Starting phenix.real_space_refine on Fri Jul 19 04:53:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo2_42425/07_2024/8uo2_42425.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo2_42425/07_2024/8uo2_42425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo2_42425/07_2024/8uo2_42425.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo2_42425/07_2024/8uo2_42425.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo2_42425/07_2024/8uo2_42425.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uo2_42425/07_2024/8uo2_42425.cif" } resolution = 3.6 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= 0.018 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 32 5.16 5 C 4126 2.51 5 N 1154 2.21 5 O 1189 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 22": "OE1" <-> "OE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 122": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6504 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 1920 Classifications: {'peptide': 283} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 6, 'TRANS': 276} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 435 Unresolved non-hydrogen angles: 536 Unresolved non-hydrogen dihedrals: 343 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 18, 'PHE:plan': 1, 'GLU:plan': 20, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 278 Chain: "B" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2396 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 242 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 7, 'ARG:plan': 9, 'ASN:plan1': 5, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 145 Chain: "G" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 341 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 1800 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 7, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 492 Unresolved non-hydrogen angles: 629 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 54 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 252 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.54, per 1000 atoms: 0.70 Number of scatterers: 6504 At special positions: 0 Unit cell: (84.1669, 135.361, 98.0501, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 3 15.00 O 1189 8.00 N 1154 7.00 C 4126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.48 Conformation dependent library (CDL) restraints added in 1.2 seconds 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 49.4% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 3.698A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 90 through 109 Processing helix chain 'A' and resid 161 through 165 removed outlier: 3.736A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 165' Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.775A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.692A pdb=" N SER A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.591A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.257A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.507A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 391 removed outlier: 3.760A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.661A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.760A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.661A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 32 through 61 removed outlier: 4.032A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 3.850A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.748A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.281A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 3.635A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 208 through 237 removed outlier: 3.746A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 4.025A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.858A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE R 298 " --> pdb=" O ILE R 294 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN R 299 " --> pdb=" O VAL R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.605A pdb=" N TYR R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 326 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 339 removed outlier: 3.505A pdb=" N LEU R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 213 removed outlier: 6.370A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.656A 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 52 removed outlier: 3.810A 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: 3.693A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 103 removed outlier: 6.951A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.865A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.970A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA B 208 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 243 removed outlier: 3.848A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 277 349 hydrogen bonds defined for protein. 1020 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: 1.76 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1697 1.33 - 1.45: 1252 1.45 - 1.57: 3635 1.57 - 1.69: 5 1.69 - 1.81: 40 Bond restraints: 6629 Sorted by residual: bond pdb=" C ALA A 366 " pdb=" N VAL A 367 " ideal model delta sigma weight residual 1.334 1.450 -0.116 1.26e-02 6.30e+03 8.45e+01 bond pdb=" CA LYS A 338 " pdb=" C LYS A 338 " ideal model delta sigma weight residual 1.524 1.483 0.040 1.27e-02 6.20e+03 1.01e+01 bond pdb=" N VAL B 133 " pdb=" CA VAL B 133 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.81e+00 bond pdb=" N ILE A 257 " pdb=" CA ILE A 257 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.19e-02 7.06e+03 9.42e+00 bond pdb=" CA SER B 245 " pdb=" CB SER B 245 " ideal model delta sigma weight residual 1.535 1.471 0.064 2.09e-02 2.29e+03 9.32e+00 ... (remaining 6624 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.83: 144 106.83 - 113.62: 3688 113.62 - 120.41: 2413 120.41 - 127.21: 2784 127.21 - 134.00: 74 Bond angle restraints: 9103 Sorted by residual: angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" C ASN A 23 " ideal model delta sigma weight residual 111.28 104.51 6.77 1.09e+00 8.42e-01 3.86e+01 angle pdb=" N GLN A 267 " pdb=" CA GLN A 267 " pdb=" C GLN A 267 " ideal model delta sigma weight residual 111.71 105.87 5.84 1.15e+00 7.56e-01 2.57e+01 angle pdb=" N GLU A 268 " pdb=" CA GLU A 268 " pdb=" C GLU A 268 " ideal model delta sigma weight residual 111.28 106.51 4.77 1.09e+00 8.42e-01 1.92e+01 angle pdb=" N SER B 245 " pdb=" CA SER B 245 " pdb=" C SER B 245 " ideal model delta sigma weight residual 109.23 115.77 -6.54 1.55e+00 4.16e-01 1.78e+01 angle pdb=" C SER R 236 " pdb=" N GLU R 237 " pdb=" CA GLU R 237 " ideal model delta sigma weight residual 123.11 117.24 5.87 1.42e+00 4.96e-01 1.71e+01 ... (remaining 9098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.33: 3757 33.33 - 66.67: 62 66.67 - 100.00: 4 100.00 - 133.33: 1 133.33 - 166.67: 2 Dihedral angle restraints: 3826 sinusoidal: 1036 harmonic: 2790 Sorted by residual: dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -97.40 166.67 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -54.17 158.76 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" O5' GTP A 401 " pdb=" O3A GTP A 401 " pdb=" PA GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 274.12 159.15 114.97 1 2.00e+01 2.50e-03 3.41e+01 ... (remaining 3823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 898 0.055 - 0.110: 165 0.110 - 0.165: 39 0.165 - 0.220: 5 0.220 - 0.275: 1 Chirality restraints: 1108 Sorted by residual: chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA ILE A 257 " pdb=" N ILE A 257 " pdb=" C ILE A 257 " pdb=" CB ILE A 257 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA VAL B 133 " pdb=" N VAL B 133 " pdb=" C VAL B 133 " pdb=" CB VAL B 133 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1105 not shown) Planarity restraints: 1167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 366 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C ALA A 366 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA A 366 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 367 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 219 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C ARG B 219 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG B 219 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN B 220 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 266 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.84e+00 pdb=" C LEU A 266 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU A 266 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN A 267 " -0.013 2.00e-02 2.50e+03 ... (remaining 1164 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1204 2.77 - 3.30: 6111 3.30 - 3.83: 10308 3.83 - 4.37: 10547 4.37 - 4.90: 19304 Nonbonded interactions: 47474 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.237 2.440 nonbonded pdb=" O LEU A 45 " pdb=" CG2 VAL A 224 " model vdw 2.274 3.460 nonbonded pdb=" OG SER R 203 " pdb=" OAL G1I R 501 " model vdw 2.309 2.440 nonbonded pdb=" NE2 HIS B 142 " pdb=" OG SER B 161 " model vdw 2.374 2.520 nonbonded pdb=" N SER A 54 " pdb=" O1B GTP A 401 " model vdw 2.377 2.520 ... (remaining 47469 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 2.990 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.850 Find NCS groups from input model: 0.070 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.005 0.116 6629 Z= 0.354 Angle : 0.761 10.646 9103 Z= 0.488 Chirality : 0.047 0.275 1108 Planarity : 0.003 0.035 1167 Dihedral : 13.649 166.667 2005 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.40 % Allowed : 1.20 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.28), residues: 936 helix: 2.46 (0.25), residues: 414 sheet: -0.21 (0.42), residues: 168 loop : -0.52 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE A 246 TYR 0.011 0.001 TYR R 316 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.705 Fit side-chains REVERT: G 48 ASP cc_start: 0.9036 (t70) cc_final: 0.8362 (t0) REVERT: R 217 PHE cc_start: 0.7921 (t80) cc_final: 0.7677 (t80) outliers start: 2 outliers final: 0 residues processed: 96 average time/residue: 0.1289 time to fit residues: 18.2822 Evaluate side-chains 73 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 44 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 chunk 85 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6629 Z= 0.246 Angle : 0.496 6.007 9103 Z= 0.277 Chirality : 0.042 0.185 1108 Planarity : 0.003 0.038 1167 Dihedral : 9.072 157.849 1031 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.80 % Allowed : 11.22 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.28), residues: 936 helix: 2.72 (0.25), residues: 418 sheet: -0.26 (0.41), residues: 169 loop : -0.86 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 PHE 0.016 0.002 PHE B 235 TYR 0.023 0.001 TYR R 308 ARG 0.003 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.752 Fit side-chains REVERT: A 344 GLU cc_start: 0.8208 (tp30) cc_final: 0.7995 (tp30) REVERT: B 298 ASP cc_start: 0.8493 (t0) cc_final: 0.7896 (t0) REVERT: G 48 ASP cc_start: 0.9046 (t70) cc_final: 0.8383 (t0) REVERT: R 209 TYR cc_start: 0.8020 (m-80) cc_final: 0.7759 (m-10) outliers start: 9 outliers final: 8 residues processed: 83 average time/residue: 0.1359 time to fit residues: 16.4872 Evaluate side-chains 76 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 0.0570 chunk 58 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6629 Z= 0.160 Angle : 0.430 5.960 9103 Z= 0.237 Chirality : 0.040 0.134 1108 Planarity : 0.003 0.040 1167 Dihedral : 8.740 155.106 1031 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.80 % Allowed : 15.63 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.54 (0.28), residues: 936 helix: 2.94 (0.25), residues: 420 sheet: -0.30 (0.39), residues: 169 loop : -0.75 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE A 246 TYR 0.021 0.001 TYR R 308 ARG 0.006 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.718 Fit side-chains REVERT: B 262 MET cc_start: 0.8512 (tpp) cc_final: 0.8244 (tpp) REVERT: B 298 ASP cc_start: 0.8452 (t0) cc_final: 0.7798 (t0) REVERT: G 48 ASP cc_start: 0.9075 (t70) cc_final: 0.8300 (t0) REVERT: R 209 TYR cc_start: 0.8090 (m-80) cc_final: 0.7855 (m-10) outliers start: 9 outliers final: 8 residues processed: 79 average time/residue: 0.1444 time to fit residues: 16.4625 Evaluate side-chains 77 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6629 Z= 0.308 Angle : 0.502 6.099 9103 Z= 0.280 Chirality : 0.042 0.140 1108 Planarity : 0.003 0.047 1167 Dihedral : 8.757 156.256 1031 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.81 % Allowed : 16.63 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.28), residues: 936 helix: 2.79 (0.26), residues: 423 sheet: -0.44 (0.39), residues: 170 loop : -0.95 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.005 0.001 HIS B 142 PHE 0.018 0.002 PHE B 235 TYR 0.021 0.002 TYR R 308 ARG 0.011 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.653 Fit side-chains REVERT: B 262 MET cc_start: 0.8616 (tpp) cc_final: 0.8384 (tpp) REVERT: G 48 ASP cc_start: 0.9067 (t70) cc_final: 0.8274 (t0) REVERT: R 312 ASN cc_start: 0.8379 (t0) cc_final: 0.8005 (t0) outliers start: 14 outliers final: 13 residues processed: 83 average time/residue: 0.1714 time to fit residues: 21.7573 Evaluate side-chains 86 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6629 Z= 0.176 Angle : 0.430 5.912 9103 Z= 0.238 Chirality : 0.040 0.135 1108 Planarity : 0.003 0.045 1167 Dihedral : 8.509 154.079 1031 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.41 % Allowed : 17.84 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.43 (0.28), residues: 936 helix: 2.91 (0.26), residues: 425 sheet: -0.31 (0.40), residues: 168 loop : -0.97 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 313 HIS 0.002 0.001 HIS A 220 PHE 0.011 0.001 PHE B 199 TYR 0.023 0.001 TYR R 308 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 1.261 Fit side-chains REVERT: B 61 MET cc_start: 0.9184 (tmm) cc_final: 0.8968 (tmm) REVERT: B 262 MET cc_start: 0.8590 (tpp) cc_final: 0.8213 (tpp) REVERT: B 333 ASP cc_start: 0.7842 (p0) cc_final: 0.7636 (p0) REVERT: G 48 ASP cc_start: 0.9050 (t70) cc_final: 0.8317 (t0) REVERT: R 316 TYR cc_start: 0.8580 (m-10) cc_final: 0.8302 (m-10) outliers start: 17 outliers final: 15 residues processed: 87 average time/residue: 0.1876 time to fit residues: 23.3170 Evaluate side-chains 86 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 71 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.0170 chunk 87 optimal weight: 0.9980 overall best weight: 0.7818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 6629 Z= 0.136 Angle : 0.417 5.915 9103 Z= 0.226 Chirality : 0.039 0.130 1108 Planarity : 0.003 0.041 1167 Dihedral : 8.222 151.303 1031 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.61 % Allowed : 19.04 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.28), residues: 936 helix: 3.04 (0.25), residues: 425 sheet: -0.24 (0.40), residues: 168 loop : -0.92 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.002 0.001 HIS B 225 PHE 0.020 0.001 PHE R 217 TYR 0.024 0.001 TYR R 308 ARG 0.009 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.691 Fit side-chains REVERT: B 262 MET cc_start: 0.8563 (tpp) cc_final: 0.8176 (tpp) REVERT: B 333 ASP cc_start: 0.7804 (p0) cc_final: 0.7530 (p0) REVERT: G 48 ASP cc_start: 0.9020 (t70) cc_final: 0.8247 (t0) outliers start: 13 outliers final: 12 residues processed: 86 average time/residue: 0.1573 time to fit residues: 19.5356 Evaluate side-chains 85 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6629 Z= 0.152 Angle : 0.418 5.894 9103 Z= 0.229 Chirality : 0.040 0.131 1108 Planarity : 0.003 0.039 1167 Dihedral : 8.053 150.236 1031 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.61 % Allowed : 18.64 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.62 (0.28), residues: 936 helix: 3.13 (0.25), residues: 424 sheet: -0.33 (0.40), residues: 169 loop : -0.90 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.002 0.000 HIS A 220 PHE 0.017 0.001 PHE R 217 TYR 0.023 0.001 TYR R 308 ARG 0.008 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 0.767 Fit side-chains REVERT: B 262 MET cc_start: 0.8577 (tpp) cc_final: 0.8258 (tpp) REVERT: B 333 ASP cc_start: 0.7842 (p0) cc_final: 0.7529 (p0) REVERT: G 48 ASP cc_start: 0.9006 (t70) cc_final: 0.8201 (t0) outliers start: 13 outliers final: 12 residues processed: 84 average time/residue: 0.1626 time to fit residues: 19.9499 Evaluate side-chains 85 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 0.0170 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 84 optimal weight: 0.0040 overall best weight: 0.4830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6629 Z= 0.110 Angle : 0.406 5.855 9103 Z= 0.218 Chirality : 0.039 0.130 1108 Planarity : 0.003 0.037 1167 Dihedral : 7.779 147.304 1031 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.81 % Allowed : 18.44 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.82 (0.28), residues: 936 helix: 3.34 (0.25), residues: 418 sheet: -0.27 (0.40), residues: 169 loop : -0.75 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.002 0.000 HIS B 225 PHE 0.019 0.001 PHE R 217 TYR 0.024 0.001 TYR R 308 ARG 0.008 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.718 Fit side-chains REVERT: B 262 MET cc_start: 0.8539 (tpp) cc_final: 0.8138 (tpp) REVERT: B 333 ASP cc_start: 0.7759 (p0) cc_final: 0.7450 (p0) REVERT: G 48 ASP cc_start: 0.8968 (t70) cc_final: 0.8477 (t0) outliers start: 14 outliers final: 13 residues processed: 85 average time/residue: 0.1373 time to fit residues: 17.7615 Evaluate side-chains 85 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 174 TYR Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 25 optimal weight: 0.0370 chunk 76 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6629 Z= 0.111 Angle : 0.403 5.871 9103 Z= 0.218 Chirality : 0.039 0.137 1108 Planarity : 0.003 0.037 1167 Dihedral : 7.624 146.057 1031 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.20 % Allowed : 19.24 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.28), residues: 936 helix: 3.39 (0.25), residues: 418 sheet: -0.19 (0.40), residues: 169 loop : -0.78 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 109 HIS 0.002 0.000 HIS B 225 PHE 0.018 0.001 PHE R 217 TYR 0.024 0.001 TYR R 308 ARG 0.007 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.788 Fit side-chains REVERT: B 262 MET cc_start: 0.8555 (tpp) cc_final: 0.8144 (tpp) REVERT: B 333 ASP cc_start: 0.7788 (p0) cc_final: 0.7461 (p0) REVERT: G 48 ASP cc_start: 0.8953 (t70) cc_final: 0.8451 (t0) outliers start: 11 outliers final: 10 residues processed: 83 average time/residue: 0.1333 time to fit residues: 16.5826 Evaluate side-chains 82 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 317 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 0.0050 chunk 93 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6629 Z= 0.110 Angle : 0.407 5.849 9103 Z= 0.218 Chirality : 0.039 0.128 1108 Planarity : 0.003 0.036 1167 Dihedral : 7.437 144.900 1031 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.00 % Allowed : 19.44 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.90 (0.28), residues: 936 helix: 3.41 (0.25), residues: 418 sheet: -0.15 (0.40), residues: 169 loop : -0.76 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 313 HIS 0.001 0.000 HIS B 225 PHE 0.018 0.001 PHE R 217 TYR 0.023 0.001 TYR R 308 ARG 0.007 0.000 ARG R 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.759 Fit side-chains REVERT: B 262 MET cc_start: 0.8567 (tpp) cc_final: 0.8169 (tpp) REVERT: B 333 ASP cc_start: 0.7789 (p0) cc_final: 0.7456 (p0) REVERT: G 48 ASP cc_start: 0.8954 (t70) cc_final: 0.8453 (t0) outliers start: 10 outliers final: 10 residues processed: 82 average time/residue: 0.1346 time to fit residues: 16.3871 Evaluate side-chains 82 residues out of total 829 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain R residue 130 ASP Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 220 SER Chi-restraints excluded: chain R residue 275 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 65 optimal weight: 0.0030 chunk 4 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.113062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.089088 restraints weight = 14264.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.091753 restraints weight = 7849.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.093625 restraints weight = 5366.053| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6629 Z= 0.289 Angle : 0.485 5.848 9103 Z= 0.268 Chirality : 0.042 0.133 1108 Planarity : 0.003 0.043 1167 Dihedral : 7.662 149.419 1031 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.40 % Allowed : 19.84 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.62 (0.29), residues: 936 helix: 3.18 (0.26), residues: 424 sheet: -0.31 (0.40), residues: 167 loop : -0.96 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.002 PHE R 217 TYR 0.023 0.002 TYR R 308 ARG 0.008 0.001 ARG R 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1614.26 seconds wall clock time: 29 minutes 50.28 seconds (1790.28 seconds total)