Starting phenix.real_space_refine on Fri Jul 19 04:51:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unl_42408/07_2024/8unl_42408.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unl_42408/07_2024/8unl_42408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unl_42408/07_2024/8unl_42408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unl_42408/07_2024/8unl_42408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unl_42408/07_2024/8unl_42408.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unl_42408/07_2024/8unl_42408.cif" } resolution = 3.3 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= 0.027 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 40 5.16 5 C 4219 2.51 5 N 1122 2.21 5 O 1166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 138": "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: 6550 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1692 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 5, 'TRANS': 225} Chain breaks: 4 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 161 Chain: "B" Number of atoms: 2400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2400 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 185 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 8, 'ASN:plan1': 3, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 118 Chain: "G" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 320 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2090 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 7, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 107 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 4.73, per 1000 atoms: 0.72 Number of scatterers: 6550 At special positions: 0 Unit cell: (83.2992, 134.493, 97.1824, 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 40 16.00 P 3 15.00 O 1166 8.00 N 1122 7.00 C 4219 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: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 47.8% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.876A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.506A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.864A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 295 through 302 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.829A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.790A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.505A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.815A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.516A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 24 removed outlier: 3.854A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.518A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 61 removed outlier: 3.538A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 97 removed outlier: 3.525A pdb=" N TYR R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.678A 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: 3.926A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.536A pdb=" N LEU R 145 " --> pdb=" O TYR R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.608A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU R 155 " --> pdb=" O ARG R 151 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.576A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 175 removed outlier: 3.546A pdb=" N ARG R 175 " --> pdb=" O HIS R 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 172 through 175' Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.872A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 299 removed outlier: 3.821A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.489A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 318 removed outlier: 3.538A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 321 through 327 Processing helix chain 'R' and resid 329 through 339 removed outlier: 3.575A 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 214 removed outlier: 7.218A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.190A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.593A 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: 6.656A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.094A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.912A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.973A 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 150 removed outlier: 6.878A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.713A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.586A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.869A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 1005 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: 1.79 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1033 1.32 - 1.44: 1900 1.44 - 1.56: 3696 1.56 - 1.69: 7 1.69 - 1.81: 54 Bond restraints: 6690 Sorted by residual: bond pdb=" CA THR A 320 " pdb=" C THR A 320 " ideal model delta sigma weight residual 1.528 1.468 0.060 1.18e-02 7.18e+03 2.60e+01 bond pdb=" CA ASN R 148 " pdb=" C ASN R 148 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.30e-02 5.92e+03 2.50e+01 bond pdb=" CA LEU R 145 " pdb=" C LEU R 145 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.23e-02 6.61e+03 2.34e+01 bond pdb=" C5 GTP A 401 " pdb=" C6 GTP A 401 " ideal model delta sigma weight residual 1.390 1.476 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" CA GLN A 59 " pdb=" C GLN A 59 " ideal model delta sigma weight residual 1.524 1.475 0.048 1.27e-02 6.20e+03 1.45e+01 ... (remaining 6685 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.50: 217 107.50 - 114.60: 3941 114.60 - 121.69: 3496 121.69 - 128.79: 1439 128.79 - 135.88: 61 Bond angle restraints: 9154 Sorted by residual: angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 111.28 123.06 -11.78 1.09e+00 8.42e-01 1.17e+02 angle pdb=" N ALA A 351 " pdb=" CA ALA A 351 " pdb=" C ALA A 351 " ideal model delta sigma weight residual 111.28 118.61 -7.33 1.09e+00 8.42e-01 4.53e+01 angle pdb=" N THR A 320 " pdb=" CA THR A 320 " pdb=" C THR A 320 " ideal model delta sigma weight residual 110.08 101.63 8.45 1.38e+00 5.25e-01 3.75e+01 angle pdb=" N SER R 143 " pdb=" CA SER R 143 " pdb=" C SER R 143 " ideal model delta sigma weight residual 111.28 117.78 -6.50 1.09e+00 8.42e-01 3.56e+01 angle pdb=" N THR R 146 " pdb=" CA THR R 146 " pdb=" C THR R 146 " ideal model delta sigma weight residual 109.50 100.99 8.51 1.58e+00 4.01e-01 2.90e+01 ... (remaining 9149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.00: 3780 31.00 - 62.01: 71 62.01 - 93.01: 2 93.01 - 124.02: 0 124.02 - 155.02: 5 Dihedral angle restraints: 3858 sinusoidal: 1250 harmonic: 2608 Sorted by residual: 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 -50.43 155.02 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" C4' GTP A 401 " pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " ideal model delta sinusoidal sigma weight residual 260.87 124.05 136.82 1 2.00e+01 2.50e-03 4.15e+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 -85.88 44.74 -130.62 1 2.00e+01 2.50e-03 3.96e+01 ... (remaining 3855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 838 0.046 - 0.091: 205 0.091 - 0.137: 57 0.137 - 0.182: 4 0.182 - 0.228: 1 Chirality restraints: 1105 Sorted by residual: chirality pdb=" CA SER A 352 " pdb=" N SER A 352 " pdb=" C SER A 352 " pdb=" CB SER A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA HIS A 357 " pdb=" N HIS A 357 " pdb=" C HIS A 357 " pdb=" CB HIS A 357 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 chirality pdb=" CA ILE A 62 " pdb=" N ILE A 62 " pdb=" C ILE A 62 " pdb=" CB ILE A 62 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.66e-01 ... (remaining 1102 not shown) Planarity restraints: 1138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.070 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO A 361 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 360 " 0.022 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C TYR A 360 " -0.075 2.00e-02 2.50e+03 pdb=" O TYR A 360 " 0.028 2.00e-02 2.50e+03 pdb=" N PRO A 361 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " 0.035 5.00e-02 4.00e+02 5.22e-02 4.37e+00 pdb=" N PRO A 321 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.030 5.00e-02 4.00e+02 ... (remaining 1135 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1070 2.76 - 3.30: 6023 3.30 - 3.83: 10314 3.83 - 4.37: 11100 4.37 - 4.90: 21096 Nonbonded interactions: 49603 Sorted by model distance: nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.228 2.440 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.324 2.440 nonbonded pdb=" OH TYR R 209 " pdb=" O PHE R 290 " model vdw 2.339 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.344 2.440 ... (remaining 49598 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.890 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.510 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 0.086 6690 Z= 0.307 Angle : 0.679 11.780 9154 Z= 0.419 Chirality : 0.043 0.228 1105 Planarity : 0.005 0.110 1138 Dihedral : 14.030 155.022 2159 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: 1.49 (0.29), residues: 874 helix: 2.56 (0.27), residues: 380 sheet: 0.66 (0.43), residues: 160 loop : -0.74 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 313 HIS 0.011 0.001 HIS R 296 PHE 0.010 0.001 PHE R 49 TYR 0.011 0.001 TYR R 141 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.753 Fit side-chains REVERT: A 350 THR cc_start: 0.8696 (m) cc_final: 0.8468 (p) REVERT: A 369 THR cc_start: 0.8647 (p) cc_final: 0.8419 (p) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1448 time to fit residues: 17.3805 Evaluate side-chains 74 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 0.0070 chunk 42 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN R 103 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6690 Z= 0.189 Angle : 0.474 6.043 9154 Z= 0.253 Chirality : 0.040 0.139 1105 Planarity : 0.003 0.038 1138 Dihedral : 9.324 145.193 975 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.49 % Allowed : 7.45 % Favored : 91.06 % 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: 1.52 (0.29), residues: 874 helix: 2.51 (0.27), residues: 394 sheet: 0.91 (0.46), residues: 141 loop : -0.82 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.007 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.019 0.001 TYR A 358 ARG 0.004 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 0.638 Fit side-chains REVERT: A 369 THR cc_start: 0.8694 (p) cc_final: 0.8481 (p) REVERT: R 82 MET cc_start: 0.8379 (ttm) cc_final: 0.8085 (ttp) outliers start: 9 outliers final: 7 residues processed: 78 average time/residue: 0.1347 time to fit residues: 15.6091 Evaluate side-chains 78 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.0050 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6690 Z= 0.152 Angle : 0.435 5.500 9154 Z= 0.233 Chirality : 0.040 0.135 1105 Planarity : 0.003 0.037 1138 Dihedral : 8.070 141.507 975 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.66 % Allowed : 8.44 % Favored : 89.90 % 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 (0.29), residues: 874 helix: 2.64 (0.27), residues: 394 sheet: 0.75 (0.45), residues: 146 loop : -0.81 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.005 0.001 HIS A 357 PHE 0.011 0.001 PHE B 199 TYR 0.014 0.001 TYR B 59 ARG 0.003 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 77 time to evaluate : 0.693 Fit side-chains REVERT: A 53 LYS cc_start: 0.8195 (mtmm) cc_final: 0.7980 (mtmm) REVERT: A 369 THR cc_start: 0.8712 (p) cc_final: 0.8506 (p) REVERT: B 258 ASP cc_start: 0.8721 (t0) cc_final: 0.8262 (t0) REVERT: R 82 MET cc_start: 0.8373 (ttm) cc_final: 0.8046 (ttp) outliers start: 10 outliers final: 8 residues processed: 80 average time/residue: 0.1384 time to fit residues: 16.2589 Evaluate side-chains 80 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.4980 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 23 optimal weight: 30.0000 chunk 71 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6690 Z= 0.243 Angle : 0.475 5.441 9154 Z= 0.256 Chirality : 0.041 0.142 1105 Planarity : 0.003 0.038 1138 Dihedral : 7.614 137.922 975 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.66 % Allowed : 10.76 % Favored : 87.58 % 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 (0.29), residues: 874 helix: 2.51 (0.27), residues: 394 sheet: 0.49 (0.41), residues: 163 loop : -0.85 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE B 241 TYR 0.012 0.001 TYR A 358 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.899 Fit side-chains REVERT: A 53 LYS cc_start: 0.8193 (mtmm) cc_final: 0.7815 (mtmm) REVERT: B 258 ASP cc_start: 0.8778 (t0) cc_final: 0.8350 (t0) REVERT: R 82 MET cc_start: 0.8402 (ttm) cc_final: 0.8116 (ttp) outliers start: 10 outliers final: 8 residues processed: 77 average time/residue: 0.1445 time to fit residues: 16.2742 Evaluate side-chains 80 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6690 Z= 0.165 Angle : 0.437 5.410 9154 Z= 0.235 Chirality : 0.040 0.134 1105 Planarity : 0.003 0.039 1138 Dihedral : 7.344 135.243 975 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.82 % Allowed : 11.26 % Favored : 86.92 % 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: 1.49 (0.29), residues: 874 helix: 2.57 (0.27), residues: 394 sheet: 0.60 (0.42), residues: 157 loop : -0.85 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE B 241 TYR 0.009 0.001 TYR R 308 ARG 0.002 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.785 Fit side-chains REVERT: B 258 ASP cc_start: 0.8786 (t0) cc_final: 0.8317 (t0) REVERT: R 82 MET cc_start: 0.8358 (ttm) cc_final: 0.8035 (ttp) outliers start: 11 outliers final: 9 residues processed: 79 average time/residue: 0.1567 time to fit residues: 18.1044 Evaluate side-chains 80 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6690 Z= 0.154 Angle : 0.430 7.491 9154 Z= 0.229 Chirality : 0.040 0.133 1105 Planarity : 0.003 0.038 1138 Dihedral : 7.001 131.025 975 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.15 % Allowed : 11.09 % Favored : 86.75 % 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: 1.53 (0.29), residues: 874 helix: 2.59 (0.27), residues: 394 sheet: 0.67 (0.43), residues: 157 loop : -0.84 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE B 241 TYR 0.009 0.001 TYR B 59 ARG 0.004 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.813 Fit side-chains REVERT: B 258 ASP cc_start: 0.8799 (t0) cc_final: 0.8333 (t0) REVERT: R 82 MET cc_start: 0.8360 (ttm) cc_final: 0.8007 (ttp) outliers start: 13 outliers final: 10 residues processed: 79 average time/residue: 0.1468 time to fit residues: 17.2873 Evaluate side-chains 81 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 71 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 72 optimal weight: 0.0570 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.0970 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6690 Z= 0.116 Angle : 0.406 6.307 9154 Z= 0.216 Chirality : 0.039 0.130 1105 Planarity : 0.002 0.038 1138 Dihedral : 6.533 124.724 975 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.66 % Allowed : 12.25 % Favored : 86.09 % 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: 1.67 (0.30), residues: 874 helix: 2.69 (0.27), residues: 395 sheet: 0.76 (0.43), residues: 157 loop : -0.78 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.003 0.000 HIS R 178 PHE 0.011 0.001 PHE B 241 TYR 0.007 0.001 TYR A 358 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.766 Fit side-chains REVERT: A 271 ASN cc_start: 0.9207 (m-40) cc_final: 0.8956 (m-40) REVERT: B 258 ASP cc_start: 0.8795 (t0) cc_final: 0.8318 (t0) REVERT: R 82 MET cc_start: 0.8358 (ttm) cc_final: 0.7968 (ttp) outliers start: 10 outliers final: 9 residues processed: 84 average time/residue: 0.1453 time to fit residues: 17.7662 Evaluate side-chains 84 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.0970 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 78 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6690 Z= 0.122 Angle : 0.411 6.312 9154 Z= 0.217 Chirality : 0.039 0.132 1105 Planarity : 0.002 0.036 1138 Dihedral : 6.205 119.724 975 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.66 % Allowed : 12.91 % Favored : 85.43 % 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: 1.72 (0.30), residues: 874 helix: 2.72 (0.27), residues: 395 sheet: 0.70 (0.42), residues: 163 loop : -0.70 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 211 HIS 0.004 0.001 HIS R 178 PHE 0.011 0.001 PHE B 241 TYR 0.007 0.001 TYR A 339 ARG 0.004 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.793 Fit side-chains REVERT: B 258 ASP cc_start: 0.8795 (t0) cc_final: 0.8322 (t0) REVERT: R 82 MET cc_start: 0.8502 (ttm) cc_final: 0.8078 (ttp) outliers start: 10 outliers final: 10 residues processed: 85 average time/residue: 0.1629 time to fit residues: 19.5960 Evaluate side-chains 86 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6690 Z= 0.261 Angle : 0.483 6.142 9154 Z= 0.257 Chirality : 0.041 0.140 1105 Planarity : 0.003 0.038 1138 Dihedral : 6.359 120.721 975 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.32 % Allowed : 13.25 % Favored : 84.44 % 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: 1.48 (0.29), residues: 874 helix: 2.53 (0.27), residues: 394 sheet: 0.59 (0.42), residues: 163 loop : -0.83 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE B 241 TYR 0.012 0.001 TYR B 59 ARG 0.005 0.000 ARG R 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.755 Fit side-chains REVERT: B 170 ASP cc_start: 0.8551 (t0) cc_final: 0.8308 (t0) REVERT: B 258 ASP cc_start: 0.8815 (t0) cc_final: 0.8380 (t0) REVERT: R 82 MET cc_start: 0.8575 (ttm) cc_final: 0.8230 (ttp) outliers start: 14 outliers final: 14 residues processed: 81 average time/residue: 0.1332 time to fit residues: 16.2331 Evaluate side-chains 86 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 314 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.0270 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6690 Z= 0.194 Angle : 0.453 6.156 9154 Z= 0.241 Chirality : 0.040 0.136 1105 Planarity : 0.003 0.038 1138 Dihedral : 6.218 117.812 975 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.15 % Allowed : 14.07 % Favored : 83.77 % 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: 1.47 (0.29), residues: 874 helix: 2.54 (0.27), residues: 394 sheet: 0.60 (0.43), residues: 157 loop : -0.86 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS R 178 PHE 0.013 0.001 PHE B 241 TYR 0.010 0.001 TYR R 308 ARG 0.005 0.000 ARG R 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.769 Fit side-chains REVERT: B 170 ASP cc_start: 0.8523 (t0) cc_final: 0.8259 (t0) REVERT: B 258 ASP cc_start: 0.8796 (t0) cc_final: 0.8359 (t0) REVERT: R 82 MET cc_start: 0.8531 (ttm) cc_final: 0.8146 (ttp) outliers start: 13 outliers final: 13 residues processed: 81 average time/residue: 0.1353 time to fit residues: 16.4187 Evaluate side-chains 86 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.121452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101620 restraints weight = 9707.401| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.82 r_work: 0.3026 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6690 Z= 0.198 Angle : 0.455 6.038 9154 Z= 0.242 Chirality : 0.040 0.137 1105 Planarity : 0.003 0.038 1138 Dihedral : 6.167 116.795 975 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.65 % Allowed : 13.74 % Favored : 83.61 % 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: 1.44 (0.29), residues: 874 helix: 2.53 (0.27), residues: 394 sheet: 0.55 (0.43), residues: 157 loop : -0.87 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 82 HIS 0.003 0.001 HIS R 178 PHE 0.013 0.001 PHE B 241 TYR 0.010 0.001 TYR R 308 ARG 0.005 0.000 ARG R 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1655.76 seconds wall clock time: 30 minutes 23.47 seconds (1823.47 seconds total)