Starting phenix.real_space_refine on Wed Mar 4 00:57:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rg9_24445/03_2026/7rg9_24445_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rg9_24445/03_2026/7rg9_24445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rg9_24445/03_2026/7rg9_24445_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rg9_24445/03_2026/7rg9_24445_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rg9_24445/03_2026/7rg9_24445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rg9_24445/03_2026/7rg9_24445.map" } resolution = 3.2 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= 0.004 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 58 5.16 5 C 6223 2.51 5 N 1677 2.21 5 O 1811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 9769 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1792 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 213} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2193 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 263} Chain breaks: 2 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 2.33, per 1000 atoms: 0.24 Number of scatterers: 9769 At special positions: 0 Unit cell: (129.792, 108.992, 104, 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 58 16.00 O 1811 8.00 N 1677 7.00 C 6223 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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: 0.89 Conformation dependent library (CDL) restraints added in 499.0 milliseconds 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2326 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 35.2% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.584A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 235 through 240 removed outlier: 4.415A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.697A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.537A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.200A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 4.098A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.811A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.749A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.539A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.722A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 169 removed outlier: 3.616A pdb=" N LEU R 144 " --> pdb=" O GLN R 140 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLY R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE R 169 " --> pdb=" O ILE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 197 removed outlier: 3.734A pdb=" N HIS R 180 " --> pdb=" O ARG R 176 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG R 190 " --> pdb=" O SER R 186 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU R 192 " --> pdb=" O ILE R 188 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER R 193 " --> pdb=" O LEU R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 202 removed outlier: 3.677A pdb=" N LEU R 201 " --> pdb=" O LYS R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 207 Processing helix chain 'R' and resid 219 through 222 Processing helix chain 'R' and resid 223 through 257 removed outlier: 3.918A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL R 229 " --> pdb=" O SER R 225 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA R 238 " --> pdb=" O GLN R 234 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU R 245 " --> pdb=" O TYR R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 291 removed outlier: 4.375A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 306 through 338 removed outlier: 3.990A pdb=" N ARG R 310 " --> pdb=" O TRP R 306 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 345 through 361 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 367 removed outlier: 3.595A pdb=" N PHE R 367 " --> pdb=" O GLU R 364 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 403 removed outlier: 3.748A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA R 399 " --> pdb=" O GLY R 395 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 419 Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 5.978A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.505A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.674A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.136A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.666A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.632A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.947A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.326A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.983A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.983A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.796A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.910A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1290 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: 1.74 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1617 1.32 - 1.44: 2812 1.44 - 1.57: 5467 1.57 - 1.69: 0 1.69 - 1.82: 82 Bond restraints: 9978 Sorted by residual: bond pdb=" CA SER B 227 " pdb=" CB SER B 227 " ideal model delta sigma weight residual 1.531 1.478 0.053 1.48e-02 4.57e+03 1.27e+01 bond pdb=" N ARG N 105 " pdb=" CA ARG N 105 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.16e-02 7.43e+03 1.12e+01 bond pdb=" C ASP G 48 " pdb=" O ASP G 48 " ideal model delta sigma weight residual 1.238 1.197 0.041 1.28e-02 6.10e+03 1.04e+01 bond pdb=" N GLU B 226 " pdb=" CA GLU B 226 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.37e+00 bond pdb=" CA SER B 74 " pdb=" CB SER B 74 " ideal model delta sigma weight residual 1.532 1.482 0.050 1.74e-02 3.30e+03 8.36e+00 ... (remaining 9973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 12874 1.81 - 3.62: 562 3.62 - 5.43: 70 5.43 - 7.24: 12 7.24 - 9.05: 4 Bond angle restraints: 13522 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.18 105.07 8.11 1.21e+00 6.83e-01 4.50e+01 angle pdb=" CA VAL B 187 " pdb=" C VAL B 187 " pdb=" O VAL B 187 " ideal model delta sigma weight residual 121.13 114.78 6.35 1.16e+00 7.43e-01 2.99e+01 angle pdb=" N ARG N 105 " pdb=" CA ARG N 105 " pdb=" C ARG N 105 " ideal model delta sigma weight residual 112.59 105.99 6.60 1.22e+00 6.72e-01 2.92e+01 angle pdb=" N ASP N 106 " pdb=" CA ASP N 106 " pdb=" CB ASP N 106 " ideal model delta sigma weight residual 110.63 102.35 8.28 1.63e+00 3.76e-01 2.58e+01 angle pdb=" CA ARG A 228 " pdb=" C ARG A 228 " pdb=" O ARG A 228 " ideal model delta sigma weight residual 121.87 116.41 5.46 1.16e+00 7.43e-01 2.21e+01 ... (remaining 13517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 5261 17.36 - 34.72: 496 34.72 - 52.08: 98 52.08 - 69.44: 16 69.44 - 86.80: 13 Dihedral angle restraints: 5884 sinusoidal: 2273 harmonic: 3611 Sorted by residual: dihedral pdb=" CA ASN G 59 " pdb=" C ASN G 59 " pdb=" N PRO G 60 " pdb=" CA PRO G 60 " ideal model delta harmonic sigma weight residual -180.00 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 154.80 25.20 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA THR R 298 " pdb=" C THR R 298 " pdb=" N ARG R 299 " pdb=" CA ARG R 299 " ideal model delta harmonic sigma weight residual -180.00 -155.11 -24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 5881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1326 0.070 - 0.141: 172 0.141 - 0.211: 15 0.211 - 0.281: 4 0.281 - 0.352: 1 Chirality restraints: 1518 Sorted by residual: chirality pdb=" CA PRO G 49 " pdb=" N PRO G 49 " pdb=" C PRO G 49 " pdb=" CB PRO G 49 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA HIS B 225 " pdb=" N HIS B 225 " pdb=" C HIS B 225 " pdb=" CB HIS B 225 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ASP B 76 " pdb=" N ASP B 76 " pdb=" C ASP B 76 " pdb=" CB ASP B 76 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1515 not shown) Planarity restraints: 1712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 224 " -0.028 2.00e-02 2.50e+03 5.43e-02 2.95e+01 pdb=" C GLY B 224 " 0.094 2.00e-02 2.50e+03 pdb=" O GLY B 224 " -0.035 2.00e-02 2.50e+03 pdb=" N HIS B 225 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 111 " 0.021 2.00e-02 2.50e+03 2.91e-02 2.12e+01 pdb=" CG TRP E 111 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP E 111 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP E 111 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 111 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP E 111 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 111 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 111 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 111 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 111 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.020 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR B 59 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.001 2.00e-02 2.50e+03 ... (remaining 1709 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 101 2.51 - 3.11: 7711 3.11 - 3.71: 14840 3.71 - 4.30: 22394 4.30 - 4.90: 36626 Nonbonded interactions: 81672 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 1.916 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 1.995 3.040 nonbonded pdb=" NH1 ARG R 299 " pdb=" OD1 ASN R 300 " model vdw 2.027 3.120 nonbonded pdb=" OD1 ASN E 157 " pdb=" N GLY E 158 " model vdw 2.182 3.120 nonbonded pdb=" O LEU R 167 " pdb=" NE2 HIS R 173 " model vdw 2.213 3.120 ... (remaining 81667 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 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 : 0.011 0.058 9983 Z= 0.482 Angle : 0.868 9.051 13532 Z= 0.516 Chirality : 0.051 0.352 1518 Planarity : 0.005 0.054 1712 Dihedral : 14.585 86.802 3543 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 0.76 % Allowed : 0.67 % Favored : 98.57 % 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: -2.49 (0.23), residues: 1218 helix: -0.74 (0.27), residues: 359 sheet: -1.60 (0.28), residues: 309 loop : -2.24 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 118 TYR 0.060 0.003 TYR B 59 PHE 0.021 0.002 PHE A 246 TRP 0.073 0.003 TRP E 111 HIS 0.020 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.01146 ( 9978) covalent geometry : angle 0.86692 (13522) SS BOND : bond 0.00394 ( 5) SS BOND : angle 1.83502 ( 10) hydrogen bonds : bond 0.12903 ( 468) hydrogen bonds : angle 7.13169 ( 1290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 205 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 TYR cc_start: 0.7146 (t80) cc_final: 0.6929 (t80) REVERT: G 42 GLU cc_start: 0.7429 (pp20) cc_final: 0.7044 (tm-30) REVERT: R 294 GLU cc_start: 0.6173 (mp0) cc_final: 0.5699 (mp0) REVERT: R 303 MET cc_start: 0.4455 (tpt) cc_final: 0.4053 (mmt) outliers start: 8 outliers final: 2 residues processed: 208 average time/residue: 0.1126 time to fit residues: 31.1541 Evaluate side-chains 166 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 226 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 220 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.157058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.132048 restraints weight = 16228.567| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.92 r_work: 0.3786 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9983 Z= 0.131 Angle : 0.637 7.712 13532 Z= 0.336 Chirality : 0.043 0.206 1518 Planarity : 0.004 0.048 1712 Dihedral : 6.007 58.116 1366 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.43 % Allowed : 8.50 % Favored : 90.07 % 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: -1.56 (0.24), residues: 1218 helix: 0.17 (0.27), residues: 370 sheet: -1.02 (0.29), residues: 300 loop : -1.85 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 118 TYR 0.012 0.001 TYR R 145 PHE 0.025 0.001 PHE R 280 TRP 0.019 0.002 TRP R 243 HIS 0.011 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9978) covalent geometry : angle 0.63710 (13522) SS BOND : bond 0.00236 ( 5) SS BOND : angle 0.93970 ( 10) hydrogen bonds : bond 0.03891 ( 468) hydrogen bonds : angle 5.59546 ( 1290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 213 GLN cc_start: 0.6430 (mt0) cc_final: 0.5707 (pp30) REVERT: A 318 TYR cc_start: 0.7033 (t80) cc_final: 0.6765 (t80) REVERT: B 197 ARG cc_start: 0.6242 (mmp80) cc_final: 0.5969 (mmp80) REVERT: G 42 GLU cc_start: 0.7843 (pp20) cc_final: 0.7629 (tm-30) REVERT: N 6 GLU cc_start: 0.5591 (OUTLIER) cc_final: 0.5229 (mp0) REVERT: R 170 ARG cc_start: 0.4908 (mmm160) cc_final: 0.4047 (mmt-90) REVERT: R 176 ARG cc_start: 0.6830 (tmm160) cc_final: 0.6544 (tmm160) REVERT: R 294 GLU cc_start: 0.6597 (mp0) cc_final: 0.6102 (mp0) outliers start: 15 outliers final: 10 residues processed: 212 average time/residue: 0.1125 time to fit residues: 31.9376 Evaluate side-chains 176 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 63 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 95 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 371 ASN B 88 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN R 320 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.151379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.125921 restraints weight = 16508.720| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 1.94 r_work: 0.3693 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9983 Z= 0.253 Angle : 0.740 7.736 13532 Z= 0.392 Chirality : 0.047 0.165 1518 Planarity : 0.005 0.060 1712 Dihedral : 6.389 58.659 1366 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.87 % Allowed : 13.09 % Favored : 84.05 % 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: -1.81 (0.24), residues: 1218 helix: -0.28 (0.26), residues: 378 sheet: -1.22 (0.28), residues: 315 loop : -1.79 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 342 TYR 0.034 0.003 TYR E 163 PHE 0.020 0.002 PHE R 184 TRP 0.021 0.003 TRP R 243 HIS 0.010 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00587 ( 9978) covalent geometry : angle 0.73948 (13522) SS BOND : bond 0.00389 ( 5) SS BOND : angle 0.92271 ( 10) hydrogen bonds : bond 0.04769 ( 468) hydrogen bonds : angle 5.85903 ( 1290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7104 (pm20) REVERT: E 17 SER cc_start: 0.7227 (m) cc_final: 0.6962 (t) REVERT: G 42 GLU cc_start: 0.7864 (pp20) cc_final: 0.7599 (tm-30) REVERT: N 39 GLN cc_start: 0.7463 (tt0) cc_final: 0.7110 (tt0) REVERT: N 118 ARG cc_start: 0.7248 (ptp-170) cc_final: 0.6883 (ptp-170) REVERT: R 205 TYR cc_start: 0.3528 (OUTLIER) cc_final: 0.2643 (m-80) REVERT: R 262 GLU cc_start: 0.6859 (tp30) cc_final: 0.6454 (tp30) REVERT: R 294 GLU cc_start: 0.6624 (mp0) cc_final: 0.6084 (mp0) outliers start: 30 outliers final: 21 residues processed: 189 average time/residue: 0.1028 time to fit residues: 26.6053 Evaluate side-chains 183 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain N residue 6 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 205 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 290 LEU Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 392 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 116 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 279 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.154210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.128533 restraints weight = 16451.174| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.00 r_work: 0.3734 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9983 Z= 0.158 Angle : 0.638 8.502 13532 Z= 0.335 Chirality : 0.043 0.142 1518 Planarity : 0.004 0.056 1712 Dihedral : 5.879 59.918 1366 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.77 % Allowed : 15.57 % Favored : 81.66 % 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: -1.52 (0.24), residues: 1218 helix: 0.08 (0.27), residues: 370 sheet: -0.99 (0.28), residues: 312 loop : -1.74 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 342 TYR 0.014 0.002 TYR E 163 PHE 0.023 0.002 PHE R 280 TRP 0.020 0.002 TRP R 243 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 9978) covalent geometry : angle 0.63817 (13522) SS BOND : bond 0.00319 ( 5) SS BOND : angle 0.70929 ( 10) hydrogen bonds : bond 0.03976 ( 468) hydrogen bonds : angle 5.49781 ( 1290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 GLU cc_start: 0.5536 (OUTLIER) cc_final: 0.5270 (pm20) REVERT: B 197 ARG cc_start: 0.6248 (mmp80) cc_final: 0.6011 (mmp80) REVERT: B 226 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6901 (mt-10) REVERT: E 17 SER cc_start: 0.7231 (m) cc_final: 0.6987 (t) REVERT: E 77 ASN cc_start: 0.6999 (OUTLIER) cc_final: 0.6738 (m-40) REVERT: R 170 ARG cc_start: 0.5053 (mmm160) cc_final: 0.4057 (mmt-90) REVERT: R 205 TYR cc_start: 0.3538 (OUTLIER) cc_final: 0.2540 (m-80) REVERT: R 294 GLU cc_start: 0.6565 (mp0) cc_final: 0.6181 (mp0) outliers start: 29 outliers final: 18 residues processed: 200 average time/residue: 0.1098 time to fit residues: 29.7709 Evaluate side-chains 182 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 205 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 332 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 29 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 279 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.155275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.129790 restraints weight = 16394.731| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.95 r_work: 0.3749 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9983 Z= 0.142 Angle : 0.614 8.730 13532 Z= 0.323 Chirality : 0.043 0.147 1518 Planarity : 0.004 0.051 1712 Dihedral : 5.642 59.622 1366 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.25 % Allowed : 16.91 % Favored : 79.85 % 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: -1.32 (0.24), residues: 1218 helix: 0.26 (0.27), residues: 371 sheet: -0.84 (0.29), residues: 310 loop : -1.67 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 105 TYR 0.020 0.002 TYR R 289 PHE 0.038 0.002 PHE R 184 TRP 0.019 0.002 TRP R 243 HIS 0.011 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9978) covalent geometry : angle 0.61426 (13522) SS BOND : bond 0.00294 ( 5) SS BOND : angle 0.69893 ( 10) hydrogen bonds : bond 0.03813 ( 468) hydrogen bonds : angle 5.34444 ( 1290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.6153 (tp40) cc_final: 0.5290 (tm-30) REVERT: A 278 ASN cc_start: 0.7794 (m-40) cc_final: 0.7522 (m110) REVERT: A 299 GLU cc_start: 0.5609 (OUTLIER) cc_final: 0.5341 (pm20) REVERT: B 197 ARG cc_start: 0.6164 (mmp80) cc_final: 0.5956 (mmp80) REVERT: B 225 HIS cc_start: 0.6396 (OUTLIER) cc_final: 0.5870 (m-70) REVERT: E 17 SER cc_start: 0.7253 (m) cc_final: 0.6976 (t) REVERT: E 77 ASN cc_start: 0.6954 (OUTLIER) cc_final: 0.6609 (m-40) REVERT: E 132 THR cc_start: 0.6426 (m) cc_final: 0.6131 (m) REVERT: N 105 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6263 (ptt180) REVERT: R 170 ARG cc_start: 0.5067 (mmm160) cc_final: 0.4098 (mmt-90) REVERT: R 205 TYR cc_start: 0.3481 (OUTLIER) cc_final: 0.2340 (m-80) REVERT: R 262 GLU cc_start: 0.6709 (tp30) cc_final: 0.6493 (tp30) REVERT: R 292 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7374 (mm-30) REVERT: R 294 GLU cc_start: 0.6573 (mp0) cc_final: 0.5949 (mp0) outliers start: 34 outliers final: 22 residues processed: 197 average time/residue: 0.1051 time to fit residues: 28.2055 Evaluate side-chains 191 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 205 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 392 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 55 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 65 optimal weight: 0.0870 chunk 7 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 overall best weight: 2.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 279 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.153737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.128029 restraints weight = 16425.544| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.99 r_work: 0.3714 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9983 Z= 0.203 Angle : 0.677 9.643 13532 Z= 0.356 Chirality : 0.045 0.159 1518 Planarity : 0.005 0.061 1712 Dihedral : 5.605 58.061 1363 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.20 % Allowed : 17.67 % Favored : 78.13 % 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: -1.43 (0.24), residues: 1218 helix: 0.13 (0.27), residues: 361 sheet: -0.95 (0.29), residues: 310 loop : -1.63 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 105 TYR 0.019 0.002 TYR E 163 PHE 0.031 0.002 PHE R 280 TRP 0.023 0.002 TRP R 243 HIS 0.010 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 9978) covalent geometry : angle 0.67704 (13522) SS BOND : bond 0.00378 ( 5) SS BOND : angle 0.73671 ( 10) hydrogen bonds : bond 0.04219 ( 468) hydrogen bonds : angle 5.55483 ( 1290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.6221 (tp40) cc_final: 0.5323 (tm-30) REVERT: A 299 GLU cc_start: 0.5507 (OUTLIER) cc_final: 0.5210 (pm20) REVERT: B 266 HIS cc_start: 0.6058 (OUTLIER) cc_final: 0.5796 (t70) REVERT: B 290 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7226 (m-30) REVERT: E 17 SER cc_start: 0.7273 (m) cc_final: 0.7062 (t) REVERT: E 77 ASN cc_start: 0.7053 (OUTLIER) cc_final: 0.6758 (m-40) REVERT: E 132 THR cc_start: 0.6496 (m) cc_final: 0.6201 (m) REVERT: N 39 GLN cc_start: 0.7626 (tp40) cc_final: 0.7290 (tp40) REVERT: R 170 ARG cc_start: 0.5272 (mmm160) cc_final: 0.4262 (mmt-90) REVERT: R 205 TYR cc_start: 0.3487 (OUTLIER) cc_final: 0.2581 (m-80) REVERT: R 294 GLU cc_start: 0.6412 (mp0) cc_final: 0.5971 (mp0) outliers start: 44 outliers final: 28 residues processed: 183 average time/residue: 0.0995 time to fit residues: 25.1931 Evaluate side-chains 183 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 163 TYR Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 205 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 392 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 42 optimal weight: 8.9990 chunk 102 optimal weight: 0.1980 chunk 100 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 279 ASN A 294 GLN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.156571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.131059 restraints weight = 16257.559| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.99 r_work: 0.3773 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9983 Z= 0.122 Angle : 0.603 11.723 13532 Z= 0.312 Chirality : 0.042 0.151 1518 Planarity : 0.004 0.049 1712 Dihedral : 5.130 59.781 1363 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.82 % Allowed : 18.05 % Favored : 78.13 % 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: -1.09 (0.24), residues: 1218 helix: 0.43 (0.27), residues: 366 sheet: -0.75 (0.29), residues: 327 loop : -1.47 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 105 TYR 0.019 0.001 TYR R 289 PHE 0.035 0.001 PHE R 280 TRP 0.022 0.002 TRP R 243 HIS 0.010 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 9978) covalent geometry : angle 0.60302 (13522) SS BOND : bond 0.00278 ( 5) SS BOND : angle 0.62229 ( 10) hydrogen bonds : bond 0.03589 ( 468) hydrogen bonds : angle 5.18748 ( 1290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.6202 (tp40) cc_final: 0.5343 (tm-30) REVERT: A 318 TYR cc_start: 0.6883 (t80) cc_final: 0.6485 (t80) REVERT: B 146 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7546 (mm) REVERT: B 225 HIS cc_start: 0.6354 (OUTLIER) cc_final: 0.5820 (m-70) REVERT: B 266 HIS cc_start: 0.5874 (OUTLIER) cc_final: 0.5578 (t70) REVERT: B 273 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.7061 (pt) REVERT: B 290 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.6614 (t0) REVERT: E 17 SER cc_start: 0.7269 (m) cc_final: 0.7042 (t) REVERT: E 77 ASN cc_start: 0.6838 (OUTLIER) cc_final: 0.6595 (m-40) REVERT: E 132 THR cc_start: 0.6418 (m) cc_final: 0.6099 (m) REVERT: G 37 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.6143 (mt) REVERT: N 105 ARG cc_start: 0.6705 (OUTLIER) cc_final: 0.5861 (ptt-90) REVERT: R 170 ARG cc_start: 0.5105 (mmm160) cc_final: 0.4152 (mmt-90) REVERT: R 205 TYR cc_start: 0.3478 (OUTLIER) cc_final: 0.2408 (m-80) REVERT: R 289 TYR cc_start: 0.4433 (t80) cc_final: 0.4103 (t80) REVERT: R 292 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7337 (mm-30) REVERT: R 294 GLU cc_start: 0.6430 (mp0) cc_final: 0.6095 (mp0) REVERT: R 404 PHE cc_start: 0.6568 (m-80) cc_final: 0.6244 (m-80) outliers start: 40 outliers final: 25 residues processed: 199 average time/residue: 0.1014 time to fit residues: 27.4046 Evaluate side-chains 189 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 205 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 392 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 0.6980 chunk 52 optimal weight: 0.0870 chunk 43 optimal weight: 7.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 279 ASN B 340 ASN N 3 GLN N 5 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.157317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.131771 restraints weight = 16273.163| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 2.00 r_work: 0.3786 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9983 Z= 0.120 Angle : 0.610 10.317 13532 Z= 0.314 Chirality : 0.042 0.150 1518 Planarity : 0.004 0.050 1712 Dihedral : 4.994 59.727 1363 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.20 % Allowed : 18.05 % Favored : 77.75 % 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: -0.99 (0.24), residues: 1218 helix: 0.55 (0.27), residues: 370 sheet: -0.69 (0.29), residues: 317 loop : -1.44 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 105 TYR 0.017 0.001 TYR R 289 PHE 0.040 0.001 PHE R 280 TRP 0.022 0.001 TRP R 243 HIS 0.009 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9978) covalent geometry : angle 0.60969 (13522) SS BOND : bond 0.00283 ( 5) SS BOND : angle 0.65356 ( 10) hydrogen bonds : bond 0.03535 ( 468) hydrogen bonds : angle 5.12362 ( 1290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 TYR cc_start: 0.6878 (t80) cc_final: 0.6495 (t80) REVERT: B 46 ARG cc_start: 0.7188 (mtm-85) cc_final: 0.6834 (mtt180) REVERT: B 225 HIS cc_start: 0.6297 (OUTLIER) cc_final: 0.5829 (m-70) REVERT: B 266 HIS cc_start: 0.5838 (OUTLIER) cc_final: 0.5543 (t70) REVERT: B 290 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.6650 (t0) REVERT: E 17 SER cc_start: 0.7244 (m) cc_final: 0.7036 (t) REVERT: E 77 ASN cc_start: 0.6737 (OUTLIER) cc_final: 0.6516 (m-40) REVERT: E 95 TYR cc_start: 0.7458 (m-80) cc_final: 0.7052 (m-80) REVERT: E 132 THR cc_start: 0.6403 (m) cc_final: 0.6061 (m) REVERT: G 37 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6156 (mt) REVERT: N 46 GLU cc_start: 0.7634 (pp20) cc_final: 0.7325 (pp20) REVERT: R 170 ARG cc_start: 0.4962 (mmm160) cc_final: 0.3982 (mmt-90) REVERT: R 205 TYR cc_start: 0.3362 (OUTLIER) cc_final: 0.2380 (m-80) REVERT: R 289 TYR cc_start: 0.4305 (t80) cc_final: 0.4005 (t80) REVERT: R 292 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7424 (mm-30) REVERT: R 294 GLU cc_start: 0.6417 (mp0) cc_final: 0.6099 (mp0) REVERT: R 404 PHE cc_start: 0.6560 (m-80) cc_final: 0.6256 (m-80) outliers start: 44 outliers final: 30 residues processed: 199 average time/residue: 0.1057 time to fit residues: 28.6640 Evaluate side-chains 195 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 205 TYR Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 392 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 88 optimal weight: 0.0570 chunk 80 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 chunk 70 optimal weight: 0.0980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 3 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.160414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.135709 restraints weight = 16254.150| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.98 r_work: 0.3840 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9983 Z= 0.107 Angle : 0.601 10.789 13532 Z= 0.308 Chirality : 0.041 0.153 1518 Planarity : 0.004 0.046 1712 Dihedral : 4.767 56.450 1363 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.96 % Allowed : 19.58 % Favored : 77.46 % 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: -0.79 (0.24), residues: 1218 helix: 0.72 (0.27), residues: 373 sheet: -0.64 (0.29), residues: 330 loop : -1.31 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 105 TYR 0.017 0.001 TYR R 289 PHE 0.037 0.001 PHE R 280 TRP 0.023 0.001 TRP R 243 HIS 0.009 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9978) covalent geometry : angle 0.60060 (13522) SS BOND : bond 0.00329 ( 5) SS BOND : angle 0.58227 ( 10) hydrogen bonds : bond 0.03360 ( 468) hydrogen bonds : angle 4.99580 ( 1290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 TYR cc_start: 0.6888 (t80) cc_final: 0.6468 (t80) REVERT: B 46 ARG cc_start: 0.7194 (mtm-85) cc_final: 0.6797 (mtt180) REVERT: B 85 TYR cc_start: 0.6501 (m-80) cc_final: 0.6224 (m-80) REVERT: B 266 HIS cc_start: 0.5691 (OUTLIER) cc_final: 0.5416 (t70) REVERT: B 290 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.6547 (t0) REVERT: E 17 SER cc_start: 0.7195 (m) cc_final: 0.6963 (t) REVERT: E 73 ASP cc_start: 0.5962 (t0) cc_final: 0.5142 (t0) REVERT: E 95 TYR cc_start: 0.7384 (m-80) cc_final: 0.7004 (m-80) REVERT: E 132 THR cc_start: 0.6276 (m) cc_final: 0.5920 (m) REVERT: G 37 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6144 (mt) REVERT: N 105 ARG cc_start: 0.6768 (ptm-80) cc_final: 0.6060 (ptt-90) REVERT: R 170 ARG cc_start: 0.4795 (mmm160) cc_final: 0.3841 (mmt-90) REVERT: R 289 TYR cc_start: 0.4376 (t80) cc_final: 0.4061 (t80) REVERT: R 294 GLU cc_start: 0.6336 (mp0) cc_final: 0.6088 (mp0) REVERT: R 404 PHE cc_start: 0.6442 (m-80) cc_final: 0.6157 (m-80) outliers start: 31 outliers final: 25 residues processed: 204 average time/residue: 0.1070 time to fit residues: 29.9031 Evaluate side-chains 191 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 349 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 114 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 279 ASN N 3 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.157878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.132605 restraints weight = 16182.707| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.98 r_work: 0.3792 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9983 Z= 0.133 Angle : 0.626 10.639 13532 Z= 0.323 Chirality : 0.043 0.149 1518 Planarity : 0.004 0.049 1712 Dihedral : 4.939 53.059 1363 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.15 % Allowed : 19.87 % Favored : 76.98 % 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: -0.83 (0.24), residues: 1218 helix: 0.71 (0.27), residues: 371 sheet: -0.68 (0.29), residues: 327 loop : -1.32 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 105 TYR 0.025 0.001 TYR E 178 PHE 0.037 0.002 PHE R 280 TRP 0.019 0.001 TRP R 243 HIS 0.009 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9978) covalent geometry : angle 0.62557 (13522) SS BOND : bond 0.00319 ( 5) SS BOND : angle 0.55898 ( 10) hydrogen bonds : bond 0.03573 ( 468) hydrogen bonds : angle 5.07987 ( 1290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2436 Ramachandran restraints generated. 1218 Oldfield, 0 Emsley, 1218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.5939 (tp40) cc_final: 0.5266 (tm-30) REVERT: A 318 TYR cc_start: 0.6954 (t80) cc_final: 0.6540 (t80) REVERT: B 46 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6824 (mtt180) REVERT: B 65 THR cc_start: 0.5967 (p) cc_final: 0.5645 (p) REVERT: B 266 HIS cc_start: 0.5786 (OUTLIER) cc_final: 0.5546 (t70) REVERT: B 290 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.6629 (t0) REVERT: E 17 SER cc_start: 0.7221 (m) cc_final: 0.6994 (t) REVERT: E 132 THR cc_start: 0.6205 (m) cc_final: 0.5864 (m) REVERT: G 37 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6239 (mt) REVERT: N 105 ARG cc_start: 0.7001 (ptm-80) cc_final: 0.6377 (ptt-90) REVERT: R 170 ARG cc_start: 0.4945 (mmm160) cc_final: 0.4016 (mmt-90) REVERT: R 289 TYR cc_start: 0.4356 (t80) cc_final: 0.4011 (t80) REVERT: R 294 GLU cc_start: 0.6419 (mp0) cc_final: 0.6104 (mp0) REVERT: R 404 PHE cc_start: 0.6589 (m-80) cc_final: 0.6319 (m-80) outliers start: 33 outliers final: 27 residues processed: 188 average time/residue: 0.1161 time to fit residues: 29.2210 Evaluate side-chains 193 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 163 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 214 VAL Chi-restraints excluded: chain E residue 217 CYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 300 ASN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain R residue 349 LEU Chi-restraints excluded: chain R residue 366 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 109 optimal weight: 0.0570 chunk 8 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.159241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.134137 restraints weight = 16374.259| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.96 r_work: 0.3815 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9983 Z= 0.122 Angle : 0.621 10.080 13532 Z= 0.319 Chirality : 0.042 0.150 1518 Planarity : 0.004 0.053 1712 Dihedral : 4.903 52.859 1363 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.87 % Allowed : 20.53 % Favored : 76.60 % 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: -0.77 (0.24), residues: 1218 helix: 0.80 (0.27), residues: 371 sheet: -0.65 (0.29), residues: 326 loop : -1.32 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 105 TYR 0.016 0.001 TYR R 289 PHE 0.037 0.001 PHE R 280 TRP 0.020 0.001 TRP R 243 HIS 0.008 0.001 HIS R 171 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9978) covalent geometry : angle 0.62122 (13522) SS BOND : bond 0.00329 ( 5) SS BOND : angle 0.51904 ( 10) hydrogen bonds : bond 0.03453 ( 468) hydrogen bonds : angle 5.03649 ( 1290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2824.43 seconds wall clock time: 49 minutes 3.33 seconds (2943.33 seconds total)