LYS cc_start: 0.8597 (mtpt) cc_final: 0.8266 (tttp) REVERT: B 254 ASP cc_start: 0.8550 (t70) cc_final: 0.8146 (t0) REVERT: C 47 GLU cc_start: 0.9309 (pt0) cc_final: 0.8864 (pm20) REVERT: C 58 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8615 (mp0) REVERT: D 3 GLN cc_start: 0.8740 (tp40) cc_final: 0.8408 (tp40) REVERT: D 43 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8451 (mmmm) REVERT: D 90 ASP cc_start: 0.9222 (m-30) cc_final: 0.8653 (m-30) REVERT: D 190 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8282 (ptt90) REVERT: D 211 ASP cc_start: 0.8432 (m-30) cc_final: 0.7942 (m-30) outliers start: 26 outliers final: 7 residues processed: 138 average time/residue: 0.6250 time to fit residues: 90.8047 Evaluate side-chains 116 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 190 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 245 HIS A 305 GLN B 340 ASN D 113 GLN D 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.070846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.053153 restraints weight = 23849.407| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.12 r_work: 0.2640 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9101 Z= 0.166 Angle : 0.587 9.228 12342 Z= 0.309 Chirality : 0.043 0.155 1412 Planarity : 0.004 0.046 1559 Dihedral : 4.360 49.785 1238 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.06 % Allowed : 14.14 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.25), residues: 1126 helix: 2.42 (0.25), residues: 409 sheet: 0.18 (0.29), residues: 290 loop : -0.67 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 206 TYR 0.025 0.001 TYR A 303 PHE 0.013 0.001 PHE R 345 TRP 0.018 0.002 TRP B 169 HIS 0.003 0.001 HIS R 218 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 9099) covalent geometry : angle 0.58683 / 0.31 (12338) SS BOND : bond 0.00474 / 0.23 ( 2) SS BOND : angle 1.12137 / 0.53 ( 4) hydrogen bonds : bond 0.04931 / 3.26 ( 461) hydrogen bonds : angle 4.73904 / 3.49 ( 1302) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 81 ASN cc_start: 0.8206 (m110) cc_final: 0.7997 (m110) REVERT: R 102 HIS cc_start: 0.8199 (m-70) cc_final: 0.7988 (m-70) REVERT: R 120 MET cc_start: 0.8212 (tpp) cc_final: 0.7542 (tpp) REVERT: R 175 LYS cc_start: 0.8352 (mppt) cc_final: 0.8108 (mppt) REVERT: R 187 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8253 (tttp) REVERT: R 228 ILE cc_start: 0.7587 (mm) cc_final: 0.7384 (mt) REVERT: B 15 LYS cc_start: 0.8964 (mtpp) cc_final: 0.8491 (mttp) REVERT: B 217 MET cc_start: 0.8953 (ptt) cc_final: 0.8564 (pmt) REVERT: B 254 ASP cc_start: 0.8531 (t70) cc_final: 0.8111 (t0) REVERT: C 13 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.8087 (mtm-85) REVERT: C 58 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8549 (mp0) REVERT: D 3 GLN cc_start: 0.8819 (tp40) cc_final: 0.8529 (tp40) REVERT: D 190 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8493 (ptt90) outliers start: 20 outliers final: 8 residues processed: 125 average time/residue: 0.6511 time to fit residues: 85.8178 Evaluate side-chains 117 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 204 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 109 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 81 ASN R 238 GLN A 305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.069287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.051200 restraints weight = 24484.733| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.19 r_work: 0.2598 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9101 Z= 0.223 Angle : 0.601 8.271 12342 Z= 0.315 Chirality : 0.043 0.195 1412 Planarity : 0.004 0.042 1559 Dihedral : 4.319 46.434 1238 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.37 % Allowed : 14.45 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.25), residues: 1126 helix: 2.50 (0.25), residues: 408 sheet: 0.25 (0.29), residues: 301 loop : -0.52 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 206 TYR 0.018 0.002 TYR R 144 PHE 0.013 0.002 PHE R 345 TRP 0.015 0.002 TRP D 47 HIS 0.004 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 ( 9099) covalent geometry : angle 0.60100 / 0.32 (12338) SS BOND : bond 0.00546 / 0.26 ( 2) SS BOND : angle 1.33110 / 0.64 ( 4) hydrogen bonds : bond 0.04900 / 3.25 ( 461) hydrogen bonds : angle 4.63790 / 3.42 ( 1302) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 53 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8277 (tp30) REVERT: R 120 MET cc_start: 0.8216 (tpp) cc_final: 0.7957 (tpp) REVERT: R 144 TYR cc_start: 0.7200 (t80) cc_final: 0.6986 (t80) REVERT: R 149 ASP cc_start: 0.7502 (OUTLIER) cc_final: 0.7152 (t0) REVERT: R 175 LYS cc_start: 0.8379 (mppt) cc_final: 0.8128 (mppt) REVERT: R 184 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8832 (mmm-85) REVERT: R 187 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8226 (tttp) REVERT: A 305 GLN cc_start: 0.9149 (tt0) cc_final: 0.8911 (tt0) REVERT: A 340 THR cc_start: 0.9032 (OUTLIER) cc_final: 0.8688 (p) REVERT: B 12 GLU cc_start: 0.9255 (tp30) cc_final: 0.8986 (tp30) REVERT: B 15 LYS cc_start: 0.9016 (mtpp) cc_final: 0.8477 (mttp) REVERT: B 217 MET cc_start: 0.9022 (ptt) cc_final: 0.8658 (pmt) REVERT: B 254 ASP cc_start: 0.8532 (t70) cc_final: 0.8140 (t0) REVERT: B 262 MET cc_start: 0.9128 (ttm) cc_final: 0.8717 (tpp) REVERT: C 58 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8632 (mp0) REVERT: D 3 GLN cc_start: 0.8850 (tp40) cc_final: 0.8641 (tp40) REVERT: D 42 GLU cc_start: 0.8568 (pp20) cc_final: 0.7797 (pp20) REVERT: D 43 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8427 (mmtm) outliers start: 23 outliers final: 9 residues processed: 125 average time/residue: 0.6946 time to fit residues: 91.6298 Evaluate side-chains 113 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 ASP Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 204 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 4.9990 chunk 102 optimal weight: 30.0000 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 259 GLN D 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.069005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.050925 restraints weight = 24560.530| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.16 r_work: 0.2598 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9101 Z= 0.221 Angle : 0.588 8.179 12342 Z= 0.310 Chirality : 0.043 0.188 1412 Planarity : 0.004 0.054 1559 Dihedral : 4.159 23.167 1238 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.37 % Allowed : 15.58 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.25), residues: 1126 helix: 2.52 (0.25), residues: 408 sheet: 0.45 (0.30), residues: 292 loop : -0.52 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 206 TYR 0.023 0.002 TYR A 303 PHE 0.012 0.001 PHE R 345 TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 ( 9099) covalent geometry : angle 0.58783 / 0.31 (12338) SS BOND : bond 0.00522 / 0.25 ( 2) SS BOND : angle 1.16932 / 0.57 ( 4) hydrogen bonds : bond 0.04818 / 3.18 ( 461) hydrogen bonds : angle 4.58782 / 3.38 ( 1302) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 107 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8363 (tp30) REVERT: R 102 HIS cc_start: 0.8147 (m-70) cc_final: 0.7748 (m-70) REVERT: R 149 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7199 (t0) REVERT: R 175 LYS cc_start: 0.8399 (mppt) cc_final: 0.8006 (mppt) REVERT: R 184 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8822 (mmm-85) REVERT: R 187 LYS cc_start: 0.8672 (mtpt) cc_final: 0.8244 (tttp) REVERT: A 305 GLN cc_start: 0.9183 (tt0) cc_final: 0.8913 (tt0) REVERT: A 340 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8726 (p) REVERT: B 217 MET cc_start: 0.9050 (ptt) cc_final: 0.8800 (pmt) REVERT: B 254 ASP cc_start: 0.8545 (t70) cc_final: 0.8168 (t0) REVERT: B 262 MET cc_start: 0.9167 (ttm) cc_final: 0.8746 (tpp) REVERT: C 58 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8625 (mp0) REVERT: D 3 GLN cc_start: 0.8901 (tp40) cc_final: 0.8631 (tp40) REVERT: D 180 MET cc_start: 0.9222 (ttp) cc_final: 0.8956 (ttp) REVERT: D 211 ASP cc_start: 0.8476 (m-30) cc_final: 0.7652 (m-30) outliers start: 23 outliers final: 12 residues processed: 121 average time/residue: 0.7512 time to fit residues: 95.7145 Evaluate side-chains 115 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 ASP Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain R residue 249 MET Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 204 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.069590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.051634 restraints weight = 24440.320| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.14 r_work: 0.2618 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9101 Z= 0.163 Angle : 0.564 8.692 12342 Z= 0.297 Chirality : 0.042 0.196 1412 Planarity : 0.004 0.057 1559 Dihedral : 3.992 18.439 1237 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.17 % Allowed : 17.65 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.25), residues: 1126 helix: 2.76 (0.25), residues: 402 sheet: 0.53 (0.30), residues: 291 loop : -0.51 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 206 TYR 0.020 0.001 TYR R 144 PHE 0.009 0.001 PHE R 345 TRP 0.015 0.001 TRP B 169 HIS 0.002 0.001 HIS D 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 ( 9099) covalent geometry : angle 0.56402 / 0.30 (12338) SS BOND : bond 0.00438 / 0.21 ( 2) SS BOND : angle 0.96665 / 0.46 ( 4) hydrogen bonds : bond 0.04506 / 2.98 ( 461) hydrogen bonds : angle 4.46668 / 3.28 ( 1302) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8304 (tp30) REVERT: R 102 HIS cc_start: 0.8060 (m-70) cc_final: 0.7667 (m-70) REVERT: R 175 LYS cc_start: 0.8352 (mppt) cc_final: 0.8107 (mppt) REVERT: R 184 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8834 (mmm-85) REVERT: R 187 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8238 (tttp) REVERT: A 305 GLN cc_start: 0.9211 (tt0) cc_final: 0.8986 (tt0) REVERT: B 23 LYS cc_start: 0.9006 (tppp) cc_final: 0.8518 (tmmt) REVERT: B 217 MET cc_start: 0.9027 (ptt) cc_final: 0.8738 (pmt) REVERT: B 226 GLU cc_start: 0.9224 (mt-10) cc_final: 0.9013 (mm-30) REVERT: B 254 ASP cc_start: 0.8507 (t70) cc_final: 0.8140 (t0) REVERT: C 21 MET cc_start: 0.9016 (ttp) cc_final: 0.8258 (tmm) REVERT: C 58 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8745 (mp0) REVERT: D 3 GLN cc_start: 0.8877 (tp40) cc_final: 0.8615 (tp40) REVERT: D 42 GLU cc_start: 0.8566 (pp20) cc_final: 0.8272 (pp20) REVERT: D 43 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8534 (mmmm) REVERT: D 58 ILE cc_start: 0.9469 (mt) cc_final: 0.9238 (mp) REVERT: D 180 MET cc_start: 0.9182 (ttp) cc_final: 0.8925 (ttp) REVERT: D 211 ASP cc_start: 0.8540 (m-30) cc_final: 0.7741 (m-30) outliers start: 21 outliers final: 11 residues processed: 126 average time/residue: 0.7014 time to fit residues: 93.3647 Evaluate side-chains 116 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 204 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.069268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.051566 restraints weight = 24349.032| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.10 r_work: 0.2617 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9101 Z= 0.176 Angle : 0.568 8.758 12342 Z= 0.300 Chirality : 0.042 0.201 1412 Planarity : 0.004 0.061 1559 Dihedral : 3.948 18.350 1237 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.65 % Allowed : 18.06 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.25), residues: 1126 helix: 2.77 (0.25), residues: 402 sheet: 0.57 (0.30), residues: 291 loop : -0.46 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 206 TYR 0.023 0.001 TYR R 144 PHE 0.008 0.001 PHE B 234 TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 9099) covalent geometry : angle 0.56820 / 0.30 (12338) SS BOND : bond 0.00445 / 0.21 ( 2) SS BOND : angle 1.01321 / 0.49 ( 4) hydrogen bonds : bond 0.04456 / 2.95 ( 461) hydrogen bonds : angle 4.41846 / 3.25 ( 1302) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: R 53 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8211 (tp30) REVERT: R 102 HIS cc_start: 0.8075 (m-70) cc_final: 0.7701 (m-70) REVERT: R 123 GLU cc_start: 0.8718 (pp20) cc_final: 0.8206 (pt0) REVERT: R 144 TYR cc_start: 0.7412 (t80) cc_final: 0.7039 (t80) REVERT: R 175 LYS cc_start: 0.8402 (mppt) cc_final: 0.8143 (mppt) REVERT: R 184 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8843 (mmm-85) REVERT: R 187 LYS cc_start: 0.8665 (mtpt) cc_final: 0.8238 (tttp) REVERT: A 305 GLN cc_start: 0.9202 (tt0) cc_final: 0.8980 (tt0) REVERT: B 23 LYS cc_start: 0.9046 (tppp) cc_final: 0.8576 (tmmt) REVERT: B 217 MET cc_start: 0.9046 (ptt) cc_final: 0.8746 (pmt) REVERT: B 226 GLU cc_start: 0.9218 (mt-10) cc_final: 0.9001 (mm-30) REVERT: B 254 ASP cc_start: 0.8471 (t70) cc_final: 0.8105 (t0) REVERT: B 325 MET cc_start: 0.9125 (tpt) cc_final: 0.8919 (tpp) REVERT: C 21 MET cc_start: 0.9116 (ttp) cc_final: 0.8331 (tmm) REVERT: C 58 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8735 (mp0) REVERT: D 3 GLN cc_start: 0.8898 (tp40) cc_final: 0.8636 (tp40) REVERT: D 42 GLU cc_start: 0.8548 (pp20) cc_final: 0.8169 (OUTLIER) REVERT: D 43 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8573 (mmmm) REVERT: D 58 ILE cc_start: 0.9466 (mt) cc_final: 0.9234 (mp) REVERT: D 180 MET cc_start: 0.9161 (ttp) cc_final: 0.8916 (ttp) REVERT: D 211 ASP cc_start: 0.8620 (m-30) cc_final: 0.7801 (m-30) outliers start: 16 outliers final: 12 residues processed: 121 average time/residue: 0.6700 time to fit residues: 85.5463 Evaluate side-chains 116 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 184 ARG Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 204 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 0.0870 chunk 39 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.071365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.053176 restraints weight = 23631.993| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.06 r_work: 0.2661 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9101 Z= 0.135 Angle : 0.588 13.468 12342 Z= 0.308 Chirality : 0.041 0.201 1412 Planarity : 0.004 0.046 1559 Dihedral : 3.844 18.141 1237 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.65 % Allowed : 18.06 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.25), residues: 1126 helix: 2.93 (0.25), residues: 393 sheet: 0.67 (0.30), residues: 291 loop : -0.40 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 209 TYR 0.023 0.001 TYR R 70 PHE 0.007 0.001 PHE D 27 TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS R 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 9099) covalent geometry : angle 0.58804 / 0.31 (12338) SS BOND : bond 0.00377 / 0.18 ( 2) SS BOND : angle 0.84067 / 0.40 ( 4) hydrogen bonds : bond 0.04185 / 2.79 ( 461) hydrogen bonds : angle 4.32324 / 3.18 ( 1302) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8211 (tp30) REVERT: R 123 GLU cc_start: 0.8708 (pp20) cc_final: 0.8119 (pt0) REVERT: R 144 TYR cc_start: 0.7558 (t80) cc_final: 0.7202 (t80) REVERT: R 165 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8342 (mt-10) REVERT: R 175 LYS cc_start: 0.8444 (mppt) cc_final: 0.8149 (mppt) REVERT: R 187 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8233 (tttp) REVERT: A 305 GLN cc_start: 0.9189 (tt0) cc_final: 0.8976 (tt0) REVERT: B 5 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.7896 (p0) REVERT: B 23 LYS cc_start: 0.9037 (tppp) cc_final: 0.8567 (tmmt) REVERT: B 217 MET cc_start: 0.9093 (ptt) cc_final: 0.8831 (pmt) REVERT: B 226 GLU cc_start: 0.9214 (mt-10) cc_final: 0.9004 (mm-30) REVERT: B 254 ASP cc_start: 0.8459 (t70) cc_final: 0.8114 (t0) REVERT: C 21 MET cc_start: 0.9112 (ttp) cc_final: 0.8325 (tmm) REVERT: C 24 ASN cc_start: 0.9257 (m-40) cc_final: 0.8743 (m-40) REVERT: C 58 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8757 (mp0) REVERT: D 3 GLN cc_start: 0.8943 (tp40) cc_final: 0.8681 (tp40) REVERT: D 58 ILE cc_start: 0.9491 (mt) cc_final: 0.9270 (mp) REVERT: D 180 MET cc_start: 0.9173 (ttp) cc_final: 0.8964 (ttp) REVERT: D 211 ASP cc_start: 0.8655 (m-30) cc_final: 0.7848 (m-30) outliers start: 16 outliers final: 9 residues processed: 120 average time/residue: 0.6631 time to fit residues: 84.0743 Evaluate side-chains 116 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 5 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 204 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 19 optimal weight: 0.0980 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.069292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.051190 restraints weight = 23974.394| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.04 r_work: 0.2620 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9101 Z= 0.234 Angle : 0.627 9.305 12342 Z= 0.329 Chirality : 0.043 0.195 1412 Planarity : 0.004 0.046 1559 Dihedral : 3.974 18.037 1237 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.96 % Allowed : 17.65 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.25), residues: 1126 helix: 2.74 (0.26), residues: 392 sheet: 0.52 (0.30), residues: 296 loop : -0.36 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 8 TYR 0.021 0.002 TYR R 70 PHE 0.011 0.001 PHE R 136 TRP 0.014 0.002 TRP D 47 HIS 0.003 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 ( 9099) covalent geometry : angle 0.62704 / 0.33 (12338) SS BOND : bond 0.00507 / 0.24 ( 2) SS BOND : angle 1.19222 / 0.59 ( 4) hydrogen bonds : bond 0.04603 / 3.06 ( 461) hydrogen bonds : angle 4.43620 / 3.27 ( 1302) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8368 (tp30) REVERT: R 123 GLU cc_start: 0.8785 (pp20) cc_final: 0.8245 (pt0) REVERT: R 165 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8452 (mt-10) REVERT: R 175 LYS cc_start: 0.8425 (mppt) cc_final: 0.8138 (mppt) REVERT: R 187 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8279 (tttp) REVERT: A 305 GLN cc_start: 0.9211 (tt0) cc_final: 0.8958 (tt0) REVERT: A 340 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8800 (p) REVERT: B 23 LYS cc_start: 0.9091 (tppp) cc_final: 0.8644 (tmmt) REVERT: B 217 MET cc_start: 0.9110 (ptt) cc_final: 0.8897 (pmt) REVERT: B 226 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8998 (mm-30) REVERT: B 254 ASP cc_start: 0.8484 (t70) cc_final: 0.8151 (t0) REVERT: C 21 MET cc_start: 0.9159 (ttp) cc_final: 0.8370 (tmm) REVERT: C 58 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8755 (mp0) REVERT: D 3 GLN cc_start: 0.8974 (tp40) cc_final: 0.8711 (tp40) REVERT: D 58 ILE cc_start: 0.9506 (mt) cc_final: 0.9282 (mp) REVERT: D 180 MET cc_start: 0.9167 (ttp) cc_final: 0.8933 (ttp) REVERT: D 211 ASP cc_start: 0.8644 (m-30) cc_final: 0.7887 (m-30) outliers start: 19 outliers final: 10 residues processed: 119 average time/residue: 0.6506 time to fit residues: 82.0028 Evaluate side-chains 115 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain R residue 304 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 88 optimal weight: 0.0670 chunk 109 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 3.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.070221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.052100 restraints weight = 23498.601| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.02 r_work: 0.2649 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9101 Z= 0.177 Angle : 0.643 11.578 12342 Z= 0.338 Chirality : 0.042 0.209 1412 Planarity : 0.004 0.058 1559 Dihedral : 3.949 19.321 1237 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.24 % Allowed : 18.27 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.25), residues: 1126 helix: 2.73 (0.26), residues: 392 sheet: 0.58 (0.30), residues: 296 loop : -0.38 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 8 TYR 0.025 0.002 TYR R 144 PHE 0.010 0.001 PHE R 136 TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS R 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 9099) covalent geometry : angle 0.64299 / 0.34 (12338) SS BOND : bond 0.00454 / 0.22 ( 2) SS BOND : angle 1.00143 / 0.48 ( 4) hydrogen bonds : bond 0.04419 / 2.94 ( 461) hydrogen bonds : angle 4.41133 / 3.23 ( 1302) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 53 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8239 (tp30) REVERT: R 165 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8422 (mt-10) REVERT: R 175 LYS cc_start: 0.8465 (mppt) cc_final: 0.8156 (mppt) REVERT: R 187 LYS cc_start: 0.8630 (mtpt) cc_final: 0.8283 (tttp) REVERT: A 305 GLN cc_start: 0.9217 (tt0) cc_final: 0.8981 (tt0) REVERT: B 23 LYS cc_start: 0.9080 (tppp) cc_final: 0.8634 (tmmt) REVERT: B 217 MET cc_start: 0.9117 (ptt) cc_final: 0.8875 (pmt) REVERT: B 226 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8980 (mm-30) REVERT: B 254 ASP cc_start: 0.8497 (t70) cc_final: 0.8187 (t0) REVERT: C 21 MET cc_start: 0.9173 (ttp) cc_final: 0.8413 (tmm) REVERT: C 24 ASN cc_start: 0.9250 (m-40) cc_final: 0.8736 (m-40) REVERT: C 58 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8774 (mp0) REVERT: D 58 ILE cc_start: 0.9518 (mt) cc_final: 0.9306 (mp) REVERT: D 180 MET cc_start: 0.9195 (ttp) cc_final: 0.8952 (ttp) REVERT: D 211 ASP cc_start: 0.8690 (m-30) cc_final: 0.7962 (m-30) outliers start: 12 outliers final: 9 residues processed: 114 average time/residue: 0.6836 time to fit residues: 82.2679 Evaluate side-chains 112 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 302 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.069692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.051525 restraints weight = 23603.632| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.03 r_work: 0.2627 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9101 Z= 0.212 Angle : 0.647 11.369 12342 Z= 0.340 Chirality : 0.044 0.207 1412 Planarity : 0.004 0.046 1559 Dihedral : 4.003 17.940 1237 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.55 % Allowed : 18.68 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1126 helix: 2.58 (0.26), residues: 393 sheet: 0.56 (0.30), residues: 296 loop : -0.38 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 209 TYR 0.024 0.002 TYR R 144 PHE 0.014 0.001 PHE R 312 TRP 0.026 0.002 TRP R 134 HIS 0.003 0.001 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 ( 9099) covalent geometry : angle 0.64685 / 0.34 (12338) SS BOND : bond 0.00488 / 0.23 ( 2) SS BOND : angle 1.16480 / 0.57 ( 4) hydrogen bonds : bond 0.04639 / 3.08 ( 461) hydrogen bonds : angle 4.51430 / 3.32 ( 1302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2668.91 seconds wall clock time: 46 minutes 20.42 seconds (2780.42 seconds total)