Starting phenix.real_space_refine on Fri Jun 13 10:20:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ouy_17205/06_2025/8ouy_17205_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ouy_17205/06_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_17205/06_2025/8ouy_17205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ouy_17205/06_2025/8ouy_17205.map" model { file = "/net/cci-nas-00/data/ceres_data/8ouy_17205/06_2025/8ouy_17205_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ouy_17205/06_2025/8ouy_17205_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.01, per 1000 atoms: 0.48 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: 3.63 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.44 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: 5.01 Time building geometry restraints manager: 4.45 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: 0.860 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: 0.250 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.980 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.790 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (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 TRP 0.006 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 PHE 0.007 0.001 PHE B 199 TYR 0.010 0.001 TYR C 72 ARG 0.002 0.000 ARG C 55 Details of bonding type rmsd hydrogen bonds : bond 0.25201 ( 338) hydrogen bonds : angle 7.38896 ( 942) covalent geometry : bond 0.00249 ( 7428) covalent geometry : angle 0.52267 (10043) *********************** 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 : 1.217 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: 0.4333 time to fit residues: 58.5535 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 : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 0.0170 chunk 82 optimal weight: 1.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 249 ASN ** 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 = 0.3611 r_free = 0.3611 target = 0.135715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114703 restraints weight = 28980.034| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.90 r_work: 0.3253 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7428 Z= 0.146 Angle : 0.532 6.205 10043 Z= 0.279 Chirality : 0.039 0.137 1177 Planarity : 0.004 0.031 1257 Dihedral : 10.497 166.297 1069 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.28), residues: 907 helix: 0.32 (0.25), residues: 428 sheet: -1.02 (0.40), residues: 152 loop : -0.83 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 268 HIS 0.005 0.001 HIS B 95 PHE 0.011 0.001 PHE B 346 TYR 0.012 0.001 TYR C 72 ARG 0.004 0.000 ARG C 232 Details of bonding type rmsd hydrogen bonds : bond 0.04756 ( 338) hydrogen bonds : angle 5.06318 ( 942) covalent geometry : bond 0.00330 ( 7428) covalent geometry : angle 0.53161 (10043) *********************** 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 112 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: B 192 HIS cc_start: 0.8068 (OUTLIER) cc_final: 0.7611 (m-70) REVERT: C 23 HIS cc_start: 0.5057 (m90) cc_final: 0.4549 (m170) REVERT: D 32 PHE cc_start: 0.8156 (m-80) cc_final: 0.7836 (m-10) outliers start: 8 outliers final: 5 residues processed: 109 average time/residue: 0.4607 time to fit residues: 68.7797 Evaluate side-chains 104 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 192 HIS 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 0 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.0370 chunk 39 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 0.0070 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- 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 = 0.3603 r_free = 0.3603 target = 0.135294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.114543 restraints weight = 28868.060| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.88 r_work: 0.3261 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1267 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= 0.119 Angle : 0.495 5.951 10043 Z= 0.256 Chirality : 0.038 0.136 1177 Planarity : 0.003 0.030 1257 Dihedral : 9.107 127.608 1069 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.12 % Allowed : 13.95 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.28), residues: 907 helix: 0.66 (0.26), residues: 428 sheet: -1.05 (0.39), residues: 157 loop : -0.80 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.004 0.001 HIS D 60 PHE 0.010 0.001 PHE B 346 TYR 0.011 0.001 TYR C 72 ARG 0.003 0.000 ARG C 232 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 338) hydrogen bonds : angle 4.56722 ( 942) covalent geometry : bond 0.00266 ( 7428) covalent geometry : angle 0.49534 (10043) *********************** 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: 9 poor density : 102 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.5076 (m90) cc_final: 0.4635 (m170) REVERT: C 191 GLN cc_start: 0.5909 (tp40) cc_final: 0.5664 (tt0) REVERT: D 32 PHE cc_start: 0.8179 (m-80) cc_final: 0.7901 (m-10) outliers start: 9 outliers final: 5 residues processed: 110 average time/residue: 0.4187 time to fit residues: 62.5709 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 : 1.193 ------------------------------------------------------------------------------- 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 2 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.135314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115043 restraints weight = 29117.707| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.86 r_work: 0.3242 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7428 Z= 0.153 Angle : 0.517 6.135 10043 Z= 0.269 Chirality : 0.039 0.139 1177 Planarity : 0.004 0.033 1257 Dihedral : 8.963 113.961 1069 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.74 % Allowed : 13.95 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.28), residues: 907 helix: 0.64 (0.26), residues: 428 sheet: -1.27 (0.38), residues: 157 loop : -0.94 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.005 0.001 HIS D 60 PHE 0.011 0.001 PHE B 346 TYR 0.013 0.001 TYR C 72 ARG 0.007 0.000 ARG D 64 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 338) hydrogen bonds : angle 4.55220 ( 942) covalent geometry : bond 0.00354 ( 7428) covalent geometry : angle 0.51688 (10043) *********************** 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 117 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: B 94 GLU cc_start: 0.7767 (tt0) cc_final: 0.7503 (tt0) REVERT: C 23 HIS cc_start: 0.5051 (m90) cc_final: 0.4608 (m90) REVERT: C 191 GLN cc_start: 0.5882 (tp40) cc_final: 0.5659 (tt0) REVERT: D 32 PHE cc_start: 0.8229 (m-80) cc_final: 0.7950 (m-10) REVERT: D 59 TYR cc_start: 0.8399 (m-80) cc_final: 0.8151 (m-10) outliers start: 14 outliers final: 11 residues processed: 112 average time/residue: 0.4292 time to fit residues: 64.9449 Evaluate side-chains 111 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 111 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.134473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113729 restraints weight = 29355.167| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.89 r_work: 0.3234 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7428 Z= 0.165 Angle : 0.523 6.321 10043 Z= 0.273 Chirality : 0.039 0.140 1177 Planarity : 0.004 0.032 1257 Dihedral : 8.867 102.706 1069 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.87 % Allowed : 14.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.28), residues: 907 helix: 0.56 (0.26), residues: 431 sheet: -1.20 (0.40), residues: 143 loop : -1.08 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.004 0.001 HIS D 60 PHE 0.012 0.001 PHE B 346 TYR 0.013 0.001 TYR C 72 ARG 0.002 0.000 ARG B 319 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 338) hydrogen bonds : angle 4.54504 ( 942) covalent geometry : bond 0.00383 ( 7428) covalent geometry : angle 0.52335 (10043) *********************** 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 113 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.030 Fit side-chains REVERT: B 94 GLU cc_start: 0.7763 (tt0) cc_final: 0.7455 (tt0) REVERT: C 23 HIS cc_start: 0.5096 (m90) cc_final: 0.4649 (m90) REVERT: D 32 PHE cc_start: 0.8240 (m-80) cc_final: 0.7925 (m-10) outliers start: 15 outliers final: 12 residues processed: 108 average time/residue: 0.4071 time to fit residues: 61.1878 Evaluate side-chains 108 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 C residue 307 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 27 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.136471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115587 restraints weight = 29056.967| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.89 r_work: 0.3255 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7428 Z= 0.107 Angle : 0.478 5.966 10043 Z= 0.246 Chirality : 0.037 0.135 1177 Planarity : 0.003 0.032 1257 Dihedral : 8.351 84.728 1069 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.25 % Allowed : 14.94 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.29), residues: 907 helix: 0.96 (0.26), residues: 422 sheet: -1.44 (0.38), residues: 157 loop : -0.79 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 PHE 0.010 0.001 PHE B 346 TYR 0.009 0.001 TYR C 72 ARG 0.004 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 338) hydrogen bonds : angle 4.25694 ( 942) covalent geometry : bond 0.00241 ( 7428) covalent geometry : angle 0.47815 (10043) *********************** 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 111 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.226 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.5031 (m90) cc_final: 0.4410 (m90) REVERT: C 306 GLN cc_start: 0.7196 (mt0) cc_final: 0.6980 (mt0) REVERT: D 32 PHE cc_start: 0.8204 (m-80) cc_final: 0.7936 (m-10) outliers start: 10 outliers final: 9 residues processed: 108 average time/residue: 0.3882 time to fit residues: 58.3710 Evaluate side-chains 107 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 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 = 0.3609 r_free = 0.3609 target = 0.135811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114943 restraints weight = 29238.279| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.89 r_work: 0.3250 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7428 Z= 0.125 Angle : 0.490 6.146 10043 Z= 0.253 Chirality : 0.038 0.137 1177 Planarity : 0.003 0.032 1257 Dihedral : 8.209 76.695 1069 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.62 % Allowed : 15.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.28), residues: 907 helix: 0.97 (0.26), residues: 422 sheet: -1.47 (0.39), residues: 152 loop : -0.85 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.004 0.001 HIS D 60 PHE 0.010 0.001 PHE B 346 TYR 0.011 0.001 TYR D 59 ARG 0.003 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 338) hydrogen bonds : angle 4.26814 ( 942) covalent geometry : bond 0.00290 ( 7428) covalent geometry : angle 0.49040 (10043) *********************** 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 111 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.5034 (m90) cc_final: 0.4494 (m170) REVERT: C 306 GLN cc_start: 0.7156 (mt0) cc_final: 0.6932 (mt0) REVERT: D 32 PHE cc_start: 0.8191 (m-80) cc_final: 0.7932 (m-10) outliers start: 13 outliers final: 12 residues processed: 106 average time/residue: 0.3940 time to fit residues: 57.9562 Evaluate side-chains 109 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3578 r_free = 0.3578 target = 0.133052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112468 restraints weight = 29443.625| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.87 r_work: 0.3220 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7428 Z= 0.209 Angle : 0.562 6.564 10043 Z= 0.295 Chirality : 0.040 0.144 1177 Planarity : 0.004 0.035 1257 Dihedral : 8.557 82.947 1069 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.12 % Allowed : 14.94 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.28), residues: 907 helix: 0.53 (0.26), residues: 425 sheet: -1.41 (0.41), residues: 138 loop : -1.27 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 268 HIS 0.005 0.001 HIS D 60 PHE 0.013 0.002 PHE B 346 TYR 0.016 0.002 TYR C 72 ARG 0.004 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 338) hydrogen bonds : angle 4.61609 ( 942) covalent geometry : bond 0.00492 ( 7428) covalent geometry : angle 0.56197 (10043) *********************** 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 119 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: B 192 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7257 (m-70) REVERT: B 196 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6950 (mt) REVERT: C 23 HIS cc_start: 0.5207 (m90) cc_final: 0.4647 (m90) REVERT: D 32 PHE cc_start: 0.8223 (m-80) cc_final: 0.7918 (m-10) outliers start: 17 outliers final: 12 residues processed: 111 average time/residue: 0.3841 time to fit residues: 59.2792 Evaluate side-chains 113 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 192 HIS 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 199 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 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 = 0.3599 r_free = 0.3599 target = 0.134763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114226 restraints weight = 29000.599| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.86 r_work: 0.3240 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7428 Z= 0.137 Angle : 0.505 6.254 10043 Z= 0.263 Chirality : 0.038 0.138 1177 Planarity : 0.003 0.033 1257 Dihedral : 8.153 74.979 1069 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.37 % Allowed : 15.69 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.28), residues: 907 helix: 0.73 (0.26), residues: 425 sheet: -1.34 (0.41), residues: 138 loop : -1.14 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 317 HIS 0.004 0.001 HIS C 126 PHE 0.010 0.001 PHE B 346 TYR 0.012 0.001 TYR C 72 ARG 0.002 0.000 ARG B 193 Details of bonding type rmsd hydrogen bonds : bond 0.03592 ( 338) hydrogen bonds : angle 4.41027 ( 942) covalent geometry : bond 0.00315 ( 7428) covalent geometry : angle 0.50503 (10043) *********************** 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 107 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: B 246 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7421 (t80) REVERT: C 23 HIS cc_start: 0.5138 (m90) cc_final: 0.4615 (m170) REVERT: C 241 LEU cc_start: 0.8131 (mt) cc_final: 0.7866 (mt) REVERT: D 32 PHE cc_start: 0.8185 (m-80) cc_final: 0.7916 (m-10) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 0.4127 time to fit residues: 59.0736 Evaluate side-chains 105 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 246 PHE 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 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 54 optimal weight: 0.0770 chunk 27 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.137161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116316 restraints weight = 29207.247| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.90 r_work: 0.3269 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 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 : 0.002 0.020 7428 Z= 0.092 Angle : 0.470 5.807 10043 Z= 0.241 Chirality : 0.037 0.134 1177 Planarity : 0.003 0.033 1257 Dihedral : 7.526 63.543 1069 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.87 % Allowed : 16.31 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.29), residues: 907 helix: 1.19 (0.27), residues: 416 sheet: -1.26 (0.42), residues: 140 loop : -0.88 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 PHE 0.010 0.001 PHE B 346 TYR 0.011 0.001 TYR D 59 ARG 0.003 0.000 ARG B 193 Details of bonding type rmsd hydrogen bonds : bond 0.02862 ( 338) hydrogen bonds : angle 4.12250 ( 942) covalent geometry : bond 0.00204 ( 7428) covalent geometry : angle 0.46974 (10043) ********************** 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 99 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 1.320 Fit side-chains revert: symmetry clash REVERT: C 241 LEU cc_start: 0.7973 (mt) cc_final: 0.7710 (mt) REVERT: D 32 PHE cc_start: 0.8142 (m-80) cc_final: 0.7913 (m-10) outliers start: 7 outliers final: 6 residues processed: 99 average time/residue: 0.4423 time to fit residues: 61.5545 Evaluate side-chains 94 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 1.327 ------------------------------------------------------------------------------- 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 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 0.0170 chunk 2 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.137135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.116152 restraints weight = 29124.782| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.90 r_work: 0.3260 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7428 Z= 0.106 Angle : 0.478 5.925 10043 Z= 0.246 Chirality : 0.037 0.135 1177 Planarity : 0.003 0.032 1257 Dihedral : 7.667 65.874 1069 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.00 % Allowed : 16.06 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.29), residues: 907 helix: 1.22 (0.27), residues: 416 sheet: -1.46 (0.40), residues: 152 loop : -0.84 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.003 0.001 HIS D 237 PHE 0.010 0.001 PHE B 346 TYR 0.011 0.001 TYR D 59 ARG 0.003 0.000 ARG B 193 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 338) hydrogen bonds : angle 4.13283 ( 942) covalent geometry : bond 0.00242 ( 7428) covalent geometry : angle 0.47796 (10043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7377.22 seconds wall clock time: 126 minutes 46.16 seconds (7606.16 seconds total)