Starting phenix.real_space_refine on Sat Aug 3 02:35:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unw_42419/08_2024/8unw_42419.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unw_42419/08_2024/8unw_42419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unw_42419/08_2024/8unw_42419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unw_42419/08_2024/8unw_42419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unw_42419/08_2024/8unw_42419.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unw_42419/08_2024/8unw_42419.cif" } resolution = 3.4 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= 0.023 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 41 5.16 5 C 4277 2.51 5 N 1146 2.21 5 O 1180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 138": "OE1" <-> "OE2" Residue "R GLU 237": "OE1" <-> "OE2" Residue "R GLU 306": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6647 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1711 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 1699 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 14, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 146 Conformer: "B" Number of residues, atoms: 231, 1699 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 14, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 146 bond proxies already assigned to first conformer: 1718 Chain: "B" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2403 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 4, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 122 Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 352 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "R" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2133 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 83 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} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 360 " occ=0.51 ... (22 atoms not shown) pdb=" OH BTYR A 360 " occ=0.49 Time building chain proxies: 7.61, per 1000 atoms: 1.14 Number of scatterers: 6647 At special positions: 0 Unit cell: (82.4315, 131.89, 99.7855, 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 41 16.00 P 3 15.00 O 1180 8.00 N 1146 7.00 C 4277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " 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: 2.69 Conformation dependent library (CDL) restraints added in 1.8 seconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 8 sheets defined 48.2% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.886A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.520A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.660A pdb=" N ILE A 235 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.555A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.928A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 308 through 316 Proline residue: A 313 - end of helix Processing helix chain 'A' and resid 333 through 353 removed outlier: 3.637A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.938A 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 25 removed outlier: 3.740A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.909A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.619A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 61 removed outlier: 3.580A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 65 removed outlier: 3.514A pdb=" N GLN R 65 " --> pdb=" O GLU R 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 62 through 65' Processing helix chain 'R' and resid 68 through 97 removed outlier: 3.911A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.564A 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: 3.935A pdb=" N ILE R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU R 122 " --> pdb=" O THR R 118 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 140 through 145 Processing helix chain 'R' and resid 146 through 164 removed outlier: 3.808A pdb=" N ARG R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL R 152 " --> pdb=" O ASN R 148 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.637A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 187 Processing helix chain 'R' and resid 196 through 208 removed outlier: 3.557A pdb=" N SER R 204 " --> pdb=" O ALA R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 238 removed outlier: 3.706A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET R 215 " --> pdb=" O PRO R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 287 removed outlier: 4.048A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.695A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 removed outlier: 3.535A pdb=" N VAL R 317 " --> pdb=" O TRP R 313 " (cutoff:3.500A) Processing helix chain 'R' and resid 318 through 320 No H-bonds generated for 'chain 'R' and resid 318 through 320' Processing helix chain 'R' and resid 321 through 327 removed outlier: 3.556A pdb=" N CYS R 327 " --> pdb=" O PRO R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 339 removed outlier: 3.665A pdb=" N LEU R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 7.202A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.738A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.649A 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: 3.945A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.761A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.080A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.716A 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: 6.818A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.795A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.735A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) 358 hydrogen bonds defined for protein. 1029 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: 1.78 Time building geometry restraints manager: 3.00 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: 1598 1.33 - 1.45: 1418 1.45 - 1.57: 3714 1.57 - 1.69: 5 1.69 - 1.81: 56 Bond restraints: 6791 Sorted by residual: bond pdb=" C ARG A 231 " pdb=" N ARG A 232 " ideal model delta sigma weight residual 1.331 1.393 -0.063 1.66e-02 3.63e+03 1.43e+01 bond pdb=" C ARG A 232 " pdb=" N LYS A 233 " ideal model delta sigma weight residual 1.334 1.387 -0.053 1.49e-02 4.50e+03 1.25e+01 bond pdb=" N GLU A 330 " pdb=" CA GLU A 330 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.21e-02 6.83e+03 1.02e+01 bond pdb=" N VAL A 301 " pdb=" CA VAL A 301 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.40e+00 bond pdb=" N ILE B 18 " pdb=" CA ILE B 18 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.36e+00 ... (remaining 6786 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.06: 174 107.06 - 113.80: 3822 113.80 - 120.54: 2720 120.54 - 127.28: 2492 127.28 - 134.02: 75 Bond angle restraints: 9283 Sorted by residual: angle pdb=" N LEU G 19 " pdb=" CA LEU G 19 " pdb=" C LEU G 19 " ideal model delta sigma weight residual 111.71 103.18 8.53 1.15e+00 7.56e-01 5.50e+01 angle pdb=" N LEU G 15 " pdb=" CA LEU G 15 " pdb=" C LEU G 15 " ideal model delta sigma weight residual 111.28 104.28 7.00 1.09e+00 8.42e-01 4.12e+01 angle pdb=" N TYR A 253 " pdb=" CA TYR A 253 " pdb=" C TYR A 253 " ideal model delta sigma weight residual 113.72 105.47 8.25 1.30e+00 5.92e-01 4.03e+01 angle pdb=" N ASN A 264 " pdb=" CA ASN A 264 " pdb=" C ASN A 264 " ideal model delta sigma weight residual 110.35 101.86 8.49 1.36e+00 5.41e-01 3.90e+01 angle pdb=" CA PHE A 212 " pdb=" CB PHE A 212 " pdb=" CG PHE A 212 " ideal model delta sigma weight residual 113.80 119.12 -5.32 1.00e+00 1.00e+00 2.83e+01 ... (remaining 9278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 3867 35.25 - 70.51: 55 70.51 - 105.76: 1 105.76 - 141.02: 0 141.02 - 176.27: 5 Dihedral angle restraints: 3928 sinusoidal: 1298 harmonic: 2630 Sorted by residual: dihedral pdb=" O3A GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PB GTP A 401 " pdb=" PG GTP A 401 " ideal model delta sinusoidal sigma weight residual 303.79 127.52 176.27 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2G GTP A 401 " pdb=" O3B GTP A 401 " pdb=" PG GTP A 401 " pdb=" PB GTP A 401 " ideal model delta sinusoidal sigma weight residual 177.30 15.15 162.15 1 2.00e+01 2.50e-03 4.68e+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 -57.10 161.70 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 3925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 851 0.056 - 0.111: 190 0.111 - 0.166: 45 0.166 - 0.222: 19 0.222 - 0.277: 4 Chirality restraints: 1109 Sorted by residual: chirality pdb=" CA LEU G 15 " pdb=" N LEU G 15 " pdb=" C LEU G 15 " pdb=" CB LEU G 15 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA ILE A 308 " pdb=" N ILE A 308 " pdb=" C ILE A 308 " pdb=" CB ILE A 308 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ARG A 231 " pdb=" N ARG A 231 " pdb=" C ARG A 231 " pdb=" CB ARG A 231 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1106 not shown) Planarity restraints: 1157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 348 " -0.015 2.00e-02 2.50e+03 2.97e-02 8.81e+00 pdb=" C ILE A 348 " 0.051 2.00e-02 2.50e+03 pdb=" O ILE A 348 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 349 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 212 " 0.011 2.00e-02 2.50e+03 2.36e-02 5.57e+00 pdb=" C ASP B 212 " -0.041 2.00e-02 2.50e+03 pdb=" O ASP B 212 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL B 213 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN G 18 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.11e+00 pdb=" C GLN G 18 " 0.039 2.00e-02 2.50e+03 pdb=" O GLN G 18 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU G 19 " -0.013 2.00e-02 2.50e+03 ... (remaining 1154 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 797 2.75 - 3.29: 6336 3.29 - 3.83: 10423 3.83 - 4.36: 11413 4.36 - 4.90: 21090 Nonbonded interactions: 50059 Sorted by model distance: nonbonded pdb=" O ASN A 264 " pdb=" OD1 ASN A 264 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR R 326 " pdb=" O HOH R 601 " model vdw 2.231 3.040 nonbonded pdb=" OH TYR R 219 " pdb=" O HOH R 601 " model vdw 2.268 3.040 nonbonded pdb=" O THR A 55 " pdb=" N LYS A 58 " model vdw 2.344 3.120 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.349 3.040 ... (remaining 50054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.870 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 26.370 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 0.063 6791 Z= 0.358 Angle : 0.917 11.708 9283 Z= 0.622 Chirality : 0.056 0.277 1109 Planarity : 0.004 0.059 1157 Dihedral : 15.253 176.272 2214 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.16 % Allowed : 1.78 % Favored : 98.06 % 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: 0.86 (0.29), residues: 885 helix: 2.13 (0.28), residues: 378 sheet: -0.07 (0.40), residues: 179 loop : -0.90 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 173 HIS 0.004 0.001 HIS R 296 PHE 0.022 0.001 PHE A 212 TYR 0.017 0.001 TYR R 308 ARG 0.005 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.688 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.1802 time to fit residues: 28.1063 Evaluate side-chains 91 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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: 5.9990 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 239 ASN R 196 ASN R 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6791 Z= 0.246 Angle : 0.528 6.951 9283 Z= 0.287 Chirality : 0.042 0.148 1109 Planarity : 0.003 0.041 1157 Dihedral : 11.599 163.868 989 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.94 % Allowed : 8.91 % Favored : 89.14 % 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: 0.96 (0.29), residues: 885 helix: 2.16 (0.27), residues: 387 sheet: -0.05 (0.41), residues: 176 loop : -0.85 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.013 0.001 PHE B 241 TYR 0.012 0.001 TYR R 316 ARG 0.003 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 0.793 Fit side-chains REVERT: B 59 TYR cc_start: 0.8668 (m-10) cc_final: 0.8276 (m-10) REVERT: R 82 MET cc_start: 0.7554 (ttt) cc_final: 0.7285 (ttt) outliers start: 12 outliers final: 10 residues processed: 107 average time/residue: 0.1679 time to fit residues: 24.6948 Evaluate side-chains 97 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 294 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 55 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.0010 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 178 HIS R 196 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6791 Z= 0.138 Angle : 0.475 8.807 9283 Z= 0.253 Chirality : 0.040 0.145 1109 Planarity : 0.003 0.035 1157 Dihedral : 11.075 161.100 989 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.94 % Allowed : 11.35 % Favored : 86.71 % 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: 1.09 (0.29), residues: 885 helix: 2.34 (0.27), residues: 386 sheet: -0.05 (0.40), residues: 177 loop : -0.83 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.010 0.001 PHE B 241 TYR 0.014 0.001 TYR B 111 ARG 0.003 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.201 Fit side-chains REVERT: B 59 TYR cc_start: 0.8558 (m-10) cc_final: 0.8267 (m-10) REVERT: R 82 MET cc_start: 0.7505 (ttt) cc_final: 0.7251 (ttt) outliers start: 12 outliers final: 9 residues processed: 103 average time/residue: 0.1578 time to fit residues: 22.7752 Evaluate side-chains 96 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 87 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 298 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: 0.6980 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 54 optimal weight: 0.2980 chunk 81 optimal weight: 7.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 71 optimal weight: 0.0270 chunk 48 optimal weight: 0.7980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 196 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6791 Z= 0.128 Angle : 0.456 8.024 9283 Z= 0.243 Chirality : 0.039 0.141 1109 Planarity : 0.003 0.034 1157 Dihedral : 10.611 165.900 989 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.27 % Allowed : 12.80 % Favored : 84.93 % 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: 1.19 (0.29), residues: 885 helix: 2.42 (0.28), residues: 386 sheet: -0.04 (0.39), residues: 177 loop : -0.74 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.009 0.001 PHE B 241 TYR 0.009 0.001 TYR A 358 ARG 0.003 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.739 Fit side-chains REVERT: A 221 MET cc_start: 0.7552 (ttm) cc_final: 0.7286 (ttp) REVERT: B 59 TYR cc_start: 0.8531 (m-10) cc_final: 0.8270 (m-10) REVERT: R 82 MET cc_start: 0.7525 (ttt) cc_final: 0.7217 (ttt) outliers start: 14 outliers final: 13 residues processed: 109 average time/residue: 0.1942 time to fit residues: 29.0064 Evaluate side-chains 101 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 0.0470 chunk 73 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6791 Z= 0.177 Angle : 0.471 7.346 9283 Z= 0.248 Chirality : 0.040 0.138 1109 Planarity : 0.003 0.037 1157 Dihedral : 10.196 170.311 989 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.59 % Allowed : 14.10 % Favored : 83.31 % 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: 1.20 (0.29), residues: 885 helix: 2.41 (0.28), residues: 386 sheet: -0.04 (0.39), residues: 177 loop : -0.70 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.012 0.001 PHE B 241 TYR 0.008 0.001 TYR A 339 ARG 0.004 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.716 Fit side-chains REVERT: R 61 PHE cc_start: 0.7017 (m-10) cc_final: 0.6673 (m-10) REVERT: R 82 MET cc_start: 0.7544 (ttt) cc_final: 0.7243 (ttp) outliers start: 16 outliers final: 13 residues processed: 105 average time/residue: 0.1708 time to fit residues: 24.6492 Evaluate side-chains 101 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 0.0470 chunk 9 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6791 Z= 0.194 Angle : 0.480 6.947 9283 Z= 0.254 Chirality : 0.040 0.138 1109 Planarity : 0.003 0.038 1157 Dihedral : 9.885 174.395 989 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.59 % Allowed : 14.59 % Favored : 82.82 % 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: 1.21 (0.29), residues: 885 helix: 2.46 (0.28), residues: 379 sheet: -0.01 (0.39), residues: 176 loop : -0.70 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.013 0.001 PHE B 241 TYR 0.008 0.001 TYR A 339 ARG 0.004 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.746 Fit side-chains REVERT: R 61 PHE cc_start: 0.6987 (m-10) cc_final: 0.6661 (m-10) REVERT: R 82 MET cc_start: 0.7548 (ttt) cc_final: 0.7228 (ttp) outliers start: 16 outliers final: 15 residues processed: 102 average time/residue: 0.1645 time to fit residues: 23.1828 Evaluate side-chains 102 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 87 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6791 Z= 0.205 Angle : 0.483 6.697 9283 Z= 0.256 Chirality : 0.040 0.138 1109 Planarity : 0.003 0.040 1157 Dihedral : 9.586 177.485 989 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.59 % Allowed : 15.07 % Favored : 82.33 % 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: 1.19 (0.29), residues: 885 helix: 2.41 (0.28), residues: 380 sheet: -0.04 (0.40), residues: 176 loop : -0.67 (0.32), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.013 0.001 PHE B 241 TYR 0.008 0.001 TYR A 339 ARG 0.003 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.736 Fit side-chains REVERT: R 61 PHE cc_start: 0.7021 (m-10) cc_final: 0.6684 (m-10) REVERT: R 82 MET cc_start: 0.7562 (ttt) cc_final: 0.7238 (ttp) outliers start: 16 outliers final: 15 residues processed: 104 average time/residue: 0.1724 time to fit residues: 24.9033 Evaluate side-chains 101 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 82 optimal weight: 0.2980 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6791 Z= 0.139 Angle : 0.463 6.664 9283 Z= 0.245 Chirality : 0.040 0.138 1109 Planarity : 0.003 0.037 1157 Dihedral : 9.229 179.362 989 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.27 % Allowed : 16.21 % Favored : 81.52 % 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: 1.25 (0.29), residues: 885 helix: 2.46 (0.28), residues: 380 sheet: -0.03 (0.40), residues: 176 loop : -0.62 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.001 PHE A 212 TYR 0.007 0.001 TYR R 316 ARG 0.003 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.779 Fit side-chains REVERT: R 61 PHE cc_start: 0.6969 (m-10) cc_final: 0.6623 (m-10) REVERT: R 82 MET cc_start: 0.7523 (ttt) cc_final: 0.7190 (ttp) outliers start: 14 outliers final: 14 residues processed: 100 average time/residue: 0.1788 time to fit residues: 24.4636 Evaluate side-chains 98 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 298 ILE 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: 0.9980 chunk 24 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 84 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6791 Z= 0.194 Angle : 0.478 6.638 9283 Z= 0.254 Chirality : 0.040 0.137 1109 Planarity : 0.003 0.039 1157 Dihedral : 8.972 178.104 989 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.43 % Allowed : 16.05 % Favored : 81.52 % 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: 1.22 (0.29), residues: 885 helix: 2.41 (0.28), residues: 380 sheet: -0.04 (0.39), residues: 176 loop : -0.61 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.008 0.001 TYR A 339 ARG 0.003 0.000 ARG R 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.683 Fit side-chains REVERT: R 61 PHE cc_start: 0.7045 (m-10) cc_final: 0.6723 (m-10) REVERT: R 82 MET cc_start: 0.7567 (ttt) cc_final: 0.7250 (ttp) outliers start: 15 outliers final: 14 residues processed: 97 average time/residue: 0.1728 time to fit residues: 22.9876 Evaluate side-chains 100 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.0040 chunk 70 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6791 Z= 0.135 Angle : 0.466 6.682 9283 Z= 0.248 Chirality : 0.040 0.159 1109 Planarity : 0.003 0.040 1157 Dihedral : 8.809 176.885 989 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.11 % Allowed : 16.21 % Favored : 81.69 % 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: 1.27 (0.29), residues: 885 helix: 2.47 (0.28), residues: 380 sheet: 0.00 (0.39), residues: 176 loop : -0.61 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 173 HIS 0.006 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.007 0.001 TYR R 316 ARG 0.003 0.000 ARG R 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.723 Fit side-chains REVERT: R 61 PHE cc_start: 0.6988 (m-10) cc_final: 0.6692 (m-10) REVERT: R 82 MET cc_start: 0.7529 (ttt) cc_final: 0.7200 (ttp) outliers start: 13 outliers final: 13 residues processed: 99 average time/residue: 0.1770 time to fit residues: 24.0111 Evaluate side-chains 99 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 196 ASN Chi-restraints excluded: chain R residue 298 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.4980 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.098339 restraints weight = 46464.734| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 5.88 r_work: 0.2996 rms_B_bonded: 5.72 restraints_weight: 2.0000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6791 Z= 0.159 Angle : 0.471 6.753 9283 Z= 0.252 Chirality : 0.040 0.143 1109 Planarity : 0.003 0.053 1157 Dihedral : 8.728 175.178 989 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.11 % Allowed : 15.88 % Favored : 82.01 % 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: 1.27 (0.29), residues: 885 helix: 2.47 (0.28), residues: 380 sheet: 0.01 (0.39), residues: 176 loop : -0.61 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 173 HIS 0.006 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.007 0.001 TYR A 339 ARG 0.003 0.000 ARG R 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1729.93 seconds wall clock time: 34 minutes 53.62 seconds (2093.62 seconds total)