Starting phenix.real_space_refine on Sat Aug 23 21:47:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ouy_17205/08_2025/8ouy_17205_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ouy_17205/08_2025/8ouy_17205.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ouy_17205/08_2025/8ouy_17205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ouy_17205/08_2025/8ouy_17205.map" model { file = "/net/cci-nas-00/data/ceres_data/8ouy_17205/08_2025/8ouy_17205_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ouy_17205/08_2025/8ouy_17205_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 7 Type Number sf(0) Gaussians P 8 5.49 5 Mg 3 5.21 5 S 50 5.16 5 C 4608 2.51 5 N 1268 2.21 5 O 1378 1.98 5 H 7380 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14695 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1131 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "B" Number of atoms: 4977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4977 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain breaks: 2 Chain: "C" Number of atoms: 4722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4722 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 7, 'TRANS': 300} Chain breaks: 1 Chain: "D" Number of atoms: 3773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 3773 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.45, per 1000 atoms: 0.17 Number of scatterers: 14695 At special positions: 0 Unit cell: (98.28, 104.76, 95.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 50 16.00 P 8 15.00 Mg 3 11.99 O 1378 8.00 N 1268 7.00 C 4608 6.00 H 7380 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 422.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 51.1% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 removed outlier: 3.775A pdb=" N VAL A 9 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5 through 10' Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 26 through 32 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 34 through 38 Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.992A pdb=" N LYS B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.627A pdb=" N ARG B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 97 Processing helix chain 'B' and resid 104 through 111 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 165 through 188 removed outlier: 3.545A pdb=" N VAL B 169 " --> pdb=" O MET B 165 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 183 " --> pdb=" O HIS B 179 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 199 removed outlier: 3.817A pdb=" N GLU B 197 " --> pdb=" O ARG B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 206 Processing helix chain 'B' and resid 215 through 233 Proline residue: B 227 - end of helix removed outlier: 3.763A pdb=" N SER B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 removed outlier: 3.751A pdb=" N SER B 256 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 removed outlier: 5.281A pdb=" N MET B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 308 removed outlier: 3.683A pdb=" N GLY B 306 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 removed outlier: 4.297A pdb=" N LEU C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 46 through 61 Processing helix chain 'C' and resid 68 through 79 removed outlier: 3.602A pdb=" N GLU C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 93 Processing helix chain 'C' and resid 112 through 127 Processing helix chain 'C' and resid 142 through 152 Processing helix chain 'C' and resid 156 through 165 Processing helix chain 'C' and resid 174 through 192 Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 221 through 242 removed outlier: 3.746A pdb=" N ALA C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 270 removed outlier: 4.087A pdb=" N PHE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.501A pdb=" N ILE D 27 " --> pdb=" O SER D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 67 Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 88 through 100 removed outlier: 3.611A pdb=" N ILE D 95 " --> pdb=" O ARG D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 113 removed outlier: 4.384A pdb=" N TYR D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 138 removed outlier: 3.639A pdb=" N GLU D 134 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N SER D 135 " --> pdb=" O TYR D 131 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 137 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 3.570A pdb=" N VAL D 160 " --> pdb=" O TRP D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 170 through 187 removed outlier: 3.590A pdb=" N LYS D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 233 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.635A pdb=" N GLU B 154 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N VAL B 239 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 156 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL B 241 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE B 158 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR B 121 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG B 312 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 316 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 337 " --> pdb=" O ALA B 324 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N CYS B 335 " --> pdb=" O LEU B 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 340 through 342 Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67 removed outlier: 7.522A pdb=" N LEU D 146 " --> pdb=" O PHE D 192 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR D 194 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU D 148 " --> pdb=" O THR D 194 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE D 43 " --> pdb=" O HIS D 237 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N MET D 239 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU D 45 " --> pdb=" O MET D 239 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N PHE D 241 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N HIS D 47 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N LYS D 243 " --> pdb=" O HIS D 47 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER D 254 " --> pdb=" O SER D 242 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER D 257 " --> pdb=" O LYS D 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 81 through 82 Processing sheet with id=AA5, first strand: chain 'C' and resid 167 through 171 removed outlier: 6.812A pdb=" N LEU C 133 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP C 206 " --> pdb=" O LEU C 133 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N VAL C 135 " --> pdb=" O ASP C 206 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL C 203 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR C 248 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N THR C 103 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASN C 249 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE C 105 " --> pdb=" O ASN C 249 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C 274 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ARG C 275 " --> pdb=" O ALA C 296 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 252 through 253 338 hydrogen bonds defined for protein. 942 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: 2.81 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7352 1.03 - 1.23: 34 1.23 - 1.42: 2983 1.42 - 1.62: 4367 1.62 - 1.81: 72 Bond restraints: 14808 Sorted by residual: bond pdb=" N GLY C 2 " pdb=" CA GLY C 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.40e+00 bond pdb=" N GLY D 20 " pdb=" CA GLY D 20 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.08e+00 bond pdb=" N LYS A 4 " pdb=" CA LYS A 4 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.79e+00 bond pdb=" N GLY D 20 " pdb=" H GLY D 20 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" N GLY C 2 " pdb=" H GLY C 2 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.25e+00 ... (remaining 14803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.72: 26780 11.72 - 23.44: 0 23.44 - 35.16: 0 35.16 - 46.88: 0 46.88 - 58.60: 1 Bond angle restraints: 26781 Sorted by residual: angle pdb=" C MET B 10 " pdb=" N GLN B 11 " pdb=" H GLN B 11 " ideal model delta sigma weight residual 123.68 65.08 58.60 3.00e+00 1.11e-01 3.82e+02 angle pdb=" C3' ATP C 401 " pdb=" C4' ATP C 401 " pdb=" O4' ATP C 401 " ideal model delta sigma weight residual 105.22 101.39 3.83 1.30e+00 5.94e-01 8.72e+00 angle pdb=" C2' ATP C 401 " pdb=" C3' ATP C 401 " pdb=" O3' ATP C 401 " ideal model delta sigma weight residual 111.83 105.17 6.66 2.67e+00 1.40e-01 6.23e+00 angle pdb=" C3' ATP C 401 " pdb=" C2' ATP C 401 " pdb=" O2' ATP C 401 " ideal model delta sigma weight residual 111.83 105.41 6.42 2.67e+00 1.40e-01 5.78e+00 angle pdb=" C1' ATP D 302 " pdb=" C2' ATP D 302 " pdb=" O2' ATP D 302 " ideal model delta sigma weight residual 110.58 103.86 6.72 2.79e+00 1.28e-01 5.78e+00 ... (remaining 26776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.12: 6589 31.12 - 62.23: 292 62.23 - 93.35: 33 93.35 - 124.46: 1 124.46 - 155.58: 2 Dihedral angle restraints: 6917 sinusoidal: 3881 harmonic: 3036 Sorted by residual: dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 95.58 -155.58 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 88.76 -148.76 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 -176.52 116.52 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 6914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1057 0.060 - 0.120: 102 0.120 - 0.179: 12 0.179 - 0.239: 1 0.239 - 0.299: 5 Chirality restraints: 1177 Sorted by residual: chirality pdb=" C2' ATP D 302 " pdb=" C1' ATP D 302 " pdb=" C3' ATP D 302 " pdb=" O2' ATP D 302 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" C3' ATP C 401 " pdb=" C2' ATP C 401 " pdb=" C4' ATP C 401 " pdb=" O3' ATP C 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C2' ATP C 401 " pdb=" C1' ATP C 401 " pdb=" C3' ATP C 401 " pdb=" O2' ATP C 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1174 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 10 " 0.092 2.00e-02 2.50e+03 2.32e-01 5.39e+02 pdb=" N GLN B 11 " -0.399 2.00e-02 2.50e+03 pdb=" CA GLN B 11 " 0.135 2.00e-02 2.50e+03 pdb=" H GLN B 11 " 0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 246 " 0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO B 247 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 247 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 247 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 37 " -0.018 5.00e-02 4.00e+02 2.77e-02 1.23e+00 pdb=" N PRO D 38 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO D 38 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 38 " -0.016 5.00e-02 4.00e+02 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 340 2.13 - 2.75: 26698 2.75 - 3.37: 39756 3.37 - 3.98: 50200 3.98 - 4.60: 79939 Nonbonded interactions: 196933 Sorted by model distance: nonbonded pdb=" OE1 GLU D 164 " pdb=" H GLU D 164 " model vdw 1.513 2.450 nonbonded pdb=" HG1 THR C 209 " pdb=" OD1 ASN C 249 " model vdw 1.625 2.450 nonbonded pdb=" OD1 ASP C 279 " pdb=" H THR C 280 " model vdw 1.631 2.450 nonbonded pdb=" O LEU D 58 " pdb=" HG1 THR D 62 " model vdw 1.636 2.450 nonbonded pdb=" OE1 GLU D 28 " pdb=" H ASN D 30 " model vdw 1.636 2.450 ... (remaining 196928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.050 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.360 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.002 0.040 7428 Z= 0.117 Angle : 0.523 6.715 10043 Z= 0.264 Chirality : 0.042 0.299 1177 Planarity : 0.003 0.031 1257 Dihedral : 17.648 155.580 2809 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 14.45 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.28), residues: 907 helix: 0.06 (0.27), residues: 407 sheet: -1.02 (0.41), residues: 153 loop : -0.79 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 55 TYR 0.010 0.001 TYR C 72 PHE 0.007 0.001 PHE B 199 TRP 0.006 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7428) covalent geometry : angle 0.52267 (10043) hydrogen bonds : bond 0.25201 ( 338) hydrogen bonds : angle 7.38896 ( 942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 32 PHE cc_start: 0.7807 (m-10) cc_final: 0.7538 (m-10) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2170 time to fit residues: 29.2066 Evaluate side-chains 100 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114629 restraints weight = 29072.862| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.89 r_work: 0.3254 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7428 Z= 0.145 Angle : 0.530 6.136 10043 Z= 0.280 Chirality : 0.039 0.137 1177 Planarity : 0.004 0.030 1257 Dihedral : 10.536 167.391 1069 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.87 % Allowed : 13.57 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.28), residues: 907 helix: 0.35 (0.25), residues: 428 sheet: -0.99 (0.40), residues: 152 loop : -0.82 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 232 TYR 0.011 0.001 TYR C 72 PHE 0.010 0.001 PHE B 346 TRP 0.004 0.001 TRP B 317 HIS 0.004 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 7428) covalent geometry : angle 0.52953 (10043) hydrogen bonds : bond 0.04732 ( 338) hydrogen bonds : angle 5.08541 ( 942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7130 (m-30) cc_final: 0.5858 (t70) REVERT: C 23 HIS cc_start: 0.5025 (m90) cc_final: 0.4518 (m170) REVERT: C 279 ASP cc_start: 0.8005 (t0) cc_final: 0.7799 (t0) REVERT: D 32 PHE cc_start: 0.8150 (m-80) cc_final: 0.7837 (m-10) outliers start: 7 outliers final: 5 residues processed: 108 average time/residue: 0.2178 time to fit residues: 31.7284 Evaluate side-chains 102 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain D residue 111 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 72 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.116091 restraints weight = 29222.852| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.88 r_work: 0.3264 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7428 Z= 0.116 Angle : 0.494 5.917 10043 Z= 0.254 Chirality : 0.038 0.135 1177 Planarity : 0.003 0.030 1257 Dihedral : 9.059 127.350 1069 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.00 % Allowed : 13.82 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.28), residues: 907 helix: 0.70 (0.26), residues: 428 sheet: -1.06 (0.39), residues: 156 loop : -0.77 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 232 TYR 0.010 0.001 TYR C 72 PHE 0.010 0.001 PHE B 346 TRP 0.005 0.001 TRP B 317 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7428) covalent geometry : angle 0.49372 (10043) hydrogen bonds : bond 0.03722 ( 338) hydrogen bonds : angle 4.52521 ( 942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 103 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.5072 (m90) cc_final: 0.4633 (m170) REVERT: D 32 PHE cc_start: 0.8174 (m-80) cc_final: 0.7913 (m-10) outliers start: 8 outliers final: 5 residues processed: 110 average time/residue: 0.2361 time to fit residues: 34.2629 Evaluate side-chains 102 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 97 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 111 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 70 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115719 restraints weight = 29140.403| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.90 r_work: 0.3260 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7428 Z= 0.117 Angle : 0.487 5.918 10043 Z= 0.251 Chirality : 0.038 0.135 1177 Planarity : 0.003 0.031 1257 Dihedral : 8.702 112.617 1069 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.74 % Allowed : 13.82 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.28), residues: 907 helix: 0.86 (0.26), residues: 428 sheet: -1.06 (0.39), residues: 157 loop : -0.83 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 64 TYR 0.010 0.001 TYR C 72 PHE 0.010 0.001 PHE B 346 TRP 0.004 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7428) covalent geometry : angle 0.48698 (10043) hydrogen bonds : bond 0.03443 ( 338) hydrogen bonds : angle 4.37072 ( 942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.4957 (m90) cc_final: 0.4520 (m90) REVERT: C 191 GLN cc_start: 0.5869 (tp40) cc_final: 0.5637 (tt0) REVERT: C 306 GLN cc_start: 0.7231 (mt0) cc_final: 0.7008 (mt0) REVERT: D 32 PHE cc_start: 0.8206 (m-80) cc_final: 0.7947 (m-10) REVERT: D 59 TYR cc_start: 0.8378 (m-80) cc_final: 0.8172 (m-10) outliers start: 14 outliers final: 12 residues processed: 110 average time/residue: 0.2060 time to fit residues: 30.9981 Evaluate side-chains 110 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 111 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.136200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115304 restraints weight = 29040.402| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.89 r_work: 0.3265 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7428 Z= 0.110 Angle : 0.479 5.936 10043 Z= 0.246 Chirality : 0.038 0.136 1177 Planarity : 0.003 0.029 1257 Dihedral : 8.417 98.232 1069 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.12 % Allowed : 14.82 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.29), residues: 907 helix: 1.04 (0.26), residues: 423 sheet: -1.13 (0.38), residues: 157 loop : -0.68 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 64 TYR 0.009 0.001 TYR C 72 PHE 0.010 0.001 PHE B 346 TRP 0.004 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7428) covalent geometry : angle 0.47877 (10043) hydrogen bonds : bond 0.03249 ( 338) hydrogen bonds : angle 4.26337 ( 942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8124 (mtt) cc_final: 0.7793 (mtm) REVERT: C 23 HIS cc_start: 0.4969 (m90) cc_final: 0.4369 (m90) REVERT: D 32 PHE cc_start: 0.8247 (m-80) cc_final: 0.7983 (m-10) REVERT: D 59 TYR cc_start: 0.8407 (m-10) cc_final: 0.8197 (m-10) outliers start: 9 outliers final: 7 residues processed: 112 average time/residue: 0.1946 time to fit residues: 29.8863 Evaluate side-chains 106 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 111 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115563 restraints weight = 29138.574| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.86 r_work: 0.3248 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7428 Z= 0.137 Angle : 0.499 6.067 10043 Z= 0.258 Chirality : 0.038 0.138 1177 Planarity : 0.003 0.030 1257 Dihedral : 8.521 82.740 1069 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.24 % Allowed : 14.20 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.29), residues: 907 helix: 0.94 (0.26), residues: 423 sheet: -1.31 (0.38), residues: 157 loop : -0.76 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 64 TYR 0.010 0.001 TYR C 72 PHE 0.011 0.001 PHE B 346 TRP 0.004 0.001 TRP C 268 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 7428) covalent geometry : angle 0.49926 (10043) hydrogen bonds : bond 0.03528 ( 338) hydrogen bonds : angle 4.33895 ( 942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.8127 (mtt) cc_final: 0.7796 (mtm) REVERT: C 23 HIS cc_start: 0.5042 (m90) cc_final: 0.4438 (m90) REVERT: D 32 PHE cc_start: 0.8250 (m-80) cc_final: 0.7980 (m-10) outliers start: 18 outliers final: 13 residues processed: 116 average time/residue: 0.2060 time to fit residues: 32.5469 Evaluate side-chains 112 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 111 CYS Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 20 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 75 optimal weight: 0.0970 chunk 49 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.137245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.116385 restraints weight = 28772.141| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.89 r_work: 0.3268 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7428 Z= 0.102 Angle : 0.475 6.015 10043 Z= 0.244 Chirality : 0.038 0.137 1177 Planarity : 0.003 0.045 1257 Dihedral : 7.947 78.127 1069 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.49 % Allowed : 14.45 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.29), residues: 907 helix: 1.09 (0.26), residues: 423 sheet: -1.26 (0.38), residues: 157 loop : -0.69 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 64 TYR 0.008 0.001 TYR C 72 PHE 0.010 0.001 PHE B 346 TRP 0.005 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 7428) covalent geometry : angle 0.47511 (10043) hydrogen bonds : bond 0.03104 ( 338) hydrogen bonds : angle 4.17971 ( 942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 55 MET cc_start: 0.8134 (mtt) cc_final: 0.7804 (mtm) REVERT: C 23 HIS cc_start: 0.4965 (m90) cc_final: 0.4393 (m170) REVERT: D 32 PHE cc_start: 0.8211 (m-80) cc_final: 0.7950 (m-10) outliers start: 12 outliers final: 11 residues processed: 110 average time/residue: 0.1816 time to fit residues: 27.4565 Evaluate side-chains 106 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 111 CYS Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 24 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112552 restraints weight = 29473.833| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.88 r_work: 0.3220 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7428 Z= 0.215 Angle : 0.568 6.541 10043 Z= 0.299 Chirality : 0.041 0.143 1177 Planarity : 0.004 0.043 1257 Dihedral : 8.553 82.902 1069 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.49 % Allowed : 14.82 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.28), residues: 907 helix: 0.57 (0.26), residues: 425 sheet: -1.29 (0.41), residues: 138 loop : -1.19 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 64 TYR 0.016 0.002 TYR C 72 PHE 0.013 0.002 PHE B 346 TRP 0.007 0.001 TRP C 268 HIS 0.006 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 7428) covalent geometry : angle 0.56826 (10043) hydrogen bonds : bond 0.04337 ( 338) hydrogen bonds : angle 4.60603 ( 942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.419 Fit side-chains REVERT: C 23 HIS cc_start: 0.5261 (m90) cc_final: 0.4700 (m90) REVERT: D 32 PHE cc_start: 0.8257 (m-80) cc_final: 0.7974 (m-10) outliers start: 12 outliers final: 9 residues processed: 109 average time/residue: 0.2078 time to fit residues: 30.9023 Evaluate side-chains 106 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 111 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 19 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114996 restraints weight = 29160.450| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.88 r_work: 0.3250 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7428 Z= 0.117 Angle : 0.487 6.108 10043 Z= 0.252 Chirality : 0.038 0.139 1177 Planarity : 0.003 0.032 1257 Dihedral : 7.952 69.553 1069 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.25 % Allowed : 15.19 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.28), residues: 907 helix: 0.85 (0.26), residues: 425 sheet: -1.23 (0.40), residues: 143 loop : -0.94 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 193 TYR 0.010 0.001 TYR C 72 PHE 0.010 0.001 PHE B 346 TRP 0.007 0.001 TRP B 317 HIS 0.003 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7428) covalent geometry : angle 0.48738 (10043) hydrogen bonds : bond 0.03332 ( 338) hydrogen bonds : angle 4.29871 ( 942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.4913 (m90) cc_final: 0.4384 (m170) REVERT: C 306 GLN cc_start: 0.7124 (mt0) cc_final: 0.6904 (mt0) REVERT: D 32 PHE cc_start: 0.8262 (m-80) cc_final: 0.8007 (m-10) outliers start: 10 outliers final: 10 residues processed: 106 average time/residue: 0.1936 time to fit residues: 28.4222 Evaluate side-chains 106 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 89 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115498 restraints weight = 29099.620| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.85 r_work: 0.3250 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7428 Z= 0.125 Angle : 0.492 6.074 10043 Z= 0.255 Chirality : 0.038 0.137 1177 Planarity : 0.003 0.031 1257 Dihedral : 7.936 71.917 1069 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.12 % Allowed : 15.44 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.28), residues: 907 helix: 0.86 (0.26), residues: 424 sheet: -1.19 (0.40), residues: 143 loop : -0.96 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 193 TYR 0.010 0.001 TYR C 72 PHE 0.011 0.001 PHE B 346 TRP 0.004 0.001 TRP B 317 HIS 0.004 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 7428) covalent geometry : angle 0.49224 (10043) hydrogen bonds : bond 0.03373 ( 338) hydrogen bonds : angle 4.29733 ( 942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1814 Ramachandran restraints generated. 907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: D 32 PHE cc_start: 0.8220 (m-80) cc_final: 0.7978 (m-10) outliers start: 9 outliers final: 9 residues processed: 102 average time/residue: 0.1999 time to fit residues: 28.1254 Evaluate side-chains 103 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 280 THR Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 88 optimal weight: 0.0980 chunk 90 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.115983 restraints weight = 28877.668| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.84 r_work: 0.3261 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7428 Z= 0.114 Angle : 0.481 6.005 10043 Z= 0.249 Chirality : 0.038 0.137 1177 Planarity : 0.003 0.031 1257 Dihedral : 7.787 67.371 1069 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.37 % Allowed : 15.44 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.29), residues: 907 helix: 1.05 (0.26), residues: 417 sheet: -1.25 (0.40), residues: 145 loop : -0.84 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 193 TYR 0.009 0.001 TYR C 72 PHE 0.011 0.001 PHE B 346 TRP 0.006 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7428) covalent geometry : angle 0.48144 (10043) hydrogen bonds : bond 0.03212 ( 338) hydrogen bonds : angle 4.21560 ( 942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3745.59 seconds wall clock time: 64 minutes 20.25 seconds (3860.25 seconds total)