Starting phenix.real_space_refine on Tue Feb 3 20:20:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9odk_70365/02_2026/9odk_70365.cif Found real_map, /net/cci-nas-00/data/ceres_data/9odk_70365/02_2026/9odk_70365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9odk_70365/02_2026/9odk_70365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9odk_70365/02_2026/9odk_70365.map" model { file = "/net/cci-nas-00/data/ceres_data/9odk_70365/02_2026/9odk_70365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9odk_70365/02_2026/9odk_70365.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.031 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 4126 2.51 5 N 1174 2.21 5 O 1238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6577 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2436 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 86} Link IDs: {'PTRANS': 4, 'TRANS': 339} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 267 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 23, 'ASP:plan': 13, 'ARG:plan': 8, 'GLN:plan1': 6, 'PHE:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 215 Chain: "B" Number of atoms: 2394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2394 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 260 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 15, 'GLN:plan1': 4, 'ARG:plan': 12, 'ASN:plan1': 2, 'HIS:plan': 1, 'ASN%COO:plan1': 1} Unresolved non-hydrogen planarities: 163 Chain: "G" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 321 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 45 Chain: "R" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1393 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 216} Link IDs: {'PTRANS': 9, 'TRANS': 253} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 773 Unresolved non-hydrogen angles: 1004 Unresolved non-hydrogen dihedrals: 642 Unresolved non-hydrogen chiralities: 100 Planarities with less than four sites: {'PHE:plan': 17, 'ASN:plan1': 12, 'TYR:plan': 13, 'ARG:plan': 12, 'ASP:plan': 6, 'GLN:plan1': 3, 'HIS:plan': 2, 'TRP:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 372 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.66, per 1000 atoms: 0.25 Number of scatterers: 6577 At special positions: 0 Unit cell: (83.52, 95.04, 146.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 3 15.00 Mg 1 11.99 O 1238 8.00 N 1174 7.00 C 4126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 208.7 milliseconds 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 11 sheets defined 48.6% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 10 through 31 removed outlier: 3.560A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 removed outlier: 4.111A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 69 through 91 removed outlier: 3.663A pdb=" N THR A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 120 through 133 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 152 through 158 removed outlier: 3.516A pdb=" N ASP A 158 " --> pdb=" O TYR A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 170 through 174 removed outlier: 3.525A pdb=" N ASP A 173 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 4.529A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.755A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.962A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.074A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.526A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 349 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 4.079A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.694A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 96 removed outlier: 3.550A pdb=" N ARG R 95 " --> pdb=" O TYR R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 100 Processing helix chain 'R' and resid 101 through 131 removed outlier: 4.152A pdb=" N ASN R 109 " --> pdb=" O ILE R 105 " (cutoff:3.500A) Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 136 through 171 removed outlier: 4.024A pdb=" N SER R 154 " --> pdb=" O ASN R 150 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE R 155 " --> pdb=" O MET R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 175 Processing helix chain 'R' and resid 180 through 205 removed outlier: 3.572A pdb=" N ALA R 184 " --> pdb=" O THR R 180 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 226 through 242 Processing helix chain 'R' and resid 242 through 260 Processing helix chain 'R' and resid 274 through 304 removed outlier: 3.875A pdb=" N THR R 279 " --> pdb=" O LEU R 275 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ARG R 280 " --> pdb=" O ARG R 276 " (cutoff:3.500A) Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 311 through 335 removed outlier: 3.800A pdb=" N THR R 315 " --> pdb=" O THR R 311 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN R 328 " --> pdb=" O LEU R 324 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N CYS R 330 " --> pdb=" O TYR R 326 " (cutoff:3.500A) Proline residue: R 333 - end of helix Processing helix chain 'R' and resid 341 through 352 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 187 removed outlier: 3.619A pdb=" N VAL A 34 " --> pdb=" O HIS A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 226 removed outlier: 6.036A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.740A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.605A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.917A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 150 through 151 removed outlier: 3.734A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.827A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.863A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 286 Processing sheet with id=AB2, first strand: chain 'R' and resid 206 through 207 383 hydrogen bonds defined for protein. 1098 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: 0.84 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2246 1.34 - 1.46: 1164 1.46 - 1.58: 3224 1.58 - 1.69: 5 1.69 - 1.81: 48 Bond restraints: 6687 Sorted by residual: bond pdb=" N ILE B 269 " pdb=" CA ILE B 269 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.19e-02 7.06e+03 8.78e+00 bond pdb=" N ILE B 270 " pdb=" CA ILE B 270 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.36e+00 bond pdb=" N ILE B 273 " pdb=" CA ILE B 273 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.24e-02 6.50e+03 7.58e+00 bond pdb=" N SER B 265 " pdb=" CA SER B 265 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.29e+00 bond pdb=" N CYS B 271 " pdb=" CA CYS B 271 " ideal model delta sigma weight residual 1.454 1.487 -0.034 1.34e-02 5.57e+03 6.28e+00 ... (remaining 6682 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 9014 2.12 - 4.24: 156 4.24 - 6.37: 16 6.37 - 8.49: 2 8.49 - 10.61: 3 Bond angle restraints: 9191 Sorted by residual: angle pdb=" N THR A 324 " pdb=" CA THR A 324 " pdb=" C THR A 324 " ideal model delta sigma weight residual 108.38 113.08 -4.70 1.35e+00 5.49e-01 1.21e+01 angle pdb=" CA ASN B 268 " pdb=" C ASN B 268 " pdb=" O ASN B 268 " ideal model delta sigma weight residual 121.84 117.91 3.93 1.16e+00 7.43e-01 1.15e+01 angle pdb=" CG1 ILE A 221 " pdb=" CB ILE A 221 " pdb=" CG2 ILE A 221 " ideal model delta sigma weight residual 110.70 100.83 9.87 3.00e+00 1.11e-01 1.08e+01 angle pdb=" CA CYS B 271 " pdb=" C CYS B 271 " pdb=" O CYS B 271 " ideal model delta sigma weight residual 121.87 118.16 3.71 1.16e+00 7.43e-01 1.03e+01 angle pdb=" CA GLN B 17 " pdb=" CB GLN B 17 " pdb=" CG GLN B 17 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.01e+01 ... (remaining 9186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.82: 3773 31.82 - 63.65: 108 63.65 - 95.47: 4 95.47 - 127.29: 2 127.29 - 159.12: 2 Dihedral angle restraints: 3889 sinusoidal: 975 harmonic: 2914 Sorted by residual: dihedral pdb=" O5' GTP A 402 " pdb=" O3A GTP A 402 " pdb=" PA GTP A 402 " pdb=" PB GTP A 402 " ideal model delta sinusoidal sigma weight residual 274.12 115.01 159.12 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C8 GTP A 402 " pdb=" C1' GTP A 402 " pdb=" N9 GTP A 402 " pdb=" O4' GTP A 402 " ideal model delta sinusoidal sigma weight residual 104.59 -23.96 128.56 1 2.00e+01 2.50e-03 3.90e+01 dihedral pdb=" O3B GTP A 402 " pdb=" O3A GTP A 402 " pdb=" PB GTP A 402 " pdb=" PA GTP A 402 " ideal model delta sinusoidal sigma weight residual 291.08 167.99 123.09 1 2.00e+01 2.50e-03 3.71e+01 ... (remaining 3886 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 883 0.048 - 0.095: 215 0.095 - 0.143: 29 0.143 - 0.190: 4 0.190 - 0.238: 1 Chirality restraints: 1132 Sorted by residual: chirality pdb=" CB ILE A 221 " pdb=" CA ILE A 221 " pdb=" CG1 ILE A 221 " pdb=" CG2 ILE A 221 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE B 269 " pdb=" N ILE B 269 " pdb=" C ILE B 269 " pdb=" CB ILE B 269 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA ILE B 270 " pdb=" N ILE B 270 " pdb=" C ILE B 270 " pdb=" CB ILE B 270 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 1129 not shown) Planarity restraints: 1198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " 0.026 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO G 60 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 140 " 0.006 2.00e-02 2.50e+03 9.52e-03 1.58e+00 pdb=" CG PHE A 140 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 140 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 140 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 140 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 140 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 140 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO B 194 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.017 5.00e-02 4.00e+02 ... (remaining 1195 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 49 2.63 - 3.20: 6045 3.20 - 3.76: 9991 3.76 - 4.33: 12218 4.33 - 4.90: 20485 Nonbonded interactions: 48788 Sorted by model distance: nonbonded pdb=" OG1 THR A 181 " pdb="MG MG A 401 " model vdw 2.061 2.170 nonbonded pdb=" OG SER A 47 " pdb="MG MG A 401 " model vdw 2.119 2.170 nonbonded pdb=" OG SER A 151 " pdb=" O2' GTP A 402 " model vdw 2.276 3.040 nonbonded pdb="MG MG A 401 " pdb=" O2G GTP A 402 " model vdw 2.323 2.170 nonbonded pdb=" OD2 ASP A 158 " pdb=" NH2 ARG A 161 " model vdw 2.324 3.120 ... (remaining 48783 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.003 0.039 6687 Z= 0.179 Angle : 0.696 10.609 9191 Z= 0.424 Chirality : 0.040 0.238 1132 Planarity : 0.003 0.040 1198 Dihedral : 15.350 159.116 1991 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.21 % Allowed : 28.21 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.28), residues: 988 helix: 2.39 (0.25), residues: 454 sheet: -2.41 (0.39), residues: 169 loop : -2.41 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 176 TYR 0.018 0.001 TYR A 230 PHE 0.022 0.001 PHE A 140 TRP 0.008 0.001 TRP R 192 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6687) covalent geometry : angle 0.69559 ( 9191) hydrogen bonds : bond 0.15722 ( 379) hydrogen bonds : angle 5.64016 ( 1098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 0.254 Fit side-chains REVERT: A 336 PHE cc_start: 0.7877 (t80) cc_final: 0.7410 (t80) REVERT: B 59 TYR cc_start: 0.8723 (m-80) cc_final: 0.8291 (m-80) REVERT: B 75 GLN cc_start: 0.8097 (mt0) cc_final: 0.7778 (mt0) outliers start: 1 outliers final: 0 residues processed: 93 average time/residue: 0.0690 time to fit residues: 8.9805 Evaluate side-chains 87 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.0970 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 16 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.126404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.090416 restraints weight = 13645.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088793 restraints weight = 16630.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.090836 restraints weight = 10764.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.092000 restraints weight = 7543.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.092071 restraints weight = 6746.117| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6687 Z= 0.106 Angle : 0.509 8.286 9191 Z= 0.266 Chirality : 0.040 0.232 1132 Planarity : 0.003 0.031 1198 Dihedral : 9.468 167.018 1052 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.84 % Allowed : 24.21 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.28), residues: 988 helix: 2.55 (0.24), residues: 458 sheet: -2.15 (0.38), residues: 172 loop : -2.32 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.014 0.001 TYR A 287 PHE 0.013 0.001 PHE A 140 TRP 0.008 0.001 TRP R 192 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 6687) covalent geometry : angle 0.50934 ( 9191) hydrogen bonds : bond 0.02936 ( 379) hydrogen bonds : angle 4.09365 ( 1098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.186 Fit side-chains REVERT: A 336 PHE cc_start: 0.7811 (t80) cc_final: 0.7345 (t80) REVERT: B 59 TYR cc_start: 0.8978 (m-80) cc_final: 0.8411 (m-80) REVERT: B 75 GLN cc_start: 0.8227 (mt0) cc_final: 0.7717 (mt0) REVERT: B 234 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8482 (m-80) outliers start: 23 outliers final: 10 residues processed: 103 average time/residue: 0.0568 time to fit residues: 8.2394 Evaluate side-chains 92 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 192 TRP Chi-restraints excluded: chain R residue 251 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.122518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.088950 restraints weight = 13764.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.086397 restraints weight = 10847.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.087235 restraints weight = 8936.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.087363 restraints weight = 8117.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.088243 restraints weight = 7027.964| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6687 Z= 0.182 Angle : 0.564 8.864 9191 Z= 0.294 Chirality : 0.042 0.235 1132 Planarity : 0.003 0.031 1198 Dihedral : 9.722 169.261 1052 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.84 % Allowed : 26.53 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.28), residues: 988 helix: 2.56 (0.25), residues: 466 sheet: -2.31 (0.37), residues: 178 loop : -2.35 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.011 0.001 TYR A 287 PHE 0.023 0.002 PHE B 199 TRP 0.007 0.001 TRP B 339 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 6687) covalent geometry : angle 0.56413 ( 9191) hydrogen bonds : bond 0.03390 ( 379) hydrogen bonds : angle 3.99987 ( 1098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 336 PHE cc_start: 0.8014 (t80) cc_final: 0.7751 (t80) REVERT: B 59 TYR cc_start: 0.9290 (m-80) cc_final: 0.8923 (m-80) REVERT: B 188 MET cc_start: 0.8080 (mtp) cc_final: 0.7723 (mtp) REVERT: B 234 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8392 (m-80) outliers start: 23 outliers final: 14 residues processed: 91 average time/residue: 0.0610 time to fit residues: 8.1803 Evaluate side-chains 89 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 192 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.121046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.084380 restraints weight = 14191.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.084728 restraints weight = 11667.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.085348 restraints weight = 9079.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.085536 restraints weight = 8055.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.085723 restraints weight = 7457.133| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6687 Z= 0.209 Angle : 0.578 8.967 9191 Z= 0.300 Chirality : 0.042 0.242 1132 Planarity : 0.003 0.030 1198 Dihedral : 9.793 172.380 1052 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 6.95 % Allowed : 24.42 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.28), residues: 988 helix: 2.56 (0.25), residues: 468 sheet: -2.31 (0.38), residues: 172 loop : -2.44 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.012 0.001 TYR B 264 PHE 0.025 0.002 PHE B 199 TRP 0.007 0.001 TRP R 192 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 6687) covalent geometry : angle 0.57752 ( 9191) hydrogen bonds : bond 0.03346 ( 379) hydrogen bonds : angle 3.96922 ( 1098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.180 Fit side-chains REVERT: B 59 TYR cc_start: 0.9309 (m-80) cc_final: 0.8607 (m-80) REVERT: B 75 GLN cc_start: 0.8408 (mt0) cc_final: 0.7642 (mt0) REVERT: B 183 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.8479 (m-70) REVERT: B 234 PHE cc_start: 0.9102 (OUTLIER) cc_final: 0.8493 (m-80) outliers start: 33 outliers final: 18 residues processed: 99 average time/residue: 0.0513 time to fit residues: 7.5511 Evaluate side-chains 92 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 192 TRP Chi-restraints excluded: chain R residue 251 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.122884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.085680 restraints weight = 14219.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.085065 restraints weight = 11167.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.085996 restraints weight = 9271.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.086669 restraints weight = 7576.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.086811 restraints weight = 6799.630| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6687 Z= 0.126 Angle : 0.517 9.957 9191 Z= 0.266 Chirality : 0.040 0.255 1132 Planarity : 0.003 0.028 1198 Dihedral : 9.559 172.973 1052 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 5.89 % Allowed : 25.89 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.28), residues: 988 helix: 2.65 (0.25), residues: 467 sheet: -2.25 (0.38), residues: 176 loop : -2.30 (0.29), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.020 0.001 TYR A 154 PHE 0.017 0.002 PHE B 292 TRP 0.011 0.001 TRP R 318 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 6687) covalent geometry : angle 0.51726 ( 9191) hydrogen bonds : bond 0.02802 ( 379) hydrogen bonds : angle 3.67703 ( 1098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.232 Fit side-chains REVERT: A 34 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8811 (m) REVERT: A 336 PHE cc_start: 0.8117 (t80) cc_final: 0.7805 (t80) REVERT: B 59 TYR cc_start: 0.9275 (m-80) cc_final: 0.8671 (m-80) REVERT: B 75 GLN cc_start: 0.8396 (mt0) cc_final: 0.7669 (mt0) REVERT: B 234 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8433 (m-80) REVERT: R 241 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7729 (m-80) outliers start: 28 outliers final: 19 residues processed: 96 average time/residue: 0.0452 time to fit residues: 6.4541 Evaluate side-chains 95 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 192 TRP Chi-restraints excluded: chain R residue 241 PHE Chi-restraints excluded: chain R residue 251 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.121927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.083531 restraints weight = 14244.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.085049 restraints weight = 9884.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.086160 restraints weight = 7630.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.086945 restraints weight = 6374.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.087289 restraints weight = 5628.913| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6687 Z= 0.161 Angle : 0.535 9.696 9191 Z= 0.277 Chirality : 0.041 0.246 1132 Planarity : 0.003 0.028 1198 Dihedral : 9.541 172.091 1052 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 6.74 % Allowed : 25.05 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.28), residues: 988 helix: 2.70 (0.24), residues: 467 sheet: -2.14 (0.38), residues: 172 loop : -2.31 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 251 TYR 0.009 0.001 TYR A 296 PHE 0.024 0.002 PHE R 108 TRP 0.010 0.001 TRP R 318 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 6687) covalent geometry : angle 0.53507 ( 9191) hydrogen bonds : bond 0.02944 ( 379) hydrogen bonds : angle 3.68898 ( 1098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.268 Fit side-chains REVERT: A 336 PHE cc_start: 0.7994 (t80) cc_final: 0.7696 (t80) REVERT: B 59 TYR cc_start: 0.9268 (m-80) cc_final: 0.8676 (m-80) REVERT: B 75 GLN cc_start: 0.8375 (mt0) cc_final: 0.7625 (mt0) REVERT: B 188 MET cc_start: 0.7969 (mtp) cc_final: 0.7645 (mtt) REVERT: B 234 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8522 (m-80) outliers start: 32 outliers final: 22 residues processed: 99 average time/residue: 0.0484 time to fit residues: 7.1737 Evaluate side-chains 97 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 192 TRP Chi-restraints excluded: chain R residue 251 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 94 optimal weight: 30.0000 chunk 85 optimal weight: 50.0000 chunk 84 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 50 optimal weight: 0.0370 chunk 22 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.2664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.121342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.084747 restraints weight = 13967.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085008 restraints weight = 11393.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.085537 restraints weight = 9134.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.085750 restraints weight = 7993.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.086008 restraints weight = 7601.839| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6687 Z= 0.181 Angle : 0.566 10.624 9191 Z= 0.290 Chirality : 0.042 0.261 1132 Planarity : 0.003 0.028 1198 Dihedral : 9.555 172.033 1052 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 7.16 % Allowed : 25.47 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.28), residues: 988 helix: 2.71 (0.25), residues: 467 sheet: -2.13 (0.39), residues: 170 loop : -2.40 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.010 0.001 TYR A 296 PHE 0.022 0.002 PHE B 199 TRP 0.019 0.001 TRP R 318 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 6687) covalent geometry : angle 0.56637 ( 9191) hydrogen bonds : bond 0.03071 ( 379) hydrogen bonds : angle 3.73103 ( 1098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 77 time to evaluate : 0.253 Fit side-chains REVERT: A 336 PHE cc_start: 0.7974 (t80) cc_final: 0.7691 (t80) REVERT: B 7 LEU cc_start: 0.9180 (mt) cc_final: 0.8970 (mt) REVERT: B 59 TYR cc_start: 0.9286 (m-80) cc_final: 0.8652 (m-80) REVERT: B 75 GLN cc_start: 0.8386 (mt0) cc_final: 0.7571 (mt0) REVERT: B 82 TRP cc_start: 0.8723 (OUTLIER) cc_final: 0.7895 (m-10) REVERT: B 183 HIS cc_start: 0.8859 (OUTLIER) cc_final: 0.8430 (m-70) REVERT: B 188 MET cc_start: 0.8061 (mtp) cc_final: 0.7720 (mtt) REVERT: B 234 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.8520 (m-80) outliers start: 34 outliers final: 26 residues processed: 104 average time/residue: 0.0540 time to fit residues: 8.3389 Evaluate side-chains 107 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 192 TRP Chi-restraints excluded: chain R residue 251 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 59 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 60 optimal weight: 0.0770 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.123835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.088383 restraints weight = 13923.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.088150 restraints weight = 11124.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.088286 restraints weight = 9330.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.088981 restraints weight = 8518.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.089022 restraints weight = 7759.224| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6687 Z= 0.104 Angle : 0.507 9.733 9191 Z= 0.259 Chirality : 0.040 0.223 1132 Planarity : 0.003 0.027 1198 Dihedral : 9.317 174.412 1052 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.42 % Allowed : 28.00 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.28), residues: 988 helix: 2.85 (0.24), residues: 464 sheet: -2.06 (0.39), residues: 173 loop : -2.19 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 251 TYR 0.019 0.001 TYR A 154 PHE 0.024 0.002 PHE B 292 TRP 0.026 0.001 TRP R 318 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 6687) covalent geometry : angle 0.50729 ( 9191) hydrogen bonds : bond 0.02548 ( 379) hydrogen bonds : angle 3.47408 ( 1098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 0.214 Fit side-chains REVERT: A 142 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8446 (ttp-110) REVERT: A 302 TYR cc_start: 0.8584 (t80) cc_final: 0.8383 (t80) REVERT: A 336 PHE cc_start: 0.7846 (t80) cc_final: 0.7614 (t80) REVERT: B 59 TYR cc_start: 0.9219 (m-80) cc_final: 0.8697 (m-80) REVERT: B 75 GLN cc_start: 0.8298 (mt0) cc_final: 0.7580 (mt0) REVERT: B 82 TRP cc_start: 0.8594 (OUTLIER) cc_final: 0.7777 (m-10) REVERT: B 234 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8507 (m-80) outliers start: 21 outliers final: 15 residues processed: 98 average time/residue: 0.0559 time to fit residues: 7.6955 Evaluate side-chains 95 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 192 TRP Chi-restraints excluded: chain R residue 251 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 62 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.120858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.084151 restraints weight = 14263.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.084445 restraints weight = 10892.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.084935 restraints weight = 8556.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.084999 restraints weight = 8197.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.085212 restraints weight = 7314.897| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6687 Z= 0.194 Angle : 0.589 11.138 9191 Z= 0.301 Chirality : 0.042 0.249 1132 Planarity : 0.003 0.029 1198 Dihedral : 9.481 173.311 1052 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 5.68 % Allowed : 27.16 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.28), residues: 988 helix: 2.82 (0.25), residues: 464 sheet: -2.10 (0.39), residues: 174 loop : -2.31 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 178 TYR 0.020 0.002 TYR A 154 PHE 0.025 0.002 PHE B 292 TRP 0.037 0.002 TRP R 318 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 6687) covalent geometry : angle 0.58902 ( 9191) hydrogen bonds : bond 0.03102 ( 379) hydrogen bonds : angle 3.69533 ( 1098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.240 Fit side-chains REVERT: A 142 ARG cc_start: 0.8654 (ttp-110) cc_final: 0.8452 (ttp-110) REVERT: A 336 PHE cc_start: 0.8000 (t80) cc_final: 0.7798 (t80) REVERT: B 7 LEU cc_start: 0.9214 (mt) cc_final: 0.9003 (mt) REVERT: B 59 TYR cc_start: 0.9274 (m-80) cc_final: 0.8654 (m-80) REVERT: B 75 GLN cc_start: 0.8376 (mt0) cc_final: 0.7584 (mt0) REVERT: B 82 TRP cc_start: 0.8739 (OUTLIER) cc_final: 0.7890 (m-10) REVERT: B 188 MET cc_start: 0.7967 (mtp) cc_final: 0.7687 (mtp) REVERT: B 234 PHE cc_start: 0.9082 (OUTLIER) cc_final: 0.8504 (m-80) outliers start: 27 outliers final: 19 residues processed: 99 average time/residue: 0.0536 time to fit residues: 7.6453 Evaluate side-chains 98 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 192 TRP Chi-restraints excluded: chain R residue 251 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 16 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 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 269 ASN B 13 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.122461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086579 restraints weight = 14028.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.085799 restraints weight = 12449.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.086229 restraints weight = 10149.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.086415 restraints weight = 8894.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.086668 restraints weight = 8102.007| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6687 Z= 0.135 Angle : 0.547 10.304 9191 Z= 0.278 Chirality : 0.041 0.226 1132 Planarity : 0.003 0.029 1198 Dihedral : 9.325 173.808 1052 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.21 % Allowed : 28.63 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.28), residues: 988 helix: 2.84 (0.25), residues: 465 sheet: -2.09 (0.39), residues: 174 loop : -2.25 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 178 TYR 0.018 0.001 TYR A 154 PHE 0.025 0.002 PHE B 292 TRP 0.035 0.001 TRP R 318 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 6687) covalent geometry : angle 0.54700 ( 9191) hydrogen bonds : bond 0.02745 ( 379) hydrogen bonds : angle 3.52645 ( 1098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1976 Ramachandran restraints generated. 988 Oldfield, 0 Emsley, 988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.148 Fit side-chains REVERT: B 59 TYR cc_start: 0.9237 (m-80) cc_final: 0.8707 (m-80) REVERT: B 75 GLN cc_start: 0.8337 (mt0) cc_final: 0.7594 (mt0) REVERT: B 82 TRP cc_start: 0.8630 (OUTLIER) cc_final: 0.7863 (m-10) REVERT: B 188 MET cc_start: 0.7856 (mtp) cc_final: 0.7559 (mtp) REVERT: B 234 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8540 (m-80) outliers start: 20 outliers final: 18 residues processed: 92 average time/residue: 0.0544 time to fit residues: 7.0811 Evaluate side-chains 95 residues out of total 863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 192 TRP Chi-restraints excluded: chain R residue 251 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.122598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.086686 restraints weight = 14051.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.085790 restraints weight = 13035.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.086247 restraints weight = 10365.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.086397 restraints weight = 8912.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.087632 restraints weight = 8305.948| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6687 Z= 0.185 Angle : 0.994 59.199 9191 Z= 0.582 Chirality : 0.048 0.865 1132 Planarity : 0.004 0.067 1198 Dihedral : 9.365 173.959 1052 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.63 % Allowed : 28.21 % Favored : 67.16 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.28), residues: 988 helix: 2.85 (0.25), residues: 465 sheet: -2.07 (0.39), residues: 174 loop : -2.24 (0.29), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 142 TYR 0.039 0.002 TYR A 74 PHE 0.023 0.002 PHE B 292 TRP 0.035 0.001 TRP R 318 HIS 0.002 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6687) covalent geometry : angle 0.99412 ( 9191) hydrogen bonds : bond 0.02736 ( 379) hydrogen bonds : angle 3.51963 ( 1098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1027.86 seconds wall clock time: 18 minutes 23.40 seconds (1103.40 seconds total)