Starting phenix.real_space_refine on Thu Jul 2 08:05:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t6d_25713/07_2026/7t6d_25713.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t6d_25713/07_2026/7t6d_25713.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/7t6d_25713/07_2026/7t6d_25713.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t6d_25713/07_2026/7t6d_25713.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7t6d_25713/07_2026/7t6d_25713.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t6d_25713/07_2026/7t6d_25713.cif" model { file = "/net/cci-nas-00/data/ceres_data/7t6d_25713/07_2026/7t6d_25713.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t6d_25713/07_2026/7t6d_25713.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= 0.008 sd= 0.059 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 2 5.49 5 S 21 5.16 5 C 4842 2.51 5 N 1362 2.21 5 O 1339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7566 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2185 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 389, 2181 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 382} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 973 Unresolved non-hydrogen angles: 1230 Unresolved non-hydrogen dihedrals: 804 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLU:plan': 30, 'GLN:plan1': 19, 'ASP:plan': 25, 'ASN:plan1': 5, 'ARG:plan': 25, 'HIS:plan': 7, 'TYR:plan': 10, 'PHE:plan': 6, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 588 Conformer: "B" Number of residues, atoms: 389, 2181 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 260} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 382} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 973 Unresolved non-hydrogen angles: 1230 Unresolved non-hydrogen dihedrals: 804 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLU:plan': 30, 'GLN:plan1': 19, 'ASP:plan': 25, 'ASN:plan1': 5, 'ARG:plan': 25, 'HIS:plan': 7, 'TYR:plan': 10, 'PHE:plan': 6, 'TRP:plan': 4} Unresolved non-hydrogen planarities: 588 bond proxies already assigned to first conformer: 2188 Chain: "B" Number of atoms: 2406 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 381, 2404 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 5, 'TRANS': 375} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 668 Unresolved non-hydrogen angles: 834 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ARG:plan': 22, 'ASP:plan': 21, 'ASN:plan1': 3, 'GLN:plan1': 12, 'GLU:plan': 24, 'TYR:plan': 6, 'HIS:plan': 4, 'PHE:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 414 Conformer: "B" Number of residues, atoms: 381, 2404 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 5, 'TRANS': 375} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 668 Unresolved non-hydrogen angles: 834 Unresolved non-hydrogen dihedrals: 550 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'ARG:plan': 22, 'ASP:plan': 21, 'ASN:plan1': 3, 'GLN:plan1': 12, 'GLU:plan': 24, 'TYR:plan': 6, 'HIS:plan': 4, 'PHE:plan': 2, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 414 bond proxies already assigned to first conformer: 2428 Chain: "C" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1544 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 8, 'TRANS': 204} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 257 Unresolved non-hydrogen angles: 334 Unresolved non-hydrogen dihedrals: 222 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PHE:plan': 6, 'ASP:plan': 4, 'TRP:plan': 3, 'ARG:plan': 8, 'GLN:plan1': 3, 'GLU:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 158 Chain: "D" Number of atoms: 1336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1336 Classifications: {'peptide': 198} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 86} Link IDs: {'PTRANS': 7, 'TRANS': 190} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 344 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'ARG:plan': 12, 'GLN:plan1': 4, 'PHE:plan': 6, 'ASP:plan': 4, 'TRP:plan': 3, 'TYR:plan': 3, 'GLU:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 196 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'LPP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'PGV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.74, per 1000 atoms: 0.36 Number of scatterers: 7566 At special positions: 0 Unit cell: (91.528, 114.41, 162.866, 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 21 16.00 P 2 15.00 O 1339 8.00 N 1362 7.00 C 4842 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 329.2 milliseconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 2 sheets defined 83.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 2 through 48 removed outlier: 4.187A pdb=" N LEU A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) Proline residue: A 10 - end of helix Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.712A pdb=" N ASP A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 83 Processing helix chain 'A' and resid 84 through 97 removed outlier: 3.640A pdb=" N GLU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 121 Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 139 through 155 Processing helix chain 'A' and resid 157 through 171 Processing helix chain 'A' and resid 175 through 190 Processing helix chain 'A' and resid 195 through 210 removed outlier: 3.937A pdb=" N THR A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 227 removed outlier: 3.985A pdb=" N SER A 217 " --> pdb=" O SER A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 removed outlier: 4.015A pdb=" N ILE A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.840A pdb=" N VAL A 248 " --> pdb=" O ARG A 245 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 249 " --> pdb=" O GLU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 263 removed outlier: 3.660A pdb=" N LEU A 262 " --> pdb=" O CYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 281 through 297 removed outlier: 3.547A pdb=" N GLU A 285 " --> pdb=" O GLY A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 312 Processing helix chain 'A' and resid 314 through 329 Processing helix chain 'A' and resid 332 through 352 Processing helix chain 'B' and resid 4 through 27 Proline residue: B 10 - end of helix Processing helix chain 'B' and resid 37 through 48 Processing helix chain 'B' and resid 50 through 62 Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 84 through 97 removed outlier: 3.574A pdb=" N GLU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 121 Processing helix chain 'B' and resid 122 through 131 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 139 through 154 Processing helix chain 'B' and resid 156 through 171 Processing helix chain 'B' and resid 175 through 192 removed outlier: 4.313A pdb=" N ALA B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 213 through 228 removed outlier: 3.694A pdb=" N SER B 217 " --> pdb=" O SER B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 239 Processing helix chain 'B' and resid 239 through 244 Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 277 Processing helix chain 'B' and resid 281 through 297 removed outlier: 3.654A pdb=" N GLU B 285 " --> pdb=" O GLY B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 312 Processing helix chain 'B' and resid 314 through 329 Processing helix chain 'B' and resid 333 through 352 Processing helix chain 'C' and resid 3 through 41 removed outlier: 3.735A pdb=" N ARG C 7 " --> pdb=" O THR C 3 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 78 removed outlier: 3.643A pdb=" N SER C 53 " --> pdb=" O GLY C 49 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) Proline residue: C 75 - end of helix removed outlier: 3.982A pdb=" N PHE C 78 " --> pdb=" O PHE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 112 removed outlier: 3.868A pdb=" N MET C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 124 Processing helix chain 'C' and resid 134 through 159 Proline residue: C 143 - end of helix Processing helix chain 'C' and resid 159 through 166 Processing helix chain 'C' and resid 166 through 194 removed outlier: 3.984A pdb=" N ALA C 170 " --> pdb=" O ARG C 166 " (cutoff:3.500A) Proline residue: C 172 - end of helix removed outlier: 4.139A pdb=" N ASN C 194 " --> pdb=" O TRP C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 203 removed outlier: 3.784A pdb=" N THR C 200 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 221 removed outlier: 3.547A pdb=" N HIS C 221 " --> pdb=" O PHE C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 41 removed outlier: 3.593A pdb=" N VAL D 32 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 78 removed outlier: 3.642A pdb=" N SER D 53 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N PHE D 74 " --> pdb=" O LEU D 70 " (cutoff:3.500A) Proline residue: D 75 - end of helix removed outlier: 3.982A pdb=" N PHE D 78 " --> pdb=" O PHE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 112 removed outlier: 3.867A pdb=" N MET D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 124 Processing helix chain 'D' and resid 134 through 159 Proline residue: D 143 - end of helix Processing helix chain 'D' and resid 159 through 166 Processing helix chain 'D' and resid 166 through 194 removed outlier: 3.985A pdb=" N ALA D 170 " --> pdb=" O ARG D 166 " (cutoff:3.500A) Proline residue: D 172 - end of helix removed outlier: 4.139A pdb=" N ASN D 194 " --> pdb=" O TRP D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 removed outlier: 3.784A pdb=" N THR D 200 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AA2, first strand: chain 'B' and resid 363 through 364 removed outlier: 3.867A pdb=" N TYR B 355 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS B 381 " --> pdb=" O ARG B 356 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2078 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: 1.05 Time building geometry restraints manager: 0.80 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: 1253 1.32 - 1.44: 1980 1.44 - 1.57: 4401 1.57 - 1.69: 3 1.69 - 1.81: 41 Bond restraints: 7678 Sorted by residual: bond pdb=" O5 LPP A 401 " pdb=" P1 LPP A 401 " ideal model delta sigma weight residual 2.278 1.629 0.649 2.00e-02 2.50e+03 1.05e+03 bond pdb=" O4 LPP A 401 " pdb=" P1 LPP A 401 " ideal model delta sigma weight residual 1.764 1.503 0.261 2.00e-02 2.50e+03 1.70e+02 bond pdb=" C6 LPP A 401 " pdb=" O5 LPP A 401 " ideal model delta sigma weight residual 1.243 1.466 -0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C LEU B 8 " pdb=" N LEU B 9 " ideal model delta sigma weight residual 1.332 1.387 -0.055 1.50e-02 4.44e+03 1.33e+01 bond pdb=" C VAL D 32 " pdb=" O VAL D 32 " ideal model delta sigma weight residual 1.237 1.279 -0.042 1.19e-02 7.06e+03 1.24e+01 ... (remaining 7673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.29: 10520 8.29 - 16.58: 5 16.58 - 24.87: 0 24.87 - 33.15: 1 33.15 - 41.44: 2 Bond angle restraints: 10528 Sorted by residual: angle pdb=" O4 LPP A 401 " pdb=" P1 LPP A 401 " pdb=" O5 LPP A 401 " ideal model delta sigma weight residual 62.99 104.43 -41.44 3.00e+00 1.11e-01 1.91e+02 angle pdb=" C6 LPP A 401 " pdb=" O5 LPP A 401 " pdb=" P1 LPP A 401 " ideal model delta sigma weight residual 82.33 120.43 -38.10 3.00e+00 1.11e-01 1.61e+02 angle pdb=" O2 LPP A 401 " pdb=" P1 LPP A 401 " pdb=" O3 LPP A 401 " ideal model delta sigma weight residual 142.11 112.60 29.51 3.00e+00 1.11e-01 9.68e+01 angle pdb=" N PRO C 211 " pdb=" CA PRO C 211 " pdb=" CB PRO C 211 " ideal model delta sigma weight residual 103.25 95.88 7.37 1.05e+00 9.07e-01 4.93e+01 angle pdb=" N GLY B 67 " pdb=" CA GLY B 67 " pdb=" C GLY B 67 " ideal model delta sigma weight residual 115.36 107.52 7.84 1.33e+00 5.65e-01 3.47e+01 ... (remaining 10523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.13: 4292 23.13 - 46.27: 160 46.27 - 69.40: 29 69.40 - 92.53: 3 92.53 - 115.66: 1 Dihedral angle restraints: 4485 sinusoidal: 1023 harmonic: 3462 Sorted by residual: dihedral pdb=" CD ARG C 161 " pdb=" NE ARG C 161 " pdb=" CZ ARG C 161 " pdb=" NH1 ARG C 161 " ideal model delta sinusoidal sigma weight residual 0.00 82.22 -82.22 1 1.00e+01 1.00e-02 8.30e+01 dihedral pdb=" C TYR D 210 " pdb=" N TYR D 210 " pdb=" CA TYR D 210 " pdb=" CB TYR D 210 " ideal model delta harmonic sigma weight residual -122.60 -110.64 -11.96 0 2.50e+00 1.60e-01 2.29e+01 dihedral pdb=" C TYR C 210 " pdb=" N TYR C 210 " pdb=" CA TYR C 210 " pdb=" CB TYR C 210 " ideal model delta harmonic sigma weight residual -122.60 -110.67 -11.93 0 2.50e+00 1.60e-01 2.28e+01 ... (remaining 4482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1181 0.074 - 0.147: 109 0.147 - 0.221: 13 0.221 - 0.294: 3 0.294 - 0.368: 4 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CA LEU A 2 " pdb=" N LEU A 2 " pdb=" C LEU A 2 " pdb=" CB LEU A 2 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CA LEU B 2 " pdb=" N LEU B 2 " pdb=" C LEU B 2 " pdb=" CB LEU B 2 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA TYR D 210 " pdb=" N TYR D 210 " pdb=" C TYR D 210 " pdb=" CB TYR D 210 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 1307 not shown) Planarity restraints: 1369 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 PGV C 601 " 0.222 2.00e-02 2.50e+03 2.18e-01 4.77e+02 pdb=" C11 PGV C 601 " -0.234 2.00e-02 2.50e+03 pdb=" C12 PGV C 601 " -0.202 2.00e-02 2.50e+03 pdb=" C13 PGV C 601 " 0.214 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 161 " -1.090 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG C 161 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG C 161 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG C 161 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 161 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 22 " -0.371 9.50e-02 1.11e+02 1.66e-01 1.70e+01 pdb=" NE ARG A 22 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A 22 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 22 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 22 " -0.013 2.00e-02 2.50e+03 ... (remaining 1366 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 202 2.72 - 3.26: 7994 3.26 - 3.81: 12449 3.81 - 4.35: 12953 4.35 - 4.90: 22478 Nonbonded interactions: 56076 Sorted by model distance: nonbonded pdb=" O LEU A 2 " pdb=" CD2 PHE A 6 " model vdw 2.172 3.340 nonbonded pdb=" O VAL D 16 " pdb=" ND1 HIS D 20 " model vdw 2.177 3.120 nonbonded pdb=" NE ARG A 22 " pdb=" O2 LPP A 401 " model vdw 2.219 3.120 nonbonded pdb=" CZ ARG A 22 " pdb=" O2 LPP A 401 " model vdw 2.220 3.270 nonbonded pdb=" NH1 ARG A 37 " pdb=" OD2 ASP B 138 " model vdw 2.239 3.120 ... (remaining 56071 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 27 or resid 36 or (resid 37 through 38 and (name \ N or name CA or name C or name O or name CB )) or resid 39 through 60 or (resid \ 61 through 66 and (name N or name CA or name C or name O or name CB )) or resid \ 67 through 114 or (resid 115 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name NE )) or resid 116 through 121 or (resid 122 t \ hrough 128 and (name N or name CA or name C or name O or name CB )) or resid 129 \ through 235 or resid 237 through 266 or resid 268 through 389)) selection = (chain 'B' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 54 or (resid 55 through 56 and (name N or name CA \ or name C or name O or name CB )) or resid 57 through 58 or (resid 59 through 6 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 67 or (resid \ 68 through 72 and (name N or name CA or name C or name O or name CB )) or resid \ 73 through 92 or (resid 93 through 106 and (name N or name CA or name C or name \ O or name CB )) or resid 107 through 122 or (resid 123 through 128 and (name N \ or name CA or name C or name O or name CB )) or resid 129 through 133 or (resid \ 134 through 141 and (name N or name CA or name C or name O or name CB )) or (res \ id 142 through 145 and (name N or name CA or name C or name O or name CB )) or r \ esid 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) \ or resid 148 through 153 or (resid 154 through 170 and (name N or name CA or nam \ e C or name O or name CB )) or resid 171 or (resid 172 through 205 and (name N o \ r name CA or name C or name O or name CB )) or (resid 206 through 220 and (name \ N or name CA or name C or name O or name CB )) or resid 221 or (resid 222 throug \ h 227 and (name N or name CA or name C or name O or name CB )) or (resid 228 thr \ ough 235 and (name N or name CA or name C or name O or name CB )) or (resid 237 \ through 262 and (name N or name CA or name C or name O or name CB )) or resid 26 \ 3 through 266 or (resid 268 through 280 and (name N or name CA or name C or name \ O or name CB )) or resid 281 through 389)) } ncs_group { reference = (chain 'C' and ((resid 5 through 7 and (name N or name CA or name C or name O or \ name CB )) or resid 8 through 28 or (resid 29 through 33 and (name N or name CA \ or name C or name O or name CB )) or resid 34 or (resid 35 and (name N or name \ CA or name C or name O or name CB )) or resid 36 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )) or resid 55 through 75 or (res \ id 76 and (name N or name CA or name C or name O or name CB )) or resid 77 throu \ gh 90 or (resid 91 through 92 and (name N or name CA or name C or name O or name \ CB )) or resid 93 through 94 or (resid 95 through 96 and (name N or name CA or \ name C or name O or name CB )) or resid 97 through 101 or (resid 102 through 107 \ and (name N or name CA or name C or name O or name CB )) or resid 108 through 1 \ 13 or (resid 114 through 123 and (name N or name CA or name C or name O or name \ CB )) or (resid 124 and (name N or name CA or name C or name O )) or (resid 133 \ through 144 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 5 through 148 or (resid 149 through 151 and (name N or name CA or name C or name \ O or name CB )) or resid 152 through 153 or (resid 154 and (name N or name CA o \ r name C or name O or name CB )) or resid 155 through 160 or (resid 161 through \ 171 and (name N or name CA or name C or name O or name CB )) or resid 172 throug \ h 187 or (resid 188 and (name N or name CA or name C or name O or name CB )) or \ resid 189 through 200 or (resid 201 through 202 and (name N or name CA or name C \ or name O or name CB )) or resid 203 through 210)) selection = (chain 'D' and (resid 5 through 82 or (resid 83 through 92 and (name N or name C \ A or name C or name O or name CB )) or resid 93 through 98 or (resid 99 and (nam \ e N or name CA or name C or name O or name CB )) or resid 100 through 210)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.17 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: 0.540 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.580 Find NCS groups from input model: 0.170 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 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 : 0.014 0.845 7679 Z= 1.121 Angle : 1.038 41.443 10528 Z= 0.579 Chirality : 0.051 0.368 1310 Planarity : 0.016 0.488 1369 Dihedral : 13.291 115.664 2229 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.91 % Favored : 97.00 % Rotamer: Outliers : 1.42 % Allowed : 1.42 % Favored : 97.16 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.14 (0.24), residues: 1170 helix: 1.38 (0.17), residues: 924 sheet: -2.39 (1.21), residues: 20 loop : -1.43 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 80 TYR 0.020 0.002 TYR C 210 PHE 0.017 0.001 PHE A 45 TRP 0.021 0.001 TRP C 18 HIS 0.007 0.001 HIS C 4 Details of bonding type rmsd/Z covalent geometry : bond 0.01015 / 0.57 ( 7678) covalent geometry : angle 1.03824 / 0.58 (10528) hydrogen bonds : bond 0.11648 / 8.19 ( 702) hydrogen bonds : angle 5.11208 / 3.86 ( 2078) Misc. bond : bond 0.84539 / 44.49 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 169 time to evaluate : 0.187 Fit side-chains REVERT: B 45 PHE cc_start: 0.7963 (m-80) cc_final: 0.7703 (m-80) REVERT: C 27 ILE cc_start: 0.7613 (tt) cc_final: 0.7366 (tt) REVERT: C 159 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8779 (tppt) REVERT: C 168 ARG cc_start: 0.8490 (ttp-110) cc_final: 0.8088 (ttp80) REVERT: D 18 TRP cc_start: 0.6662 (t60) cc_final: 0.5967 (t60) REVERT: D 27 ILE cc_start: 0.7398 (tt) cc_final: 0.7097 (tt) REVERT: D 172 PRO cc_start: 0.7242 (Cg_exo) cc_final: 0.6816 (Cg_endo) outliers start: 6 outliers final: 2 residues processed: 174 average time/residue: 0.0700 time to fit residues: 16.4754 Evaluate side-chains 126 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 124 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 ARG Chi-restraints excluded: chain C residue 3 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.0170 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS A 111 GLN A 112 GLN A 131 ASN B 152 GLN B 181 HIS C 205 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.228656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.212843 restraints weight = 17438.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.212214 restraints weight = 25343.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.209129 restraints weight = 14703.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.210230 restraints weight = 13736.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.210452 restraints weight = 8153.492| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4384 r_free = 0.4384 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4383 r_free = 0.4383 target_work(ls_wunit_k1) = 0.210 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (7 function evaluations) r_final: 0.4383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7679 Z= 0.139 Angle : 0.560 8.610 10528 Z= 0.297 Chirality : 0.037 0.238 1310 Planarity : 0.005 0.112 1369 Dihedral : 8.548 105.002 1321 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.63 % Favored : 98.29 % Rotamer: Outliers : 2.84 % Allowed : 15.37 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.97 (0.25), residues: 1170 helix: 1.90 (0.17), residues: 938 sheet: -1.39 (2.02), residues: 10 loop : -1.11 (0.42), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 140 TYR 0.017 0.002 TYR B 117 PHE 0.045 0.002 PHE A 6 TRP 0.019 0.001 TRP D 18 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 7678) covalent geometry : angle 0.55968 / 0.30 (10528) hydrogen bonds : bond 0.03781 / 2.71 ( 702) hydrogen bonds : angle 3.88505 / 2.92 ( 2078) Misc. bond : bond 0.00125 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.265 Fit side-chains REVERT: C 31 LEU cc_start: 0.8838 (mt) cc_final: 0.8613 (mt) REVERT: C 36 ARG cc_start: 0.7774 (ttt180) cc_final: 0.7454 (ttt90) REVERT: C 188 TYR cc_start: 0.8403 (t80) cc_final: 0.8196 (t80) REVERT: D 18 TRP cc_start: 0.6627 (t60) cc_final: 0.6222 (t60) REVERT: D 27 ILE cc_start: 0.7269 (tt) cc_final: 0.7004 (tt) REVERT: D 172 PRO cc_start: 0.7529 (Cg_exo) cc_final: 0.7258 (Cg_endo) outliers start: 12 outliers final: 7 residues processed: 137 average time/residue: 0.0552 time to fit residues: 10.7301 Evaluate side-chains 123 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain D residue 179 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 39 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 27 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 82 optimal weight: 0.2980 chunk 114 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 GLN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** 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 = 0.4511 r_free = 0.4511 target = 0.225452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.208471 restraints weight = 25048.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.207301 restraints weight = 21701.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.205371 restraints weight = 15876.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.204368 restraints weight = 16489.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.203645 restraints weight = 13663.373| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4353 r_free = 0.4353 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4353 r_free = 0.4353 target_work(ls_wunit_k1) = 0.206 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.4353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 7679 Z= 0.135 Angle : 0.531 8.384 10528 Z= 0.277 Chirality : 0.035 0.205 1310 Planarity : 0.004 0.118 1369 Dihedral : 8.036 106.365 1316 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.37 % Favored : 98.54 % Rotamer: Outliers : 2.36 % Allowed : 17.02 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 2.37 (0.25), residues: 1170 helix: 2.14 (0.17), residues: 939 sheet: -1.75 (1.51), residues: 15 loop : -0.73 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 22 TYR 0.017 0.001 TYR B 117 PHE 0.022 0.002 PHE A 6 TRP 0.014 0.001 TRP D 18 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 7678) covalent geometry : angle 0.53101 / 0.28 (10528) hydrogen bonds : bond 0.03615 / 2.62 ( 702) hydrogen bonds : angle 3.68107 / 2.77 ( 2078) Misc. bond : bond 0.00455 / 0.24 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: B 74 THR cc_start: 0.9222 (m) cc_final: 0.8943 (m) REVERT: B 161 ILE cc_start: 0.8891 (mm) cc_final: 0.8654 (mm) REVERT: C 36 ARG cc_start: 0.7999 (ttt180) cc_final: 0.7629 (ttt90) REVERT: D 18 TRP cc_start: 0.6486 (t60) cc_final: 0.6146 (t60) outliers start: 10 outliers final: 7 residues processed: 125 average time/residue: 0.0658 time to fit residues: 11.5134 Evaluate side-chains 121 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 83 GLN Chi-restraints excluded: chain D residue 179 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 32 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** 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 = 0.4493 r_free = 0.4493 target = 0.223437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.207069 restraints weight = 29510.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.205782 restraints weight = 25534.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.204362 restraints weight = 19607.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.205319 restraints weight = 16429.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.205921 restraints weight = 10832.947| |-----------------------------------------------------------------------------| r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4340 r_free = 0.4340 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4340 r_free = 0.4340 target_work(ls_wunit_k1) = 0.205 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7679 Z= 0.131 Angle : 0.515 8.082 10528 Z= 0.270 Chirality : 0.035 0.153 1310 Planarity : 0.003 0.047 1369 Dihedral : 7.637 106.745 1316 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.84 % Allowed : 18.91 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 4.00 % 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: 2.66 (0.25), residues: 1170 helix: 2.30 (0.17), residues: 942 sheet: -2.94 (1.58), residues: 10 loop : -0.42 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 140 TYR 0.019 0.002 TYR B 117 PHE 0.017 0.002 PHE D 22 TRP 0.013 0.001 TRP D 18 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 7678) covalent geometry : angle 0.51539 / 0.27 (10528) hydrogen bonds : bond 0.03393 / 2.45 ( 702) hydrogen bonds : angle 3.48492 / 2.62 ( 2078) Misc. bond : bond 0.00064 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.220 Fit side-chains REVERT: B 74 THR cc_start: 0.9156 (m) cc_final: 0.8891 (m) REVERT: B 170 LEU cc_start: 0.8334 (tp) cc_final: 0.7052 (tp) REVERT: C 36 ARG cc_start: 0.7941 (ttt180) cc_final: 0.7548 (ttt90) REVERT: D 61 PHE cc_start: 0.6920 (OUTLIER) cc_final: 0.6245 (t80) REVERT: D 203 ARG cc_start: 0.5989 (ttm110) cc_final: 0.5574 (mmt180) outliers start: 12 outliers final: 9 residues processed: 124 average time/residue: 0.0558 time to fit residues: 9.9436 Evaluate side-chains 121 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 179 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 71 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 113 optimal weight: 0.5980 chunk 9 optimal weight: 0.0470 chunk 34 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.224153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.207911 restraints weight = 27043.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.206570 restraints weight = 22963.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.205233 restraints weight = 14913.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.204895 restraints weight = 13398.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.203684 restraints weight = 12376.741| |-----------------------------------------------------------------------------| r_work (final): 0.4319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4319 r_free = 0.4319 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4319 r_free = 0.4319 target_work(ls_wunit_k1) = 0.203 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7679 Z= 0.117 Angle : 0.495 7.419 10528 Z= 0.260 Chirality : 0.035 0.167 1310 Planarity : 0.003 0.060 1369 Dihedral : 7.308 104.603 1316 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.07 % Allowed : 19.86 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 4.00 % 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: 2.84 (0.25), residues: 1170 helix: 2.45 (0.17), residues: 940 sheet: -3.08 (1.51), residues: 10 loop : -0.45 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 165 TYR 0.020 0.001 TYR B 117 PHE 0.015 0.001 PHE D 22 TRP 0.033 0.001 TRP D 18 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 7678) covalent geometry : angle 0.49520 / 0.26 (10528) hydrogen bonds : bond 0.03238 / 2.35 ( 702) hydrogen bonds : angle 3.38809 / 2.55 ( 2078) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.255 Fit side-chains REVERT: B 74 THR cc_start: 0.9150 (m) cc_final: 0.8883 (m) REVERT: B 170 LEU cc_start: 0.8341 (tp) cc_final: 0.7010 (tp) REVERT: D 61 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.5917 (t80) REVERT: D 203 ARG cc_start: 0.6078 (ttm110) cc_final: 0.5589 (mmt180) outliers start: 13 outliers final: 6 residues processed: 128 average time/residue: 0.0536 time to fit residues: 9.9412 Evaluate side-chains 118 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 83 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 66 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 40.0000 chunk 57 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.221677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.203331 restraints weight = 21027.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.202017 restraints weight = 21263.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.199688 restraints weight = 17646.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.199507 restraints weight = 16242.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.199025 restraints weight = 11861.144| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4281 r_free = 0.4281 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4281 r_free = 0.4281 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7679 Z= 0.135 Angle : 0.520 8.238 10528 Z= 0.272 Chirality : 0.035 0.173 1310 Planarity : 0.003 0.059 1369 Dihedral : 7.238 104.490 1316 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.60 % Allowed : 21.04 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 2.88 (0.25), residues: 1170 helix: 2.46 (0.17), residues: 938 sheet: -2.99 (1.52), residues: 10 loop : -0.35 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 165 TYR 0.019 0.001 TYR B 117 PHE 0.014 0.002 PHE A 58 TRP 0.034 0.001 TRP D 18 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 7678) covalent geometry : angle 0.52046 / 0.27 (10528) hydrogen bonds : bond 0.03317 / 2.38 ( 702) hydrogen bonds : angle 3.40638 / 2.58 ( 2078) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.234 Fit side-chains REVERT: B 74 THR cc_start: 0.9155 (m) cc_final: 0.8894 (m) REVERT: B 170 LEU cc_start: 0.8393 (tp) cc_final: 0.7087 (tp) REVERT: D 61 PHE cc_start: 0.6620 (OUTLIER) cc_final: 0.5963 (t80) REVERT: D 203 ARG cc_start: 0.6460 (ttm110) cc_final: 0.5946 (mmt180) outliers start: 11 outliers final: 6 residues processed: 121 average time/residue: 0.0530 time to fit residues: 9.3382 Evaluate side-chains 116 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 179 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 115 optimal weight: 0.0980 chunk 110 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 56 optimal weight: 0.3980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 202 GLN D 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.222749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.207072 restraints weight = 27248.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.204542 restraints weight = 23479.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.203659 restraints weight = 19448.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.204748 restraints weight = 15290.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.205015 restraints weight = 10552.099| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4326 r_free = 0.4326 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4326 r_free = 0.4326 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7679 Z= 0.118 Angle : 0.513 8.399 10528 Z= 0.267 Chirality : 0.035 0.167 1310 Planarity : 0.003 0.055 1369 Dihedral : 7.009 101.669 1316 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.60 % Allowed : 22.93 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 3.01 (0.25), residues: 1170 helix: 2.57 (0.17), residues: 940 sheet: -1.45 (1.37), residues: 15 loop : -0.46 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 165 TYR 0.018 0.001 TYR B 117 PHE 0.013 0.001 PHE C 63 TRP 0.035 0.001 TRP D 18 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7678) covalent geometry : angle 0.51346 / 0.27 (10528) hydrogen bonds : bond 0.03156 / 2.29 ( 702) hydrogen bonds : angle 3.36506 / 2.54 ( 2078) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.254 Fit side-chains REVERT: B 74 THR cc_start: 0.9129 (m) cc_final: 0.8849 (m) REVERT: B 139 PHE cc_start: 0.8570 (m-80) cc_final: 0.8364 (m-10) REVERT: B 170 LEU cc_start: 0.8513 (tp) cc_final: 0.7186 (tp) REVERT: D 61 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.5925 (t80) REVERT: D 203 ARG cc_start: 0.6388 (ttm110) cc_final: 0.6067 (mmt180) outliers start: 11 outliers final: 6 residues processed: 123 average time/residue: 0.0550 time to fit residues: 9.7970 Evaluate side-chains 118 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 61 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 109 optimal weight: 40.0000 chunk 49 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 115 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** 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 = 0.4483 r_free = 0.4483 target = 0.222766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.206732 restraints weight = 30352.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.206649 restraints weight = 24995.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.205370 restraints weight = 15166.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.206561 restraints weight = 12702.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.205268 restraints weight = 10202.170| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4325 r_free = 0.4325 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4325 r_free = 0.4325 target_work(ls_wunit_k1) = 0.204 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7679 Z= 0.127 Angle : 0.531 8.901 10528 Z= 0.274 Chirality : 0.035 0.175 1310 Planarity : 0.003 0.053 1369 Dihedral : 6.976 100.294 1316 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.60 % Allowed : 23.64 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 3.08 (0.25), residues: 1170 helix: 2.60 (0.17), residues: 942 sheet: -1.46 (1.37), residues: 15 loop : -0.36 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 165 TYR 0.023 0.001 TYR B 117 PHE 0.019 0.002 PHE D 22 TRP 0.037 0.001 TRP D 18 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7678) covalent geometry : angle 0.53056 / 0.27 (10528) hydrogen bonds : bond 0.03202 / 2.31 ( 702) hydrogen bonds : angle 3.36554 / 2.55 ( 2078) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.199 Fit side-chains REVERT: B 74 THR cc_start: 0.9134 (m) cc_final: 0.8887 (m) REVERT: B 118 MET cc_start: 0.8439 (ttm) cc_final: 0.8123 (ttm) REVERT: B 139 PHE cc_start: 0.8575 (m-80) cc_final: 0.8371 (m-10) REVERT: B 170 LEU cc_start: 0.8535 (tp) cc_final: 0.7196 (tp) REVERT: C 188 TYR cc_start: 0.8196 (t80) cc_final: 0.7979 (t80) REVERT: C 203 ARG cc_start: 0.8073 (ptt90) cc_final: 0.7769 (ttp-110) REVERT: D 61 PHE cc_start: 0.6651 (OUTLIER) cc_final: 0.5859 (t80) REVERT: D 203 ARG cc_start: 0.6437 (ttm110) cc_final: 0.5982 (tpp-160) outliers start: 11 outliers final: 8 residues processed: 125 average time/residue: 0.0590 time to fit residues: 10.7877 Evaluate side-chains 123 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 61 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 105 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 111 GLN ** 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 = 0.4472 r_free = 0.4472 target = 0.221561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.205588 restraints weight = 24649.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.204226 restraints weight = 22688.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.203301 restraints weight = 12917.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.201790 restraints weight = 13894.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.201050 restraints weight = 12841.292| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4296 r_free = 0.4296 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4296 r_free = 0.4296 target_work(ls_wunit_k1) = 0.201 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7679 Z= 0.127 Angle : 0.529 9.262 10528 Z= 0.273 Chirality : 0.035 0.180 1310 Planarity : 0.003 0.051 1369 Dihedral : 6.813 97.461 1316 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.55 % Allowed : 22.93 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 3.16 (0.25), residues: 1170 helix: 2.65 (0.17), residues: 941 sheet: -1.45 (1.37), residues: 15 loop : -0.28 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 165 TYR 0.025 0.001 TYR B 117 PHE 0.013 0.002 PHE D 152 TRP 0.041 0.002 TRP D 18 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 7678) covalent geometry : angle 0.52890 / 0.27 (10528) hydrogen bonds : bond 0.03182 / 2.31 ( 702) hydrogen bonds : angle 3.34963 / 2.53 ( 2078) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.199 Fit side-chains REVERT: B 74 THR cc_start: 0.9139 (m) cc_final: 0.8883 (m) REVERT: B 139 PHE cc_start: 0.8570 (m-80) cc_final: 0.8354 (m-10) REVERT: B 170 LEU cc_start: 0.8508 (tp) cc_final: 0.7126 (tp) REVERT: C 203 ARG cc_start: 0.8002 (ptt90) cc_final: 0.7617 (ttp-110) REVERT: D 18 TRP cc_start: 0.6671 (t60) cc_final: 0.6020 (t60) REVERT: D 61 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6059 (t80) REVERT: D 203 ARG cc_start: 0.6388 (ttm110) cc_final: 0.6026 (tpp-160) outliers start: 15 outliers final: 11 residues processed: 124 average time/residue: 0.0535 time to fit residues: 9.5918 Evaluate side-chains 124 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 61 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 42 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 0.2980 chunk 77 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.222681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.204798 restraints weight = 19655.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.203036 restraints weight = 19527.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.201433 restraints weight = 15176.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.200670 restraints weight = 15046.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.199893 restraints weight = 13193.141| |-----------------------------------------------------------------------------| r_work (final): 0.4278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4278 r_free = 0.4278 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4278 r_free = 0.4278 target_work(ls_wunit_k1) = 0.199 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7679 Z= 0.119 Angle : 0.526 9.728 10528 Z= 0.270 Chirality : 0.035 0.205 1310 Planarity : 0.003 0.049 1369 Dihedral : 6.563 93.376 1316 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.60 % Allowed : 22.93 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 3.27 (0.25), residues: 1170 helix: 2.70 (0.17), residues: 945 sheet: -1.42 (1.36), residues: 15 loop : -0.17 (0.44), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 165 TYR 0.023 0.001 TYR B 117 PHE 0.012 0.001 PHE C 63 TRP 0.038 0.001 TRP D 18 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 7678) covalent geometry : angle 0.52649 / 0.27 (10528) hydrogen bonds : bond 0.03094 / 2.25 ( 702) hydrogen bonds : angle 3.31380 / 2.51 ( 2078) Misc. bond : bond 0.00042 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.291 Fit side-chains REVERT: A 118 MET cc_start: 0.8225 (tpt) cc_final: 0.7747 (tpt) REVERT: B 74 THR cc_start: 0.9144 (m) cc_final: 0.8883 (m) REVERT: B 135 ASP cc_start: 0.7930 (t0) cc_final: 0.7455 (m-30) REVERT: B 139 PHE cc_start: 0.8568 (m-80) cc_final: 0.8336 (m-10) REVERT: B 170 LEU cc_start: 0.8521 (tp) cc_final: 0.7133 (tp) REVERT: C 203 ARG cc_start: 0.8162 (ptt90) cc_final: 0.7777 (ttp-110) REVERT: C 210 TYR cc_start: 0.7203 (m-80) cc_final: 0.6986 (m-10) REVERT: D 61 PHE cc_start: 0.6909 (OUTLIER) cc_final: 0.6092 (t80) REVERT: D 71 LEU cc_start: 0.8374 (mt) cc_final: 0.7906 (mt) REVERT: D 203 ARG cc_start: 0.6309 (ttm110) cc_final: 0.5979 (tpp-160) outliers start: 11 outliers final: 8 residues processed: 120 average time/residue: 0.0572 time to fit residues: 10.4679 Evaluate side-chains 119 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 61 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 83 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 81 optimal weight: 0.1980 chunk 70 optimal weight: 0.0170 chunk 74 optimal weight: 10.0000 chunk 2 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.224070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.207389 restraints weight = 22184.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.205995 restraints weight = 21000.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.205424 restraints weight = 15074.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.203594 restraints weight = 14508.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.202852 restraints weight = 13934.722| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4305 r_free = 0.4305 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4305 r_free = 0.4305 target_work(ls_wunit_k1) = 0.202 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7679 Z= 0.109 Angle : 0.540 9.523 10528 Z= 0.272 Chirality : 0.035 0.172 1310 Planarity : 0.003 0.047 1369 Dihedral : 6.289 88.601 1316 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.36 % Allowed : 23.40 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 3.31 (0.25), residues: 1170 helix: 2.73 (0.17), residues: 945 sheet: -1.40 (1.36), residues: 15 loop : -0.14 (0.45), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 165 TYR 0.016 0.001 TYR B 117 PHE 0.030 0.001 PHE D 22 TRP 0.040 0.001 TRP D 18 HIS 0.003 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 7678) covalent geometry : angle 0.53959 / 0.27 (10528) hydrogen bonds : bond 0.03017 / 2.19 ( 702) hydrogen bonds : angle 3.27438 / 2.48 ( 2078) Misc. bond : bond 0.00038 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1059.63 seconds wall clock time: 18 minutes 50.74 seconds (1130.74 seconds total)