Starting phenix.real_space_refine on Tue Mar 3 20:31:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vdl_31922/03_2026/7vdl_31922.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vdl_31922/03_2026/7vdl_31922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vdl_31922/03_2026/7vdl_31922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vdl_31922/03_2026/7vdl_31922.map" model { file = "/net/cci-nas-00/data/ceres_data/7vdl_31922/03_2026/7vdl_31922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vdl_31922/03_2026/7vdl_31922.cif" } resolution = 3.22 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= 0.006 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 64 5.16 5 C 5513 2.51 5 N 1440 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8598 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1727 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2590 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} 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: "S" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1757 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2036 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "L" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 45 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.18, per 1000 atoms: 0.25 Number of scatterers: 8598 At special positions: 0 Unit cell: (117.52, 104, 106.08, 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 64 16.00 O 1581 8.00 N 1440 7.00 C 5513 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.07 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " 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: 0.64 Conformation dependent library (CDL) restraints added in 317.0 milliseconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.7% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.577A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.586A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.055A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.734A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.097A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 5.520A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.724A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.622A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.664A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.663A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.135A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'R' and resid 31 through 58 Processing helix chain 'R' and resid 62 through 94 removed outlier: 3.601A pdb=" N VAL R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR R 67 " --> pdb=" O ALA R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 4.018A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 169 Processing helix chain 'R' and resid 176 through 213 removed outlier: 4.007A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 235 Processing helix chain 'R' and resid 236 through 245 removed outlier: 4.594A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 249 Processing helix chain 'R' and resid 254 through 280 removed outlier: 4.342A pdb=" N CYS R 258 " --> pdb=" O ASP R 254 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS R 261 " --> pdb=" O PHE R 257 " (cutoff:3.500A) Proline residue: R 262 - end of helix removed outlier: 3.540A pdb=" N VAL R 265 " --> pdb=" O HIS R 261 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 38 removed outlier: 3.651A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 220 through 226 removed outlier: 5.518A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.555A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.027A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.759A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.584A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.546A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.712A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 277 removed outlier: 4.002A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.547A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.677A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.677A pdb=" N GLY S 10 " --> pdb=" O THR S 116 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR S 115 " --> pdb=" O TYR S 94 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 129 through 130 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.552A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 437 hydrogen bonds defined for protein. 1230 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: 1.37 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2693 1.34 - 1.47: 2328 1.47 - 1.60: 3678 1.60 - 1.74: 1 1.74 - 1.87: 88 Bond restraints: 8788 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.647 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CA ARG R 61 " pdb=" C ARG R 61 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" C HIS R 261 " pdb=" N PRO R 262 " ideal model delta sigma weight residual 1.336 1.369 -0.033 1.20e-02 6.94e+03 7.45e+00 bond pdb=" CA ARG B 52 " pdb=" CB ARG B 52 " ideal model delta sigma weight residual 1.527 1.589 -0.061 2.48e-02 1.63e+03 6.14e+00 bond pdb=" CA PHE R 281 " pdb=" C PHE R 281 " ideal model delta sigma weight residual 1.524 1.493 0.031 1.29e-02 6.01e+03 5.74e+00 ... (remaining 8783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 11568 2.99 - 5.99: 288 5.99 - 8.98: 42 8.98 - 11.97: 11 11.97 - 14.97: 4 Bond angle restraints: 11913 Sorted by residual: angle pdb=" N TYR R 279 " pdb=" CA TYR R 279 " pdb=" C TYR R 279 " ideal model delta sigma weight residual 111.36 119.24 -7.88 1.09e+00 8.42e-01 5.23e+01 angle pdb=" N ILE R 278 " pdb=" CA ILE R 278 " pdb=" C ILE R 278 " ideal model delta sigma weight residual 110.42 117.13 -6.71 9.60e-01 1.09e+00 4.88e+01 angle pdb=" N ARG R 61 " pdb=" CA ARG R 61 " pdb=" C ARG R 61 " ideal model delta sigma weight residual 109.95 119.88 -9.93 1.59e+00 3.96e-01 3.90e+01 angle pdb=" N PHE R 281 " pdb=" CA PHE R 281 " pdb=" C PHE R 281 " ideal model delta sigma weight residual 111.36 117.45 -6.09 1.09e+00 8.42e-01 3.12e+01 angle pdb=" CA CYS B 149 " pdb=" CB CYS B 149 " pdb=" SG CYS B 149 " ideal model delta sigma weight residual 114.40 127.06 -12.66 2.30e+00 1.89e-01 3.03e+01 ... (remaining 11908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4717 17.97 - 35.93: 412 35.93 - 53.90: 66 53.90 - 71.86: 10 71.86 - 89.83: 5 Dihedral angle restraints: 5210 sinusoidal: 2038 harmonic: 3172 Sorted by residual: dihedral pdb=" CA THR A 295 " pdb=" C THR A 295 " pdb=" N TYR A 296 " pdb=" CA TYR A 296 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" N ASN L 24 " pdb=" C ASN L 24 " pdb=" CA ASN L 24 " pdb=" CB ASN L 24 " ideal model delta harmonic sigma weight residual 122.80 135.03 -12.23 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" CA LEU B 261 " pdb=" C LEU B 261 " pdb=" N MET B 262 " pdb=" CA MET B 262 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 5207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1219 0.104 - 0.208: 121 0.208 - 0.311: 8 0.311 - 0.415: 5 0.415 - 0.519: 5 Chirality restraints: 1358 Sorted by residual: chirality pdb=" CA ASN L 24 " pdb=" N ASN L 24 " pdb=" C ASN L 24 " pdb=" CB ASN L 24 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" CB ILE R 32 " pdb=" CA ILE R 32 " pdb=" CG1 ILE R 32 " pdb=" CG2 ILE R 32 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA ARG R 61 " pdb=" N ARG R 61 " pdb=" C ARG R 61 " pdb=" CB ARG R 61 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.27e+00 ... (remaining 1355 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR S 103 " -0.006 2.00e-02 2.50e+03 2.31e-02 1.07e+01 pdb=" CG TYR S 103 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR S 103 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR S 103 " -0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR S 103 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 103 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR S 103 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR S 103 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET S 180 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C MET S 180 " -0.055 2.00e-02 2.50e+03 pdb=" O MET S 180 " 0.021 2.00e-02 2.50e+03 pdb=" N SER S 181 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO C 53 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " 0.042 5.00e-02 4.00e+02 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 24 2.37 - 3.01: 4227 3.01 - 3.64: 13199 3.64 - 4.27: 20292 4.27 - 4.90: 34051 Nonbonded interactions: 71793 Sorted by model distance: nonbonded pdb=" O PHE R 50 " pdb=" CD1 LEU R 54 " model vdw 1.743 3.460 nonbonded pdb=" CD1 LEU R 120 " pdb=" OH TYR R 279 " model vdw 2.062 3.460 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.217 3.040 nonbonded pdb=" O SER S 30 " pdb=" OG SER S 53 " model vdw 2.237 3.040 ... (remaining 71788 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: 0.520 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: 0.020 Process input model: 9.510 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 0.112 8791 Z= 0.352 Angle : 1.161 14.967 11919 Z= 0.621 Chirality : 0.069 0.519 1358 Planarity : 0.007 0.076 1490 Dihedral : 13.815 89.831 3155 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.11 % Allowed : 1.18 % Favored : 98.72 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 3.45 % 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: -1.82 (0.24), residues: 1082 helix: -1.14 (0.23), residues: 380 sheet: -0.84 (0.31), residues: 277 loop : -1.29 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 197 TYR 0.049 0.004 TYR S 103 PHE 0.043 0.004 PHE R 257 TRP 0.023 0.003 TRP B 297 HIS 0.004 0.002 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00777 ( 8788) covalent geometry : angle 1.15781 (11913) SS BOND : bond 0.02211 ( 3) SS BOND : angle 4.08964 ( 6) hydrogen bonds : bond 0.17422 ( 434) hydrogen bonds : angle 8.07632 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7046 (t0) cc_final: 0.6772 (t0) REVERT: A 277 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7317 (tptt) REVERT: A 304 GLN cc_start: 0.8266 (tm130) cc_final: 0.8018 (tm-30) REVERT: B 211 TRP cc_start: 0.8839 (m100) cc_final: 0.8396 (m100) REVERT: S 218 MET cc_start: 0.9086 (ttp) cc_final: 0.8818 (ttp) REVERT: R 158 LEU cc_start: 0.7832 (tp) cc_final: 0.7311 (tt) REVERT: R 163 LEU cc_start: 0.7570 (tt) cc_final: 0.7256 (tp) REVERT: R 183 PHE cc_start: 0.4481 (m-80) cc_final: 0.4103 (m-80) REVERT: L 22 CYS cc_start: 0.4938 (p) cc_final: 0.4218 (t) outliers start: 1 outliers final: 0 residues processed: 218 average time/residue: 0.1015 time to fit residues: 29.8092 Evaluate side-chains 198 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN S 3 GLN S 182 ASN L 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.184256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.147932 restraints weight = 10103.054| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.22 r_work: 0.3479 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8791 Z= 0.147 Angle : 0.679 14.313 11919 Z= 0.341 Chirality : 0.045 0.273 1358 Planarity : 0.004 0.054 1490 Dihedral : 6.640 59.421 1245 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.39 % Allowed : 8.56 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.81 (0.25), residues: 1082 helix: 0.28 (0.26), residues: 381 sheet: -0.66 (0.31), residues: 268 loop : -1.06 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 283 TYR 0.025 0.002 TYR R 279 PHE 0.032 0.002 PHE R 50 TRP 0.024 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8788) covalent geometry : angle 0.67731 (11913) SS BOND : bond 0.00983 ( 3) SS BOND : angle 2.26822 ( 6) hydrogen bonds : bond 0.04516 ( 434) hydrogen bonds : angle 5.49129 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 222 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7964 (t0) cc_final: 0.7749 (t0) REVERT: B 13 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7238 (pt0) REVERT: S 65 LYS cc_start: 0.8117 (tptt) cc_final: 0.7541 (mmtt) REVERT: S 206 ARG cc_start: 0.6913 (ptt-90) cc_final: 0.6375 (mmp80) REVERT: S 219 GLN cc_start: 0.8632 (pp30) cc_final: 0.8254 (pp30) REVERT: R 35 PHE cc_start: 0.6936 (m-80) cc_final: 0.6603 (m-80) REVERT: R 61 ARG cc_start: 0.5583 (mtm-85) cc_final: 0.5130 (mtm-85) REVERT: R 158 LEU cc_start: 0.7898 (tp) cc_final: 0.7382 (tt) REVERT: R 180 CYS cc_start: 0.7445 (t) cc_final: 0.7134 (t) REVERT: R 193 PHE cc_start: 0.8181 (t80) cc_final: 0.7888 (t80) REVERT: R 208 ARG cc_start: 0.7648 (tpt90) cc_final: 0.7440 (tpt90) REVERT: R 248 TRP cc_start: 0.7816 (m100) cc_final: 0.7605 (m100) outliers start: 13 outliers final: 7 residues processed: 226 average time/residue: 0.1046 time to fit residues: 31.4725 Evaluate side-chains 198 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 191 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain L residue 24 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 64 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 0.0020 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN S 3 GLN S 167 GLN L 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.185653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.149808 restraints weight = 9958.467| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.25 r_work: 0.3508 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8791 Z= 0.124 Angle : 0.620 13.344 11919 Z= 0.311 Chirality : 0.043 0.266 1358 Planarity : 0.004 0.043 1490 Dihedral : 6.218 59.272 1245 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.03 % Allowed : 12.73 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.28 (0.25), residues: 1082 helix: 0.98 (0.26), residues: 385 sheet: -0.53 (0.31), residues: 269 loop : -0.94 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.039 0.002 TYR A 296 PHE 0.017 0.001 PHE R 50 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8788) covalent geometry : angle 0.61990 (11913) SS BOND : bond 0.00842 ( 3) SS BOND : angle 0.86343 ( 6) hydrogen bonds : bond 0.04052 ( 434) hydrogen bonds : angle 4.98671 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: A 193 ASP cc_start: 0.8018 (t0) cc_final: 0.7785 (t0) REVERT: A 289 GLU cc_start: 0.7896 (pm20) cc_final: 0.7638 (pm20) REVERT: B 13 GLN cc_start: 0.7640 (tm-30) cc_final: 0.7177 (pt0) REVERT: B 23 LYS cc_start: 0.8393 (tppt) cc_final: 0.8185 (tppt) REVERT: S 19 LYS cc_start: 0.7698 (tttp) cc_final: 0.7080 (ttpt) REVERT: S 65 LYS cc_start: 0.8164 (tptt) cc_final: 0.7561 (mmtt) REVERT: R 35 PHE cc_start: 0.6843 (m-80) cc_final: 0.6387 (m-80) REVERT: R 59 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6508 (mtm) REVERT: R 158 LEU cc_start: 0.7906 (tp) cc_final: 0.7447 (tt) REVERT: R 180 CYS cc_start: 0.7356 (t) cc_final: 0.7032 (t) REVERT: R 183 PHE cc_start: 0.5807 (m-80) cc_final: 0.5405 (m-80) REVERT: R 193 PHE cc_start: 0.8124 (t80) cc_final: 0.7799 (t80) outliers start: 19 outliers final: 11 residues processed: 215 average time/residue: 0.1006 time to fit residues: 29.2759 Evaluate side-chains 208 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 196 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 163 LEU Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 230 LEU Chi-restraints excluded: chain L residue 22 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 57 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 340 ASN S 3 GLN R 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.180209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143451 restraints weight = 10250.957| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.19 r_work: 0.3426 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8791 Z= 0.204 Angle : 0.654 12.571 11919 Z= 0.333 Chirality : 0.045 0.281 1358 Planarity : 0.004 0.042 1490 Dihedral : 6.315 59.010 1245 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.89 % Allowed : 15.51 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.14 (0.26), residues: 1082 helix: 1.06 (0.26), residues: 393 sheet: -0.48 (0.30), residues: 284 loop : -0.82 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.036 0.002 TYR A 296 PHE 0.022 0.002 PHE R 50 TRP 0.017 0.002 TRP B 211 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8788) covalent geometry : angle 0.65380 (11913) SS BOND : bond 0.01063 ( 3) SS BOND : angle 0.76391 ( 6) hydrogen bonds : bond 0.04194 ( 434) hydrogen bonds : angle 4.97121 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.7893 (mt) cc_final: 0.7511 (mp) REVERT: A 193 ASP cc_start: 0.7862 (t0) cc_final: 0.7592 (t0) REVERT: A 289 GLU cc_start: 0.7926 (pm20) cc_final: 0.7634 (pm20) REVERT: A 312 LYS cc_start: 0.8335 (mmtp) cc_final: 0.7760 (mmmt) REVERT: B 13 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7398 (pt0) REVERT: B 23 LYS cc_start: 0.8355 (tppt) cc_final: 0.8139 (tppt) REVERT: S 65 LYS cc_start: 0.8163 (tptt) cc_final: 0.7938 (tptt) REVERT: R 35 PHE cc_start: 0.6943 (m-80) cc_final: 0.6419 (m-80) REVERT: R 45 LEU cc_start: 0.7838 (tp) cc_final: 0.7479 (tt) REVERT: R 59 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6180 (mtm) REVERT: R 61 ARG cc_start: 0.6174 (ptp-110) cc_final: 0.5151 (mtm-85) REVERT: R 158 LEU cc_start: 0.7850 (tp) cc_final: 0.7437 (tt) REVERT: R 183 PHE cc_start: 0.5760 (m-80) cc_final: 0.5265 (m-80) REVERT: R 193 PHE cc_start: 0.8213 (t80) cc_final: 0.7884 (t80) outliers start: 27 outliers final: 17 residues processed: 210 average time/residue: 0.1033 time to fit residues: 29.2219 Evaluate side-chains 208 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 212 VAL Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 87 LEU Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 102 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN S 3 GLN R 48 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.183991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147837 restraints weight = 10120.586| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.25 r_work: 0.3491 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8791 Z= 0.126 Angle : 0.591 12.238 11919 Z= 0.299 Chirality : 0.042 0.264 1358 Planarity : 0.003 0.037 1490 Dihedral : 6.055 59.865 1245 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.46 % Allowed : 17.22 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.11 (0.26), residues: 1082 helix: 1.37 (0.27), residues: 394 sheet: -0.37 (0.30), residues: 285 loop : -0.79 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.038 0.002 TYR A 296 PHE 0.012 0.001 PHE R 101 TRP 0.019 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8788) covalent geometry : angle 0.59072 (11913) SS BOND : bond 0.01002 ( 3) SS BOND : angle 0.75234 ( 6) hydrogen bonds : bond 0.03798 ( 434) hydrogen bonds : angle 4.71632 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7635 (tt0) REVERT: A 193 ASP cc_start: 0.7905 (t0) cc_final: 0.7611 (t0) REVERT: A 247 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.8221 (ttt) REVERT: A 312 LYS cc_start: 0.8344 (mmtp) cc_final: 0.7742 (mmmt) REVERT: B 13 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7430 (pt0) REVERT: B 23 LYS cc_start: 0.8310 (tppt) cc_final: 0.8087 (tppt) REVERT: S 65 LYS cc_start: 0.8199 (tptt) cc_final: 0.7589 (mmtt) REVERT: S 80 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.5856 (p90) REVERT: S 206 ARG cc_start: 0.6924 (ptt-90) cc_final: 0.6367 (mmp80) REVERT: R 35 PHE cc_start: 0.6930 (m-80) cc_final: 0.6396 (m-80) REVERT: R 45 LEU cc_start: 0.7829 (tp) cc_final: 0.7515 (tt) REVERT: R 59 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6617 (mtm) REVERT: R 158 LEU cc_start: 0.7897 (tp) cc_final: 0.7562 (tt) REVERT: R 183 PHE cc_start: 0.5719 (m-80) cc_final: 0.5158 (m-80) REVERT: R 193 PHE cc_start: 0.8130 (t80) cc_final: 0.7840 (t80) outliers start: 23 outliers final: 13 residues processed: 222 average time/residue: 0.1014 time to fit residues: 29.9219 Evaluate side-chains 219 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 81 optimal weight: 0.0870 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 3 GLN R 48 ASN R 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.183085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146761 restraints weight = 10065.624| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.29 r_work: 0.3467 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8791 Z= 0.146 Angle : 0.613 14.714 11919 Z= 0.308 Chirality : 0.043 0.263 1358 Planarity : 0.003 0.036 1490 Dihedral : 6.024 59.098 1245 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.67 % Allowed : 18.07 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.24 (0.26), residues: 1082 helix: 1.52 (0.27), residues: 394 sheet: -0.35 (0.30), residues: 285 loop : -0.71 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.038 0.002 TYR A 296 PHE 0.015 0.001 PHE R 101 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8788) covalent geometry : angle 0.61344 (11913) SS BOND : bond 0.01058 ( 3) SS BOND : angle 0.71470 ( 6) hydrogen bonds : bond 0.03828 ( 434) hydrogen bonds : angle 4.69168 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8005 (mt-10) REVERT: A 188 HIS cc_start: 0.7281 (OUTLIER) cc_final: 0.6683 (m-70) REVERT: A 193 ASP cc_start: 0.7911 (t0) cc_final: 0.7618 (t0) REVERT: A 247 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8215 (ttt) REVERT: A 312 LYS cc_start: 0.8397 (mmtp) cc_final: 0.7766 (mmmt) REVERT: B 13 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7473 (pt0) REVERT: B 23 LYS cc_start: 0.8297 (tppt) cc_final: 0.8074 (tppt) REVERT: B 234 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8092 (m-80) REVERT: S 65 LYS cc_start: 0.8171 (tptt) cc_final: 0.7527 (mmtt) REVERT: S 73 ASP cc_start: 0.7472 (p0) cc_final: 0.6606 (t70) REVERT: S 80 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.5840 (p90) REVERT: R 35 PHE cc_start: 0.7000 (m-80) cc_final: 0.6425 (m-80) REVERT: R 59 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6350 (mtm) REVERT: R 158 LEU cc_start: 0.7820 (tp) cc_final: 0.7510 (tt) REVERT: R 167 PHE cc_start: 0.7504 (m-10) cc_final: 0.7181 (m-80) REVERT: R 183 PHE cc_start: 0.5696 (m-80) cc_final: 0.5175 (m-80) REVERT: R 193 PHE cc_start: 0.8180 (t80) cc_final: 0.7862 (t80) outliers start: 25 outliers final: 16 residues processed: 221 average time/residue: 0.1035 time to fit residues: 30.5036 Evaluate side-chains 219 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 186 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 80 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 3 GLN R 48 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.180366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144314 restraints weight = 10238.060| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.19 r_work: 0.3430 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8791 Z= 0.188 Angle : 0.648 14.202 11919 Z= 0.326 Chirality : 0.044 0.273 1358 Planarity : 0.003 0.036 1490 Dihedral : 6.148 59.723 1245 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.42 % Allowed : 18.07 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.26), residues: 1082 helix: 1.48 (0.27), residues: 395 sheet: -0.35 (0.30), residues: 285 loop : -0.73 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.039 0.002 TYR A 296 PHE 0.017 0.001 PHE R 50 TRP 0.018 0.002 TRP B 211 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8788) covalent geometry : angle 0.64794 (11913) SS BOND : bond 0.01517 ( 3) SS BOND : angle 0.82888 ( 6) hydrogen bonds : bond 0.03990 ( 434) hydrogen bonds : angle 4.75973 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8292 (mt-10) cc_final: 0.8066 (mt-10) REVERT: A 188 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.6695 (m-70) REVERT: A 193 ASP cc_start: 0.7865 (t0) cc_final: 0.7581 (t0) REVERT: A 247 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8134 (ttt) REVERT: A 312 LYS cc_start: 0.8350 (mmtp) cc_final: 0.7762 (mmmt) REVERT: B 13 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7412 (pt0) REVERT: B 23 LYS cc_start: 0.8328 (tppt) cc_final: 0.8103 (tppt) REVERT: B 234 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: S 65 LYS cc_start: 0.8160 (tptt) cc_final: 0.7937 (tptt) REVERT: S 73 ASP cc_start: 0.7456 (p0) cc_final: 0.6631 (t70) REVERT: S 80 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.5973 (p90) REVERT: R 35 PHE cc_start: 0.7139 (m-80) cc_final: 0.6524 (m-80) REVERT: R 59 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6335 (mtm) REVERT: R 158 LEU cc_start: 0.7763 (tp) cc_final: 0.7464 (tt) outliers start: 32 outliers final: 21 residues processed: 219 average time/residue: 0.0983 time to fit residues: 28.8979 Evaluate side-chains 227 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 177 ILE Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 59 MET Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 223 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 58 optimal weight: 0.0870 chunk 67 optimal weight: 5.9990 chunk 93 optimal weight: 0.0050 chunk 96 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.4972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.186577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150452 restraints weight = 9974.420| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.27 r_work: 0.3518 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8791 Z= 0.114 Angle : 0.589 12.599 11919 Z= 0.296 Chirality : 0.042 0.247 1358 Planarity : 0.003 0.034 1490 Dihedral : 5.678 57.682 1245 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.46 % Allowed : 19.36 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.42 (0.26), residues: 1082 helix: 1.70 (0.27), residues: 396 sheet: -0.04 (0.32), residues: 248 loop : -0.82 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 61 TYR 0.041 0.002 TYR A 296 PHE 0.011 0.001 PHE A 334 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8788) covalent geometry : angle 0.58893 (11913) SS BOND : bond 0.00878 ( 3) SS BOND : angle 0.76368 ( 6) hydrogen bonds : bond 0.03581 ( 434) hydrogen bonds : angle 4.55597 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7897 (mt-10) REVERT: A 35 LYS cc_start: 0.8038 (mttt) cc_final: 0.7837 (mttt) REVERT: A 52 GLN cc_start: 0.7095 (pp30) cc_final: 0.6736 (pt0) REVERT: A 188 HIS cc_start: 0.7249 (OUTLIER) cc_final: 0.6654 (m-70) REVERT: A 193 ASP cc_start: 0.7829 (t0) cc_final: 0.7578 (t0) REVERT: A 247 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8092 (ttt) REVERT: B 13 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7461 (pt0) REVERT: B 23 LYS cc_start: 0.8238 (tppt) cc_final: 0.7991 (tppt) REVERT: B 119 ASN cc_start: 0.9106 (m-40) cc_final: 0.8874 (m-40) REVERT: B 234 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8033 (m-80) REVERT: S 19 LYS cc_start: 0.7694 (tttp) cc_final: 0.7403 (tptt) REVERT: S 73 ASP cc_start: 0.7428 (p0) cc_final: 0.6673 (t70) REVERT: S 80 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.5983 (p90) REVERT: S 206 ARG cc_start: 0.6915 (ptt-90) cc_final: 0.6289 (mmp80) REVERT: R 35 PHE cc_start: 0.7335 (m-80) cc_final: 0.6816 (m-80) REVERT: R 61 ARG cc_start: 0.5727 (ptp-110) cc_final: 0.4733 (ptt180) REVERT: R 158 LEU cc_start: 0.7789 (tp) cc_final: 0.7519 (tt) REVERT: R 166 LYS cc_start: 0.8086 (tppt) cc_final: 0.7802 (tppt) REVERT: R 167 PHE cc_start: 0.6955 (m-80) cc_final: 0.6593 (m-80) REVERT: R 278 ILE cc_start: 0.7978 (mt) cc_final: 0.7738 (mt) outliers start: 23 outliers final: 15 residues processed: 225 average time/residue: 0.1009 time to fit residues: 30.3685 Evaluate side-chains 220 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 20 LEU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 230 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 78 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 17 optimal weight: 0.0670 chunk 54 optimal weight: 0.0970 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.5916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN R 48 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.186234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.150217 restraints weight = 9902.222| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.24 r_work: 0.3525 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8791 Z= 0.119 Angle : 0.615 16.118 11919 Z= 0.304 Chirality : 0.042 0.231 1358 Planarity : 0.003 0.034 1490 Dihedral : 5.438 51.872 1245 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.25 % Allowed : 20.64 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.52 (0.26), residues: 1082 helix: 1.88 (0.27), residues: 390 sheet: -0.13 (0.32), residues: 255 loop : -0.72 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 137 TYR 0.040 0.002 TYR A 296 PHE 0.036 0.001 PHE R 193 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8788) covalent geometry : angle 0.61543 (11913) SS BOND : bond 0.00913 ( 3) SS BOND : angle 0.61808 ( 6) hydrogen bonds : bond 0.03574 ( 434) hydrogen bonds : angle 4.49548 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7939 (mt-10) REVERT: A 188 HIS cc_start: 0.7193 (OUTLIER) cc_final: 0.6651 (m-70) REVERT: A 193 ASP cc_start: 0.7835 (t0) cc_final: 0.7504 (t0) REVERT: B 13 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7466 (pt0) REVERT: B 23 LYS cc_start: 0.8234 (tppt) cc_final: 0.7979 (tppt) REVERT: B 119 ASN cc_start: 0.9106 (m-40) cc_final: 0.8827 (m-40) REVERT: B 234 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: S 19 LYS cc_start: 0.7684 (tttp) cc_final: 0.7351 (tptt) REVERT: S 73 ASP cc_start: 0.7431 (p0) cc_final: 0.6683 (t70) REVERT: S 80 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6010 (p90) REVERT: S 206 ARG cc_start: 0.6959 (ptt-90) cc_final: 0.6346 (mmp80) REVERT: R 35 PHE cc_start: 0.7278 (m-80) cc_final: 0.6751 (m-80) REVERT: R 61 ARG cc_start: 0.5833 (ptp-110) cc_final: 0.4844 (ptt180) REVERT: R 104 PHE cc_start: 0.6270 (t80) cc_final: 0.5895 (t80) REVERT: R 140 ARG cc_start: 0.8463 (mtm110) cc_final: 0.8191 (mtm110) REVERT: R 166 LYS cc_start: 0.8256 (tppt) cc_final: 0.7985 (tppt) REVERT: R 167 PHE cc_start: 0.6893 (m-80) cc_final: 0.6119 (m-10) REVERT: R 278 ILE cc_start: 0.8002 (mt) cc_final: 0.7742 (mt) outliers start: 21 outliers final: 15 residues processed: 215 average time/residue: 0.1056 time to fit residues: 30.1537 Evaluate side-chains 209 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 223 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 174 GLN R 48 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.183081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.146358 restraints weight = 9994.479| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.24 r_work: 0.3478 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8791 Z= 0.160 Angle : 0.658 15.970 11919 Z= 0.325 Chirality : 0.044 0.230 1358 Planarity : 0.003 0.034 1490 Dihedral : 5.518 50.656 1245 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.93 % Allowed : 21.60 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.48 (0.26), residues: 1082 helix: 1.75 (0.27), residues: 390 sheet: -0.19 (0.32), residues: 265 loop : -0.62 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.040 0.002 TYR A 296 PHE 0.012 0.001 PHE R 64 TRP 0.017 0.001 TRP B 211 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8788) covalent geometry : angle 0.65761 (11913) SS BOND : bond 0.01301 ( 3) SS BOND : angle 0.73737 ( 6) hydrogen bonds : bond 0.03756 ( 434) hydrogen bonds : angle 4.55087 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 HIS cc_start: 0.7282 (OUTLIER) cc_final: 0.6720 (m-70) REVERT: A 193 ASP cc_start: 0.7800 (t0) cc_final: 0.7493 (t0) REVERT: A 271 LYS cc_start: 0.7604 (pttt) cc_final: 0.7230 (tttm) REVERT: B 13 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7434 (pt0) REVERT: B 23 LYS cc_start: 0.8251 (tppt) cc_final: 0.7999 (tppt) REVERT: B 119 ASN cc_start: 0.9097 (m-40) cc_final: 0.8800 (m-40) REVERT: B 234 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8118 (m-80) REVERT: S 73 ASP cc_start: 0.7504 (p0) cc_final: 0.6740 (t70) REVERT: S 80 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.6033 (p90) REVERT: R 35 PHE cc_start: 0.7392 (m-80) cc_final: 0.6888 (m-80) REVERT: R 61 ARG cc_start: 0.5861 (ptp-110) cc_final: 0.4880 (ptt180) REVERT: R 104 PHE cc_start: 0.6278 (t80) cc_final: 0.5886 (t80) REVERT: R 140 ARG cc_start: 0.8478 (mtm110) cc_final: 0.8135 (mtm110) REVERT: R 166 LYS cc_start: 0.8175 (tppt) cc_final: 0.7923 (tppt) REVERT: R 167 PHE cc_start: 0.6930 (m-80) cc_final: 0.6150 (m-10) REVERT: R 278 ILE cc_start: 0.8114 (mt) cc_final: 0.7870 (mt) outliers start: 18 outliers final: 14 residues processed: 207 average time/residue: 0.0985 time to fit residues: 27.0721 Evaluate side-chains 209 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 HIS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 80 PHE Chi-restraints excluded: chain S residue 144 SER Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 223 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 40 optimal weight: 0.0670 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN S 174 GLN R 48 ASN R 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.180386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.143415 restraints weight = 10152.622| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.27 r_work: 0.3428 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8791 Z= 0.196 Angle : 0.709 16.604 11919 Z= 0.348 Chirality : 0.045 0.242 1358 Planarity : 0.003 0.034 1490 Dihedral : 5.817 54.251 1245 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.78 % Allowed : 21.07 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.36 (0.26), residues: 1082 helix: 1.54 (0.27), residues: 389 sheet: -0.20 (0.31), residues: 280 loop : -0.62 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 208 TYR 0.041 0.002 TYR A 296 PHE 0.019 0.002 PHE R 257 TRP 0.019 0.002 TRP B 211 HIS 0.003 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 8788) covalent geometry : angle 0.70879 (11913) SS BOND : bond 0.01553 ( 3) SS BOND : angle 0.87480 ( 6) hydrogen bonds : bond 0.03946 ( 434) hydrogen bonds : angle 4.64895 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2529.93 seconds wall clock time: 43 minutes 56.88 seconds (2636.88 seconds total)