Starting phenix.real_space_refine on Fri Mar 14 07:19:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rg9_24445/03_2025/7rg9_24445_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rg9_24445/03_2025/7rg9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rg9_24445/03_2025/7rg9_24445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rg9_24445/03_2025/7rg9_24445.map" model { file = "/net/cci-nas-00/data/ceres_data/7rg9_24445/03_2025/7rg9_24445_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rg9_24445/03_2025/7rg9_24445_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'GLU:plan': 1, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 5.98, per 1000 atoms: 0.61 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: 3.16 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.09 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: 2.86 Time building geometry restraints manager: 3.63 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.750 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.560 ------------------------------------------------------------------------------- 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 9978 Z= 0.745 Angle : 0.867 9.051 13522 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 : 16.10 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.073 0.003 TRP E 111 HIS 0.020 0.002 HIS A 357 PHE 0.021 0.002 PHE A 246 TYR 0.060 0.003 TYR B 59 ARG 0.013 0.001 ARG N 118 *********************** 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 : 1.117 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: 0.6926 (t80) REVERT: G 42 GLU cc_start: 0.7429 (pp20) cc_final: 0.7045 (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: 0.4054 (mmt) outliers start: 8 outliers final: 2 residues processed: 208 average time/residue: 0.2545 time to fit residues: 70.5925 Evaluate side-chains 167 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 165 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 102 optimal weight: 0.0670 chunk 91 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.156653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.131671 restraints weight = 16137.198| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.92 r_work: 0.3781 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9978 Z= 0.186 Angle : 0.643 7.667 13522 Z= 0.340 Chirality : 0.043 0.200 1518 Planarity : 0.004 0.047 1712 Dihedral : 6.091 59.373 1366 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.15 % Allowed : 8.69 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.24), residues: 1218 helix: 0.13 (0.27), residues: 370 sheet: -1.08 (0.29), residues: 306 loop : -1.84 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 243 HIS 0.011 0.001 HIS A 357 PHE 0.025 0.001 PHE R 280 TYR 0.012 0.001 TYR R 145 ARG 0.004 0.001 ARG N 118 *********************** 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 212 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: A 318 TYR cc_start: 0.7025 (t80) cc_final: 0.6746 (t80) REVERT: B 197 ARG cc_start: 0.6257 (mmp80) cc_final: 0.5978 (mmp80) REVERT: E 183 LEU cc_start: 0.8516 (tp) cc_final: 0.8289 (mm) REVERT: G 42 GLU cc_start: 0.7836 (pp20) cc_final: 0.7625 (tm-30) REVERT: N 120 GLN cc_start: 0.6947 (pm20) cc_final: 0.6642 (pm20) REVERT: R 170 ARG cc_start: 0.4888 (mmm160) cc_final: 0.4014 (mmt-90) REVERT: R 176 ARG cc_start: 0.6825 (tmm160) cc_final: 0.6569 (tmm160) REVERT: R 292 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7440 (mm-30) REVERT: R 294 GLU cc_start: 0.6603 (mp0) cc_final: 0.6057 (mp0) REVERT: R 405 VAL cc_start: 0.6850 (m) cc_final: 0.6422 (t) outliers start: 12 outliers final: 9 residues processed: 208 average time/residue: 0.2644 time to fit residues: 73.6746 Evaluate side-chains 175 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 214 VAL Chi-restraints excluded: chain G residue 50 LEU 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 77 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.150594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.125012 restraints weight = 16684.347| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.96 r_work: 0.3679 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 9978 Z= 0.435 Angle : 0.790 7.855 13522 Z= 0.418 Chirality : 0.049 0.178 1518 Planarity : 0.005 0.064 1712 Dihedral : 6.623 57.845 1366 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.15 % Allowed : 13.37 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.24), residues: 1218 helix: -0.41 (0.27), residues: 370 sheet: -1.28 (0.28), residues: 317 loop : -1.80 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP R 243 HIS 0.011 0.002 HIS A 357 PHE 0.021 0.003 PHE N 108 TYR 0.041 0.003 TYR E 163 ARG 0.005 0.001 ARG R 421 *********************** 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 193 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 TYR cc_start: 0.7140 (t80) cc_final: 0.6866 (t80) REVERT: B 10 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7089 (pm20) REVERT: E 17 SER cc_start: 0.7175 (m) cc_final: 0.6933 (t) REVERT: E 77 ASN cc_start: 0.7216 (OUTLIER) cc_final: 0.6751 (m-40) REVERT: G 42 GLU cc_start: 0.7813 (pp20) cc_final: 0.7488 (tm-30) REVERT: N 86 LEU cc_start: 0.8219 (mm) cc_final: 0.7980 (mm) REVERT: N 105 ARG cc_start: 0.6797 (mtm110) cc_final: 0.5677 (mtm180) REVERT: R 205 TYR cc_start: 0.3660 (OUTLIER) cc_final: 0.2728 (m-80) REVERT: R 262 GLU cc_start: 0.6911 (tp30) cc_final: 0.6500 (tp30) REVERT: R 292 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7386 (mm-30) REVERT: R 294 GLU cc_start: 0.6546 (mp0) cc_final: 0.6036 (mp0) outliers start: 33 outliers final: 21 residues processed: 184 average time/residue: 0.2499 time to fit residues: 62.9960 Evaluate side-chains 174 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 187 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 77 ASN 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 64 VAL 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 392 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 68 optimal weight: 0.0770 chunk 25 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN R 240 ASN R 320 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.153083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.127580 restraints weight = 16284.226| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.98 r_work: 0.3717 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9978 Z= 0.260 Angle : 0.663 7.665 13522 Z= 0.349 Chirality : 0.044 0.148 1518 Planarity : 0.004 0.065 1712 Dihedral : 6.056 59.773 1366 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.44 % Allowed : 15.57 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.23), residues: 1218 helix: -0.06 (0.27), residues: 372 sheet: -1.07 (0.28), residues: 311 loop : -1.77 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 243 HIS 0.007 0.001 HIS A 357 PHE 0.022 0.002 PHE R 280 TYR 0.017 0.002 TYR E 163 ARG 0.004 0.000 ARG N 105 *********************** 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 204 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8331 (p0) REVERT: A 299 GLU cc_start: 0.5395 (OUTLIER) cc_final: 0.5117 (pm20) REVERT: A 318 TYR cc_start: 0.7052 (t80) cc_final: 0.6810 (t80) REVERT: B 197 ARG cc_start: 0.6196 (mmp80) cc_final: 0.5933 (mmp80) REVERT: B 226 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: E 17 SER cc_start: 0.7217 (m) cc_final: 0.6933 (t) REVERT: E 151 LYS cc_start: 0.6733 (tppt) cc_final: 0.6208 (tttm) REVERT: G 50 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6965 (mm) REVERT: N 86 LEU cc_start: 0.8110 (mm) cc_final: 0.7887 (mm) REVERT: N 105 ARG cc_start: 0.6681 (mtm110) cc_final: 0.5921 (ptt180) REVERT: R 170 ARG cc_start: 0.5079 (mmm160) cc_final: 0.4051 (mmt-90) REVERT: R 205 TYR cc_start: 0.3679 (OUTLIER) cc_final: 0.2601 (m-80) REVERT: R 292 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7457 (mm-30) REVERT: R 294 GLU cc_start: 0.6615 (mp0) cc_final: 0.6123 (mp0) outliers start: 36 outliers final: 21 residues processed: 192 average time/residue: 0.2522 time to fit residues: 65.4228 Evaluate side-chains 180 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 239 ASN 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 43 ILE Chi-restraints excluded: chain B residue 158 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 315 VAL 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 G residue 50 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 25 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 114 optimal weight: 0.0570 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.154180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.128365 restraints weight = 16329.048| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.00 r_work: 0.3724 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9978 Z= 0.243 Angle : 0.637 8.061 13522 Z= 0.335 Chirality : 0.044 0.182 1518 Planarity : 0.004 0.066 1712 Dihedral : 5.837 59.586 1366 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.01 % Allowed : 17.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.24), residues: 1218 helix: 0.07 (0.27), residues: 371 sheet: -0.94 (0.29), residues: 312 loop : -1.66 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 243 HIS 0.005 0.001 HIS A 357 PHE 0.023 0.002 PHE R 280 TYR 0.014 0.002 TYR E 163 ARG 0.003 0.000 ARG N 105 *********************** 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 211 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.5966 (tp40) cc_final: 0.5175 (tm-30) REVERT: A 239 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8319 (p0) REVERT: A 299 GLU cc_start: 0.5524 (OUTLIER) cc_final: 0.5281 (pm20) REVERT: A 318 TYR cc_start: 0.7006 (t80) cc_final: 0.6791 (t80) REVERT: B 101 MET cc_start: 0.7523 (mtm) cc_final: 0.7254 (mtm) REVERT: B 197 ARG cc_start: 0.6194 (mmp80) cc_final: 0.5932 (mmp80) REVERT: B 290 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.6505 (t0) REVERT: E 17 SER cc_start: 0.7274 (m) cc_final: 0.7020 (t) REVERT: E 77 ASN cc_start: 0.7043 (OUTLIER) cc_final: 0.6714 (m-40) REVERT: E 151 LYS cc_start: 0.6811 (tppt) cc_final: 0.6277 (tttm) REVERT: N 39 GLN cc_start: 0.7667 (tt0) cc_final: 0.7125 (tt0) REVERT: N 105 ARG cc_start: 0.6681 (mtm110) cc_final: 0.5893 (ptt180) REVERT: R 170 ARG cc_start: 0.5174 (mmm160) cc_final: 0.4144 (mmt-90) REVERT: R 205 TYR cc_start: 0.3420 (OUTLIER) cc_final: 0.2328 (m-80) REVERT: R 233 MET cc_start: 0.6238 (tpp) cc_final: 0.5645 (tpp) REVERT: R 294 GLU cc_start: 0.6499 (mp0) cc_final: 0.6086 (mp0) outliers start: 42 outliers final: 27 residues processed: 198 average time/residue: 0.2419 time to fit residues: 64.9291 Evaluate side-chains 186 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 1.126 ------------------------------------------------------------------------------- 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 239 ASN 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 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 177 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 263 THR 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 143 VAL 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 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 392 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 0.0870 chunk 79 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 13 optimal weight: 0.2980 chunk 69 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.158424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.133066 restraints weight = 16321.932| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.95 r_work: 0.3792 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9978 Z= 0.155 Angle : 0.583 9.418 13522 Z= 0.304 Chirality : 0.041 0.149 1518 Planarity : 0.004 0.056 1712 Dihedral : 4.999 59.606 1363 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.06 % Allowed : 18.91 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.24), residues: 1218 helix: 0.55 (0.27), residues: 372 sheet: -0.77 (0.29), residues: 334 loop : -1.47 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 243 HIS 0.005 0.001 HIS A 357 PHE 0.043 0.001 PHE R 184 TYR 0.011 0.001 TYR B 85 ARG 0.005 0.000 ARG A 342 *********************** 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 217 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.6081 (tp40) cc_final: 0.5255 (tm-30) REVERT: A 318 TYR cc_start: 0.6905 (t80) cc_final: 0.6703 (t80) REVERT: A 358 TYR cc_start: 0.7184 (m-80) cc_final: 0.6842 (m-80) REVERT: B 43 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.7047 (pt) REVERT: B 46 ARG cc_start: 0.7174 (mtm-85) cc_final: 0.6865 (mpt180) REVERT: B 225 HIS cc_start: 0.6168 (OUTLIER) cc_final: 0.5785 (m-70) REVERT: B 290 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6533 (t0) REVERT: E 17 SER cc_start: 0.7255 (m) cc_final: 0.7019 (t) REVERT: G 37 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6193 (mt) REVERT: N 39 GLN cc_start: 0.7524 (tt0) cc_final: 0.6890 (tt0) REVERT: R 170 ARG cc_start: 0.4870 (mmm160) cc_final: 0.3875 (mmt-90) REVERT: R 205 TYR cc_start: 0.3399 (OUTLIER) cc_final: 0.2333 (m-80) REVERT: R 233 MET cc_start: 0.6112 (tpp) cc_final: 0.5632 (tpp) REVERT: R 294 GLU cc_start: 0.6464 (mp0) cc_final: 0.5779 (mp0) REVERT: R 404 PHE cc_start: 0.6573 (m-80) cc_final: 0.6309 (m-80) outliers start: 32 outliers final: 20 residues processed: 205 average time/residue: 0.2470 time to fit residues: 68.7641 Evaluate side-chains 188 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 A residue 379 CYS Chi-restraints excluded: chain B residue 43 ILE 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 290 ASP Chi-restraints excluded: chain B residue 315 VAL 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 G residue 37 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 91 THR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 12 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 3 GLN R 171 HIS ** 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 = 0.4210 r_free = 0.4210 target = 0.157754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.132528 restraints weight = 16390.083| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.00 r_work: 0.3788 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9978 Z= 0.170 Angle : 0.592 8.996 13522 Z= 0.309 Chirality : 0.042 0.156 1518 Planarity : 0.004 0.056 1712 Dihedral : 4.952 58.112 1363 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.15 % Allowed : 20.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.24), residues: 1218 helix: 0.61 (0.27), residues: 370 sheet: -0.60 (0.29), residues: 309 loop : -1.43 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 297 HIS 0.009 0.001 HIS R 171 PHE 0.035 0.001 PHE R 280 TYR 0.023 0.001 TYR E 178 ARG 0.004 0.000 ARG N 105 *********************** 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 208 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7184 (mtm-85) cc_final: 0.6887 (mpt180) REVERT: B 290 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.6616 (t0) REVERT: E 17 SER cc_start: 0.7241 (m) cc_final: 0.6989 (t) REVERT: E 34 MET cc_start: 0.7038 (mmm) cc_final: 0.6797 (mmt) REVERT: E 95 TYR cc_start: 0.7432 (m-80) cc_final: 0.6997 (m-80) REVERT: G 37 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6285 (mt) REVERT: N 39 GLN cc_start: 0.7473 (tt0) cc_final: 0.6839 (tt0) REVERT: R 170 ARG cc_start: 0.4869 (mmm160) cc_final: 0.3923 (mmt-90) REVERT: R 289 TYR cc_start: 0.4525 (t80) cc_final: 0.3504 (t80) REVERT: R 294 GLU cc_start: 0.6323 (mp0) cc_final: 0.6096 (mp0) REVERT: R 404 PHE cc_start: 0.6539 (m-80) cc_final: 0.6262 (m-80) outliers start: 33 outliers final: 24 residues processed: 193 average time/residue: 0.2493 time to fit residues: 65.0782 Evaluate side-chains 191 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 319 THR Chi-restraints excluded: chain A residue 364 THR 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 290 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 132 THR 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 91 THR Chi-restraints excluded: chain N residue 93 VAL 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 0.0060 chunk 29 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 overall best weight: 2.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 3 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.155224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.129285 restraints weight = 16383.069| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.00 r_work: 0.3729 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9978 Z= 0.290 Angle : 0.687 9.126 13522 Z= 0.356 Chirality : 0.045 0.168 1518 Planarity : 0.004 0.063 1712 Dihedral : 5.404 55.535 1363 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.63 % Allowed : 19.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1218 helix: 0.29 (0.27), residues: 366 sheet: -0.61 (0.30), residues: 308 loop : -1.47 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 297 HIS 0.003 0.001 HIS A 357 PHE 0.034 0.002 PHE R 280 TYR 0.017 0.002 TYR E 215 ARG 0.005 0.000 ARG N 105 *********************** 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 200 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.5904 (tp40) cc_final: 0.5115 (tm-30) REVERT: A 299 GLU cc_start: 0.5479 (OUTLIER) cc_final: 0.5177 (pm20) REVERT: B 290 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.6595 (t0) REVERT: E 95 TYR cc_start: 0.7493 (m-80) cc_final: 0.7214 (m-80) REVERT: N 39 GLN cc_start: 0.7576 (tt0) cc_final: 0.6978 (tt0) REVERT: N 105 ARG cc_start: 0.6781 (mtm110) cc_final: 0.5899 (ptt180) REVERT: R 170 ARG cc_start: 0.5247 (mmm160) cc_final: 0.4138 (mmt-90) REVERT: R 205 TYR cc_start: 0.3455 (OUTLIER) cc_final: 0.2430 (m-80) REVERT: R 233 MET cc_start: 0.5757 (mmm) cc_final: 0.5556 (mmm) REVERT: R 289 TYR cc_start: 0.4584 (t80) cc_final: 0.4337 (t80) REVERT: R 292 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7788 (mm-30) REVERT: R 294 GLU cc_start: 0.6350 (mp0) cc_final: 0.5993 (mp0) outliers start: 38 outliers final: 31 residues processed: 185 average time/residue: 0.2262 time to fit residues: 57.5869 Evaluate side-chains 194 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 177 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 263 THR 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 132 THR 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 N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL 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 366 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 86 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 1 GLN N 3 GLN N 5 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.158062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.132452 restraints weight = 16256.567| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.99 r_work: 0.3790 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3675 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9978 Z= 0.174 Angle : 0.609 9.968 13522 Z= 0.315 Chirality : 0.042 0.153 1518 Planarity : 0.004 0.063 1712 Dihedral : 4.984 52.976 1363 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.34 % Allowed : 20.25 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.24), residues: 1218 helix: 0.55 (0.28), residues: 370 sheet: -0.57 (0.30), residues: 316 loop : -1.35 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 243 HIS 0.005 0.001 HIS A 357 PHE 0.035 0.002 PHE R 280 TYR 0.010 0.001 TYR E 215 ARG 0.004 0.000 ARG N 105 *********************** 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 200 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.5918 (tp40) cc_final: 0.5192 (tm-30) REVERT: B 290 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.6498 (t0) REVERT: E 77 ASN cc_start: 0.6683 (OUTLIER) cc_final: 0.6461 (m-40) REVERT: E 95 TYR cc_start: 0.7400 (m-80) cc_final: 0.7013 (m-80) REVERT: G 37 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6161 (mt) REVERT: N 39 GLN cc_start: 0.7487 (tt0) cc_final: 0.6881 (tt0) REVERT: N 105 ARG cc_start: 0.6658 (mtm110) cc_final: 0.5769 (ptt180) REVERT: R 170 ARG cc_start: 0.4935 (mmm160) cc_final: 0.3932 (mmt-90) REVERT: R 205 TYR cc_start: 0.3367 (OUTLIER) cc_final: 0.2313 (m-80) REVERT: R 294 GLU cc_start: 0.6250 (mp0) cc_final: 0.6029 (mp0) REVERT: R 404 PHE cc_start: 0.6626 (m-80) cc_final: 0.6304 (m-80) outliers start: 35 outliers final: 30 residues processed: 188 average time/residue: 0.2579 time to fit residues: 66.5119 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 : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 43 ILE 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 290 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 132 THR 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 N residue 93 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 103 optimal weight: 0.0050 chunk 106 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 3 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.157863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.132042 restraints weight = 16331.162| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.00 r_work: 0.3783 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9978 Z= 0.190 Angle : 0.625 9.498 13522 Z= 0.322 Chirality : 0.042 0.154 1518 Planarity : 0.004 0.061 1712 Dihedral : 4.935 50.618 1363 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.15 % Allowed : 20.63 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.24), residues: 1218 helix: 0.58 (0.27), residues: 372 sheet: -0.62 (0.29), residues: 321 loop : -1.31 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 243 HIS 0.004 0.001 HIS A 357 PHE 0.040 0.002 PHE R 280 TYR 0.023 0.001 TYR E 178 ARG 0.005 0.000 ARG N 105 ********************** 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 197 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 213 GLN cc_start: 0.5911 (tp40) cc_final: 0.5209 (tm-30) REVERT: B 46 ARG cc_start: 0.7297 (mtm-85) cc_final: 0.6991 (mpt180) REVERT: B 290 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.6557 (t0) REVERT: E 34 MET cc_start: 0.7166 (mmm) cc_final: 0.6929 (mmt) REVERT: E 95 TYR cc_start: 0.7424 (m-80) cc_final: 0.6997 (m-80) REVERT: N 39 GLN cc_start: 0.7507 (tt0) cc_final: 0.6888 (tt0) REVERT: R 170 ARG cc_start: 0.4937 (mmm160) cc_final: 0.3976 (mmt-90) REVERT: R 205 TYR cc_start: 0.3453 (OUTLIER) cc_final: 0.2416 (m-80) REVERT: R 292 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7855 (mm-30) REVERT: R 294 GLU cc_start: 0.6296 (mp0) cc_final: 0.6068 (mp0) REVERT: R 404 PHE cc_start: 0.6643 (m-80) cc_final: 0.6316 (m-80) outliers start: 33 outliers final: 29 residues processed: 185 average time/residue: 0.2642 time to fit residues: 66.4233 Evaluate side-chains 191 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 290 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 132 THR 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 91 THR Chi-restraints excluded: chain N residue 93 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 79 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 114 optimal weight: 0.0040 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN N 3 GLN ** R 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.159786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.134280 restraints weight = 16154.669| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 1.98 r_work: 0.3815 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9978 Z= 0.166 Angle : 0.602 9.854 13522 Z= 0.310 Chirality : 0.042 0.157 1518 Planarity : 0.004 0.058 1712 Dihedral : 4.730 50.757 1363 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.25 % Allowed : 20.34 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.25), residues: 1218 helix: 0.77 (0.28), residues: 372 sheet: -0.56 (0.29), residues: 331 loop : -1.31 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 243 HIS 0.005 0.001 HIS A 357 PHE 0.037 0.001 PHE R 280 TYR 0.010 0.001 TYR E 215 ARG 0.007 0.000 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6111.46 seconds wall clock time: 106 minutes 11.52 seconds (6371.52 seconds total)