Starting phenix.real_space_refine on Fri May 16 21:46:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ouy_17205/05_2025/8ouy_17205_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ouy_17205/05_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_17205/05_2025/8ouy_17205.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ouy_17205/05_2025/8ouy_17205.map" model { file = "/net/cci-nas-00/data/ceres_data/8ouy_17205/05_2025/8ouy_17205_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ouy_17205/05_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.76, per 1000 atoms: 0.53 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: 4.17 Conformation dependent library (CDL) restraints added in 1.7 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: 1.50 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: 5.39 Time building geometry restraints manager: 5.02 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: 1.200 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: 0.290 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 36.800 Find NCS groups from input model: 0.110 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:4.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.690 ------------------------------------------------------------------------------- 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 : 1.196 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: 0.4221 time to fit residues: 56.8835 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 : 1.071 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114704 restraints weight = 28980.029| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.90 r_work: 0.3252 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 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 : 1.155 Fit side-chains revert: symmetry clash REVERT: B 192 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7612 (m-70) REVERT: C 23 HIS cc_start: 0.5051 (m90) cc_final: 0.4542 (m170) REVERT: C 279 ASP cc_start: 0.8031 (t0) cc_final: 0.7830 (t0) REVERT: D 32 PHE cc_start: 0.8148 (m-80) cc_final: 0.7828 (m-10) outliers start: 8 outliers final: 5 residues processed: 109 average time/residue: 0.4440 time to fit residues: 65.2106 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 : 1.056 ------------------------------------------------------------------------------- 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: 0.0060 chunk 39 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 89 optimal weight: 1.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.135298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.114941 restraints weight = 29117.374| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.86 r_work: 0.3246 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1268 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= 0.147 Angle : 0.519 5.969 10043 Z= 0.270 Chirality : 0.038 0.138 1177 Planarity : 0.004 0.032 1257 Dihedral : 9.267 126.605 1069 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.12 % Allowed : 14.20 % Favored : 84.68 % 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: -0.54 (0.28), residues: 907 helix: 0.49 (0.26), residues: 428 sheet: -1.24 (0.39), residues: 156 loop : -0.87 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.003 0.000 ARG C 232 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 338) hydrogen bonds : angle 4.68154 ( 942) covalent geometry : bond 0.00337 ( 7428) covalent geometry : angle 0.51936 (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 112 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.5046 (m90) cc_final: 0.4577 (m90) REVERT: C 191 GLN cc_start: 0.5921 (tp40) cc_final: 0.5682 (tt0) REVERT: D 32 PHE cc_start: 0.8191 (m-80) cc_final: 0.7896 (m-10) outliers start: 9 outliers final: 6 residues processed: 111 average time/residue: 0.3910 time to fit residues: 60.0146 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 : 1.098 ------------------------------------------------------------------------------- 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 82 LEU 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: 2.9990 chunk 75 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.132554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111935 restraints weight = 29342.236| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.88 r_work: 0.3211 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7428 Z= 0.228 Angle : 0.586 6.561 10043 Z= 0.309 Chirality : 0.041 0.145 1177 Planarity : 0.004 0.035 1257 Dihedral : 9.376 114.478 1069 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.49 % Allowed : 14.32 % 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: -1.03 (0.27), residues: 907 helix: 0.11 (0.25), residues: 431 sheet: -1.38 (0.40), residues: 138 loop : -1.26 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 268 HIS 0.006 0.001 HIS D 60 PHE 0.013 0.002 PHE B 346 TYR 0.017 0.002 TYR C 72 ARG 0.003 0.000 ARG B 319 Details of bonding type rmsd hydrogen bonds : bond 0.04668 ( 338) hydrogen bonds : angle 4.90752 ( 942) covalent geometry : bond 0.00536 ( 7428) covalent geometry : angle 0.58557 (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 119 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 1.126 Fit side-chains REVERT: B 192 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7184 (m-70) REVERT: C 23 HIS cc_start: 0.5180 (m90) cc_final: 0.4768 (m90) REVERT: D 32 PHE cc_start: 0.8274 (m-80) cc_final: 0.7918 (m-10) outliers start: 20 outliers final: 10 residues processed: 114 average time/residue: 0.3886 time to fit residues: 62.1775 Evaluate side-chains 110 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 192 HIS 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: 0.8980 chunk 79 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.134533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113669 restraints weight = 29256.503| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.89 r_work: 0.3245 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1570 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= 0.127 Angle : 0.504 6.150 10043 Z= 0.261 Chirality : 0.038 0.139 1177 Planarity : 0.004 0.034 1257 Dihedral : 8.770 100.428 1069 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.25 % Allowed : 15.82 % 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: -0.67 (0.28), residues: 907 helix: 0.53 (0.26), residues: 429 sheet: -1.36 (0.39), residues: 143 loop : -1.18 (0.34), residues: 335 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 0.011 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 0.03617 ( 338) hydrogen bonds : angle 4.48829 ( 942) covalent geometry : bond 0.00288 ( 7428) covalent geometry : angle 0.50437 (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: 10 poor density : 103 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: B 94 GLU cc_start: 0.7737 (tt0) cc_final: 0.7464 (tt0) REVERT: C 23 HIS cc_start: 0.5051 (m90) cc_final: 0.4532 (m90) REVERT: D 32 PHE cc_start: 0.8230 (m-80) cc_final: 0.7901 (m-10) outliers start: 10 outliers final: 9 residues processed: 111 average time/residue: 0.3788 time to fit residues: 58.2961 Evaluate side-chains 109 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 22 SER Chi-restraints excluded: chain D residue 111 CYS Chi-restraints excluded: chain D residue 183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 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 = 0.3602 r_free = 0.3602 target = 0.135079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114262 restraints weight = 29142.940| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.89 r_work: 0.3244 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7428 Z= 0.126 Angle : 0.494 6.125 10043 Z= 0.256 Chirality : 0.038 0.137 1177 Planarity : 0.003 0.033 1257 Dihedral : 8.566 86.163 1069 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.37 % Allowed : 15.57 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.26), residues: 425 sheet: -1.33 (0.40), residues: 138 loop : -1.08 (0.34), residues: 344 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 0.011 0.001 PHE B 346 TYR 0.011 0.001 TYR C 72 ARG 0.003 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 338) hydrogen bonds : angle 4.37282 ( 942) covalent geometry : bond 0.00288 ( 7428) covalent geometry : angle 0.49441 (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 114 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: B 94 GLU cc_start: 0.7575 (tt0) cc_final: 0.7314 (tt0) REVERT: C 23 HIS cc_start: 0.5093 (m90) cc_final: 0.4496 (m90) REVERT: C 241 LEU cc_start: 0.8108 (mt) cc_final: 0.7847 (mt) REVERT: D 32 PHE cc_start: 0.8203 (m-80) cc_final: 0.7913 (m-10) outliers start: 11 outliers final: 9 residues processed: 111 average time/residue: 0.3926 time to fit residues: 59.7575 Evaluate side-chains 108 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 0.0370 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.137123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116065 restraints weight = 29252.181| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.92 r_work: 0.3262 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7428 Z= 0.101 Angle : 0.476 6.040 10043 Z= 0.244 Chirality : 0.038 0.134 1177 Planarity : 0.003 0.032 1257 Dihedral : 7.951 77.672 1069 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.37 % Allowed : 15.82 % 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: -0.27 (0.29), residues: 907 helix: 0.99 (0.26), residues: 424 sheet: -1.57 (0.38), residues: 152 loop : -0.91 (0.35), residues: 331 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 0.009 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 0.03096 ( 338) hydrogen bonds : angle 4.18993 ( 942) covalent geometry : bond 0.00228 ( 7428) covalent geometry : angle 0.47620 (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: 11 poor density : 100 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.5043 (m90) cc_final: 0.4506 (m170) REVERT: C 241 LEU cc_start: 0.7980 (mt) cc_final: 0.7741 (mt) REVERT: D 32 PHE cc_start: 0.8177 (m-80) cc_final: 0.7890 (m-10) outliers start: 11 outliers final: 11 residues processed: 108 average time/residue: 0.4016 time to fit residues: 59.3509 Evaluate side-chains 108 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 C residue 274 THR 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: 0.0010 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 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: 0.5980 overall best weight: 0.8588 ------------------------------------------------------------------------------- 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 = 0.136298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115251 restraints weight = 29264.440| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.91 r_work: 0.3244 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7428 Z= 0.128 Angle : 0.493 6.000 10043 Z= 0.254 Chirality : 0.038 0.137 1177 Planarity : 0.004 0.046 1257 Dihedral : 8.032 74.843 1069 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.12 % Allowed : 15.44 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.37 (0.29), residues: 907 helix: 0.93 (0.26), residues: 424 sheet: -1.61 (0.38), residues: 152 loop : -0.99 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 317 HIS 0.004 0.001 HIS C 126 PHE 0.010 0.001 PHE B 346 TYR 0.011 0.001 TYR C 72 ARG 0.010 0.000 ARG D 64 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 338) hydrogen bonds : angle 4.26007 ( 942) covalent geometry : bond 0.00296 ( 7428) covalent geometry : angle 0.49321 (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 113 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: C 23 HIS cc_start: 0.5204 (m90) cc_final: 0.4691 (m170) REVERT: C 241 LEU cc_start: 0.8045 (mt) cc_final: 0.7787 (mt) REVERT: D 32 PHE cc_start: 0.8174 (m-80) cc_final: 0.7896 (m-10) outliers start: 17 outliers final: 13 residues processed: 109 average time/residue: 0.3905 time to fit residues: 58.5136 Evaluate side-chains 110 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 307 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 8 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114373 restraints weight = 28839.779| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.89 r_work: 0.3255 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7428 Z= 0.124 Angle : 0.491 6.064 10043 Z= 0.253 Chirality : 0.038 0.137 1177 Planarity : 0.004 0.044 1257 Dihedral : 7.919 70.796 1069 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.74 % Allowed : 15.69 % Favored : 82.57 % 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: -0.27 (0.29), residues: 907 helix: 1.05 (0.27), residues: 418 sheet: -1.62 (0.38), residues: 152 loop : -0.91 (0.34), residues: 337 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 0.010 0.001 PHE B 346 TYR 0.010 0.001 TYR C 72 ARG 0.008 0.000 ARG D 64 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 338) hydrogen bonds : angle 4.23443 ( 942) covalent geometry : bond 0.00285 ( 7428) covalent geometry : angle 0.49121 (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 112 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: B 235 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7671 (mtmm) REVERT: C 23 HIS cc_start: 0.4957 (m90) cc_final: 0.4447 (m170) REVERT: C 241 LEU cc_start: 0.8063 (mt) cc_final: 0.7796 (mt) REVERT: D 32 PHE cc_start: 0.8248 (m-80) cc_final: 0.7979 (m-10) outliers start: 14 outliers final: 13 residues processed: 108 average time/residue: 0.3900 time to fit residues: 58.0168 Evaluate side-chains 109 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 235 LYS 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 274 THR Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 307 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.136596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115466 restraints weight = 29436.657| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.92 r_work: 0.3245 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1955 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 : 0.494 6.048 10043 Z= 0.255 Chirality : 0.038 0.136 1177 Planarity : 0.004 0.044 1257 Dihedral : 7.897 70.519 1069 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.87 % Allowed : 15.69 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.25 (0.28), residues: 907 helix: 1.02 (0.26), residues: 418 sheet: -1.25 (0.42), residues: 135 loop : -1.08 (0.33), residues: 354 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 C 72 ARG 0.007 0.000 ARG D 64 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 338) hydrogen bonds : angle 4.22603 ( 942) covalent geometry : bond 0.00288 ( 7428) covalent geometry : angle 0.49387 (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 112 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: B 235 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7662 (mtmm) REVERT: C 23 HIS cc_start: 0.4926 (m90) cc_final: 0.4416 (m170) REVERT: C 241 LEU cc_start: 0.8039 (mt) cc_final: 0.7787 (mt) REVERT: D 32 PHE cc_start: 0.8132 (m-80) cc_final: 0.7869 (m-10) outliers start: 15 outliers final: 13 residues processed: 108 average time/residue: 0.4204 time to fit residues: 63.0442 Evaluate side-chains 109 residues out of total 803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 235 LYS 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 274 THR Chi-restraints excluded: chain C residue 292 MET Chi-restraints excluded: chain C residue 307 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 90 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 0.0270 chunk 54 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.3633 r_free = 0.3633 target = 0.137641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116596 restraints weight = 29072.054| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.91 r_work: 0.3262 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7428 Z= 0.102 Angle : 0.480 5.906 10043 Z= 0.246 Chirality : 0.038 0.134 1177 Planarity : 0.003 0.041 1257 Dihedral : 7.653 65.087 1069 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.74 % Allowed : 15.94 % Favored : 82.32 % 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: 1.18 (0.27), residues: 416 sheet: -1.17 (0.42), residues: 135 loop : -0.97 (0.34), residues: 356 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 0.010 0.001 PHE B 346 TYR 0.010 0.001 TYR D 59 ARG 0.007 0.000 ARG D 64 Details of bonding type rmsd hydrogen bonds : bond 0.03039 ( 338) hydrogen bonds : angle 4.11989 ( 942) covalent geometry : bond 0.00231 ( 7428) covalent geometry : angle 0.48007 (10043) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7015.00 seconds wall clock time: 121 minutes 7.11 seconds (7267.11 seconds total)