Starting phenix.real_space_refine on Sat Apr 6 02:26:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfx_29987/04_2024/8gfx_29987_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfx_29987/04_2024/8gfx_29987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfx_29987/04_2024/8gfx_29987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfx_29987/04_2024/8gfx_29987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfx_29987/04_2024/8gfx_29987_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gfx_29987/04_2024/8gfx_29987_updated.pdb" } resolution = 3.0 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= 0.036 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 43 5.16 5 C 4314 2.51 5 N 1151 2.21 5 O 1214 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6725 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1743 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 143 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 13, 'ARG:plan': 8, 'PHE:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 128 Chain: "B" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2443 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 86 Chain: "G" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 348 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 2143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2143 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 139 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 75 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: 4.30, per 1000 atoms: 0.64 Number of scatterers: 6725 At special positions: 0 Unit cell: (85.0346, 133.626, 100.653, 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 43 16.00 P 3 15.00 O 1214 8.00 N 1151 7.00 C 4314 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: 2.23 Conformation dependent library (CDL) restraints added in 1.4 seconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 8 sheets defined 43.2% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.601A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.504A pdb=" N ARG A 317 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.833A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.953A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.854A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.137A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 23 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'R' and resid 36 through 60 removed outlier: 3.623A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 96 removed outlier: 4.084A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.761A 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 103 through 136 removed outlier: 3.859A pdb=" N THR R 123 " --> pdb=" O ALA R 119 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS R 125 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 126 " --> pdb=" O GLU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 163 Processing helix chain 'R' and resid 166 through 170 Processing helix chain 'R' and resid 179 through 186 Processing helix chain 'R' and resid 197 through 237 removed outlier: 5.094A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.582A pdb=" N ILE R 214 " --> pdb=" O VAL R 210 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER R 236 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 298 removed outlier: 3.702A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.251A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 320 removed outlier: 3.924A pdb=" N ASN R 318 " --> pdb=" O ILE R 314 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 326 Processing helix chain 'R' and resid 330 through 339 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.076A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 91 through 94 removed outlier: 3.561A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.167A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.826A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.771A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.624A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.522A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.624A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 960 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: 1.88 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1102 1.32 - 1.44: 1913 1.44 - 1.57: 3792 1.57 - 1.69: 5 1.69 - 1.81: 60 Bond restraints: 6872 Sorted by residual: bond pdb=" CA PHE R 332 " pdb=" C PHE R 332 " ideal model delta sigma weight residual 1.524 1.469 0.054 1.29e-02 6.01e+03 1.78e+01 bond pdb=" CA ARG R 239 " pdb=" C ARG R 239 " ideal model delta sigma weight residual 1.522 1.468 0.054 1.40e-02 5.10e+03 1.50e+01 bond pdb=" C ARG R 239 " pdb=" N PHE R 240 " ideal model delta sigma weight residual 1.335 1.290 0.045 1.36e-02 5.41e+03 1.10e+01 bond pdb=" C PHE R 332 " pdb=" O PHE R 332 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" CA ALA R 335 " pdb=" CB ALA R 335 " ideal model delta sigma weight residual 1.528 1.481 0.047 1.56e-02 4.11e+03 9.26e+00 ... (remaining 6867 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.81: 151 106.81 - 113.61: 3858 113.61 - 120.41: 2519 120.41 - 127.22: 2778 127.22 - 134.02: 79 Bond angle restraints: 9385 Sorted by residual: angle pdb=" N PHE R 332 " pdb=" CA PHE R 332 " pdb=" C PHE R 332 " ideal model delta sigma weight residual 111.36 104.48 6.88 1.09e+00 8.42e-01 3.98e+01 angle pdb=" C ILE R 334 " pdb=" CA ILE R 334 " pdb=" CB ILE R 334 " ideal model delta sigma weight residual 112.14 105.83 6.31 1.35e+00 5.49e-01 2.19e+01 angle pdb=" N GLN R 337 " pdb=" CA GLN R 337 " pdb=" C GLN R 337 " ideal model delta sigma weight residual 111.28 116.00 -4.72 1.09e+00 8.42e-01 1.88e+01 angle pdb=" N ARG R 239 " pdb=" CA ARG R 239 " pdb=" C ARG R 239 " ideal model delta sigma weight residual 112.54 116.90 -4.36 1.22e+00 6.72e-01 1.27e+01 angle pdb=" N ARG R 239 " pdb=" CA ARG R 239 " pdb=" CB ARG R 239 " ideal model delta sigma weight residual 110.39 105.00 5.39 1.66e+00 3.63e-01 1.05e+01 ... (remaining 9380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.75: 3937 33.75 - 67.49: 47 67.49 - 101.24: 7 101.24 - 134.98: 0 134.98 - 168.73: 2 Dihedral angle restraints: 3993 sinusoidal: 1381 harmonic: 2612 Sorted by residual: dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -122.00 -168.73 1 2.00e+01 2.50e-03 4.75e+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 -62.25 166.84 1 2.00e+01 2.50e-03 4.74e+01 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 -56.21 -127.50 71.29 1 2.00e+01 2.50e-03 1.63e+01 ... (remaining 3990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 784 0.041 - 0.082: 253 0.082 - 0.123: 65 0.123 - 0.164: 7 0.164 - 0.205: 1 Chirality restraints: 1110 Sorted by residual: chirality pdb=" CA PHE R 240 " pdb=" N PHE R 240 " pdb=" C PHE R 240 " pdb=" CB PHE R 240 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.55 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1107 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 239 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.77e+00 pdb=" C ARG R 239 " 0.034 2.00e-02 2.50e+03 pdb=" O ARG R 239 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE R 240 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 205 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C ILE R 205 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE R 205 " 0.011 2.00e-02 2.50e+03 pdb=" N VAL R 206 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 335 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C ALA R 335 " -0.028 2.00e-02 2.50e+03 pdb=" O ALA R 335 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE R 336 " 0.009 2.00e-02 2.50e+03 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1447 2.78 - 3.31: 5980 3.31 - 3.84: 10476 3.84 - 4.37: 12062 4.37 - 4.90: 22259 Nonbonded interactions: 52224 Sorted by model distance: nonbonded pdb=" OD1 ASP R 113 " pdb=" OH TYR R 316 " model vdw 2.248 2.440 nonbonded pdb=" OE2 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.295 2.440 nonbonded pdb=" OD2 ASP R 113 " pdb=" OAM G1I R 501 " model vdw 2.302 2.440 nonbonded pdb=" O LEU R 64 " pdb=" ND2 ASN R 69 " model vdw 2.368 2.520 nonbonded pdb=" NE2 GLN G 18 " pdb=" OE1 GLU G 22 " model vdw 2.368 2.520 ... (remaining 52219 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.100 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: 7.790 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 22.180 Find NCS groups from input model: 0.180 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:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 : 0.004 0.054 6872 Z= 0.269 Angle : 0.528 6.875 9385 Z= 0.302 Chirality : 0.042 0.205 1110 Planarity : 0.003 0.031 1175 Dihedral : 13.466 168.728 2294 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.67 (0.29), residues: 880 helix: 1.37 (0.27), residues: 398 sheet: 0.35 (0.42), residues: 171 loop : -0.65 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 99 HIS 0.006 0.001 HIS B 183 PHE 0.017 0.001 PHE B 234 TYR 0.016 0.001 TYR B 59 ARG 0.002 0.000 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.754 Fit side-chains REVERT: A 364 THR cc_start: 0.9101 (m) cc_final: 0.8854 (m) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 1.0739 time to fit residues: 116.2688 Evaluate side-chains 79 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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: 0.0980 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 220 HIS B 75 GLN R 241 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6872 Z= 0.141 Angle : 0.454 6.446 9385 Z= 0.246 Chirality : 0.040 0.146 1110 Planarity : 0.003 0.031 1175 Dihedral : 9.278 170.573 983 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.14 % Allowed : 9.65 % Favored : 88.21 % 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: 1.05 (0.29), residues: 880 helix: 1.81 (0.27), residues: 399 sheet: 0.56 (0.41), residues: 170 loop : -0.67 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE A 376 TYR 0.012 0.001 TYR B 59 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.761 Fit side-chains REVERT: R 195 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.9010 (t) outliers start: 14 outliers final: 7 residues processed: 92 average time/residue: 1.0755 time to fit residues: 105.1127 Evaluate side-chains 85 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 340 ASN R 241 HIS R 296 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6872 Z= 0.219 Angle : 0.482 6.413 9385 Z= 0.259 Chirality : 0.041 0.139 1110 Planarity : 0.003 0.033 1175 Dihedral : 9.345 172.180 983 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.91 % Allowed : 10.72 % Favored : 86.37 % 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: 880 helix: 1.83 (0.27), residues: 399 sheet: 0.60 (0.42), residues: 171 loop : -0.64 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.005 0.001 HIS B 183 PHE 0.010 0.001 PHE A 212 TYR 0.013 0.001 TYR R 209 ARG 0.004 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.955 Fit side-chains REVERT: R 195 THR cc_start: 0.9269 (OUTLIER) cc_final: 0.9058 (t) outliers start: 19 outliers final: 11 residues processed: 89 average time/residue: 1.1043 time to fit residues: 104.3697 Evaluate side-chains 88 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.0770 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 overall best weight: 1.5144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 241 HIS R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6872 Z= 0.265 Angle : 0.503 6.371 9385 Z= 0.270 Chirality : 0.042 0.143 1110 Planarity : 0.003 0.034 1175 Dihedral : 9.439 173.291 983 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.37 % Allowed : 12.40 % Favored : 84.23 % 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: 1.00 (0.29), residues: 880 helix: 1.79 (0.27), residues: 398 sheet: 0.61 (0.41), residues: 170 loop : -0.77 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 211 HIS 0.005 0.001 HIS B 183 PHE 0.011 0.001 PHE B 241 TYR 0.013 0.001 TYR R 132 ARG 0.004 0.000 ARG R 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 0.621 Fit side-chains outliers start: 22 outliers final: 16 residues processed: 91 average time/residue: 1.0222 time to fit residues: 98.8124 Evaluate side-chains 91 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 339 LEU 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: 1.9990 chunk 35 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 0.0470 chunk 77 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6872 Z= 0.148 Angle : 0.439 6.430 9385 Z= 0.237 Chirality : 0.039 0.138 1110 Planarity : 0.003 0.032 1175 Dihedral : 9.293 173.519 983 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.91 % Allowed : 13.94 % Favored : 83.15 % 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: 1.15 (0.29), residues: 880 helix: 1.98 (0.27), residues: 399 sheet: 0.51 (0.41), residues: 173 loop : -0.69 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.005 0.001 HIS A 220 PHE 0.009 0.001 PHE B 241 TYR 0.009 0.001 TYR R 132 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 0.767 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 93 average time/residue: 1.0877 time to fit residues: 107.4332 Evaluate side-chains 84 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 195 THR 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: 0.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 340 ASN R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6872 Z= 0.168 Angle : 0.452 6.433 9385 Z= 0.243 Chirality : 0.040 0.140 1110 Planarity : 0.003 0.032 1175 Dihedral : 9.303 174.301 983 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.76 % Allowed : 13.94 % 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: 1.16 (0.29), residues: 880 helix: 1.94 (0.27), residues: 399 sheet: 0.57 (0.41), residues: 172 loop : -0.63 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.004 0.001 HIS R 178 PHE 0.010 0.001 PHE B 241 TYR 0.010 0.001 TYR R 132 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 74 time to evaluate : 0.759 Fit side-chains REVERT: A 344 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8399 (mm-30) outliers start: 18 outliers final: 14 residues processed: 88 average time/residue: 1.0602 time to fit residues: 99.4567 Evaluate side-chains 87 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 340 ASN R 296 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6872 Z= 0.165 Angle : 0.451 6.428 9385 Z= 0.242 Chirality : 0.040 0.138 1110 Planarity : 0.003 0.032 1175 Dihedral : 9.291 175.498 983 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.22 % Allowed : 14.70 % Favored : 82.08 % 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: 880 helix: 1.97 (0.27), residues: 399 sheet: 0.57 (0.41), residues: 172 loop : -0.61 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 109 HIS 0.003 0.001 HIS R 178 PHE 0.010 0.001 PHE B 241 TYR 0.010 0.001 TYR R 132 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.759 Fit side-chains outliers start: 21 outliers final: 17 residues processed: 90 average time/residue: 1.1085 time to fit residues: 106.1191 Evaluate side-chains 90 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 113 ASP Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 195 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 0.0470 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 74 optimal weight: 0.3980 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6872 Z= 0.129 Angle : 0.438 6.436 9385 Z= 0.236 Chirality : 0.039 0.136 1110 Planarity : 0.003 0.031 1175 Dihedral : 9.227 176.781 983 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.91 % Allowed : 15.93 % Favored : 81.16 % 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: 1.24 (0.29), residues: 880 helix: 2.00 (0.27), residues: 402 sheet: 0.58 (0.40), residues: 177 loop : -0.61 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.004 0.001 HIS A 220 PHE 0.009 0.001 PHE A 376 TYR 0.008 0.001 TYR R 132 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.697 Fit side-chains REVERT: A 25 LYS cc_start: 0.8130 (ttmm) cc_final: 0.7684 (ttpp) outliers start: 19 outliers final: 15 residues processed: 91 average time/residue: 1.0108 time to fit residues: 98.1125 Evaluate side-chains 91 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 239 ARG Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6872 Z= 0.203 Angle : 0.482 6.385 9385 Z= 0.258 Chirality : 0.040 0.141 1110 Planarity : 0.003 0.032 1175 Dihedral : 9.335 178.737 983 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.60 % Allowed : 16.54 % Favored : 80.86 % 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: 1.18 (0.29), residues: 880 helix: 1.93 (0.27), residues: 399 sheet: 0.66 (0.41), residues: 169 loop : -0.63 (0.33), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 PHE 0.010 0.001 PHE B 241 TYR 0.012 0.001 TYR R 132 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 0.747 Fit side-chains REVERT: A 25 LYS cc_start: 0.8129 (ttmm) cc_final: 0.7675 (ttpp) outliers start: 17 outliers final: 15 residues processed: 91 average time/residue: 0.9606 time to fit residues: 93.2783 Evaluate side-chains 91 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 184 CYS Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 7 optimal weight: 0.0870 chunk 54 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6872 Z= 0.138 Angle : 0.449 6.401 9385 Z= 0.240 Chirality : 0.039 0.137 1110 Planarity : 0.003 0.031 1175 Dihedral : 9.265 179.567 983 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.30 % Allowed : 16.85 % Favored : 80.86 % 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: 880 helix: 1.97 (0.27), residues: 405 sheet: 0.52 (0.41), residues: 173 loop : -0.49 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 99 HIS 0.005 0.001 HIS A 357 PHE 0.009 0.001 PHE B 241 TYR 0.009 0.001 TYR R 132 ARG 0.006 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.793 Fit side-chains REVERT: A 25 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7640 (ttpp) outliers start: 15 outliers final: 14 residues processed: 87 average time/residue: 1.0109 time to fit residues: 93.6765 Evaluate side-chains 90 residues out of total 774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.092741 restraints weight = 8826.179| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.00 r_work: 0.2852 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6872 Z= 0.154 Angle : 0.458 6.394 9385 Z= 0.246 Chirality : 0.039 0.138 1110 Planarity : 0.003 0.031 1175 Dihedral : 9.253 179.183 983 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.45 % Allowed : 17.00 % Favored : 80.55 % 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: 880 helix: 2.02 (0.27), residues: 399 sheet: 0.49 (0.41), residues: 173 loop : -0.52 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.006 0.001 HIS A 357 PHE 0.009 0.001 PHE B 241 TYR 0.010 0.001 TYR R 132 ARG 0.006 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2548.98 seconds wall clock time: 47 minutes 45.49 seconds (2865.49 seconds total)