Starting phenix.real_space_refine on Wed Jun 4 14:32:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qwm_14189/06_2025/7qwm_14189.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qwm_14189/06_2025/7qwm_14189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qwm_14189/06_2025/7qwm_14189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qwm_14189/06_2025/7qwm_14189.map" model { file = "/net/cci-nas-00/data/ceres_data/7qwm_14189/06_2025/7qwm_14189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qwm_14189/06_2025/7qwm_14189.cif" } resolution = 2.76 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= 0.005 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 2079 2.51 5 N 519 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3255 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain: "B" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Chain: "C" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1085 Classifications: {'peptide': 135} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 132} Time building chain proxies: 3.62, per 1000 atoms: 1.11 Number of scatterers: 3255 At special positions: 0 Unit cell: (87.874, 114.402, 36.476, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 636 8.00 N 519 7.00 C 2079 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 214 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS B 214 " - pdb=" SG CYS B 253 " distance=2.04 Simple disulfide: pdb=" SG CYS C 214 " - pdb=" SG CYS C 253 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 434.8 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 66.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 126 removed outlier: 6.170A pdb=" N ILE A 121 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N LYS B 124 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A 123 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE B 126 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR A 125 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE B 121 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N LYS C 124 " --> pdb=" O ILE B 121 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL B 123 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ILE C 126 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N TYR B 125 " --> pdb=" O ILE C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 removed outlier: 6.812A pdb=" N LYS A 129 " --> pdb=" O SER B 130 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS B 129 " --> pdb=" O SER C 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 133 through 138 removed outlier: 6.415A pdb=" N SER A 134 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL B 137 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ASP A 136 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N SER B 134 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL C 137 " --> pdb=" O SER B 134 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 136 " --> pdb=" O VAL C 137 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 153 removed outlier: 7.041A pdb=" N TYR A 143 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B 144 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN A 145 " --> pdb=" O LEU B 144 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR B 143 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU C 144 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN B 145 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 156 through 160 removed outlier: 6.477A pdb=" N TYR A 157 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N VAL B 160 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER A 159 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR B 157 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL C 160 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER B 159 " --> pdb=" O VAL C 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 163 through 176 removed outlier: 6.973A pdb=" N SER A 172 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LYS B 173 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER B 172 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS C 173 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 180 through 182 removed outlier: 6.438A pdb=" N ARG A 180 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ARG B 180 " --> pdb=" O LEU C 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 187 removed outlier: 6.229A pdb=" N ILE A 186 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE B 186 " --> pdb=" O ILE C 187 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AB1, first strand: chain 'A' and resid 201 through 213 removed outlier: 9.091A pdb=" N THR A 201 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N ALA B 204 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ILE A 203 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N GLU B 206 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU A 205 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N SER B 208 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET A 207 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N MET B 210 " --> pdb=" O MET A 207 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR A 209 " --> pdb=" O MET B 210 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ASP B 212 " --> pdb=" O TYR A 209 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR A 211 " --> pdb=" O ASP B 212 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N THR B 201 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N ALA C 204 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE B 203 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N GLU C 206 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU B 205 " --> pdb=" O GLU C 206 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N SER C 208 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N MET B 207 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N MET C 210 " --> pdb=" O MET B 207 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR B 209 " --> pdb=" O MET C 210 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ASP C 212 " --> pdb=" O TYR B 209 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR B 211 " --> pdb=" O ASP C 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 216 through 219 removed outlier: 6.073A pdb=" N LEU A 216 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE B 219 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER A 218 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU B 216 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE C 219 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER B 218 " --> pdb=" O ILE C 219 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 222 through 245 removed outlier: 9.072A pdb=" N HIS A 222 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N VAL B 225 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N ILE A 224 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 9.967A pdb=" N MET B 227 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N LEU A 226 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N GLN B 229 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N MET A 228 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N THR B 231 " --> pdb=" O MET A 228 " (cutoff:3.500A) removed outlier: 8.919A pdb=" N VAL A 230 " --> pdb=" O THR B 231 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N THR B 233 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N VAL A 232 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N THR B 235 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N THR A 234 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N PHE B 237 " --> pdb=" O THR A 234 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR A 236 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N HIS B 239 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY A 238 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLU B 241 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N SER A 240 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ILE B 243 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN A 242 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N GLN B 245 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N SER A 244 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL C 230 " --> pdb=" O GLN B 229 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR B 231 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR B 235 " --> pdb=" O THR C 234 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR C 236 " --> pdb=" O THR B 235 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE B 237 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY C 238 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS B 239 " --> pdb=" O GLY C 238 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N SER C 240 " --> pdb=" O HIS B 239 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU B 241 " --> pdb=" O SER C 240 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN C 242 " --> pdb=" O GLU B 241 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE B 243 " --> pdb=" O GLN C 242 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N SER C 244 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLN B 245 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 248 through 253 removed outlier: 6.806A pdb=" N GLN A 249 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASP B 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 251 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN B 249 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ASP C 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 251 " --> pdb=" O ASP C 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 56 hydrogen bonds defined for protein. 168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 943 1.33 - 1.46: 532 1.46 - 1.58: 1798 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 3309 Sorted by residual: bond pdb=" N ILE C 146 " pdb=" CA ILE C 146 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.14e-02 7.69e+03 7.44e+00 bond pdb=" CZ ARG B 140 " pdb=" NH2 ARG B 140 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.59e+00 bond pdb=" CZ ARG B 247 " pdb=" NH2 ARG B 247 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.48e+00 bond pdb=" CZ ARG B 180 " pdb=" NH2 ARG B 180 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.47e+00 bond pdb=" CZ ARG C 140 " pdb=" NH2 ARG C 140 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.44e+00 ... (remaining 3304 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 3130 1.82 - 3.63: 1076 3.63 - 5.45: 239 5.45 - 7.26: 44 7.26 - 9.08: 8 Bond angle restraints: 4497 Sorted by residual: angle pdb=" N THR C 231 " pdb=" CA THR C 231 " pdb=" C THR C 231 " ideal model delta sigma weight residual 112.45 121.41 -8.96 1.39e+00 5.18e-01 4.16e+01 angle pdb=" CB ASN B 183 " pdb=" CG ASN B 183 " pdb=" ND2 ASN B 183 " ideal model delta sigma weight residual 116.40 107.32 9.08 1.50e+00 4.44e-01 3.66e+01 angle pdb=" N GLN B 138 " pdb=" CA GLN B 138 " pdb=" C GLN B 138 " ideal model delta sigma weight residual 108.60 117.03 -8.43 1.46e+00 4.69e-01 3.33e+01 angle pdb=" CA ASN C 145 " pdb=" CB ASN C 145 " pdb=" CG ASN C 145 " ideal model delta sigma weight residual 112.60 118.24 -5.64 1.00e+00 1.00e+00 3.18e+01 angle pdb=" CA ASN B 183 " pdb=" CB ASN B 183 " pdb=" CG ASN B 183 " ideal model delta sigma weight residual 112.60 118.15 -5.55 1.00e+00 1.00e+00 3.08e+01 ... (remaining 4492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 1782 14.90 - 29.81: 164 29.81 - 44.71: 28 44.71 - 59.61: 13 59.61 - 74.51: 8 Dihedral angle restraints: 1995 sinusoidal: 777 harmonic: 1218 Sorted by residual: dihedral pdb=" CA GLU A 206 " pdb=" C GLU A 206 " pdb=" N MET A 207 " pdb=" CA MET A 207 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA GLU C 206 " pdb=" C GLU C 206 " pdb=" N MET C 207 " pdb=" CA MET C 207 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA GLU B 206 " pdb=" C GLU B 206 " pdb=" N MET B 207 " pdb=" CA MET B 207 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 1992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 415 0.112 - 0.224: 104 0.224 - 0.337: 13 0.337 - 0.449: 5 0.449 - 0.561: 3 Chirality restraints: 540 Sorted by residual: chirality pdb=" CA THR A 231 " pdb=" N THR A 231 " pdb=" C THR A 231 " pdb=" CB THR A 231 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CA THR C 231 " pdb=" N THR C 231 " pdb=" C THR C 231 " pdb=" CB THR C 231 " both_signs ideal model delta sigma weight residual False 2.53 2.01 0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CA LYS B 193 " pdb=" N LYS B 193 " pdb=" C LYS B 193 " pdb=" CB LYS B 193 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.14e+00 ... (remaining 537 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 250 " 0.056 2.00e-02 2.50e+03 3.68e-02 2.71e+01 pdb=" CG TYR A 250 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 250 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 250 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 250 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR A 250 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 250 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 250 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 171 " 0.053 2.00e-02 2.50e+03 3.25e-02 1.85e+01 pdb=" CG PHE A 171 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 171 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 PHE A 171 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 171 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 171 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 171 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 248 " -0.054 2.00e-02 2.50e+03 2.93e-02 1.71e+01 pdb=" CG TYR B 248 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR B 248 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR B 248 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 248 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 248 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 248 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 248 " -0.044 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1535 2.98 - 3.46: 2771 3.46 - 3.94: 5653 3.94 - 4.42: 5664 4.42 - 4.90: 10689 Nonbonded interactions: 26312 Sorted by model distance: nonbonded pdb=" OG SER A 120 " pdb=" OE2 GLU B 161 " model vdw 2.502 3.040 nonbonded pdb=" OG SER B 120 " pdb=" OE2 GLU C 161 " model vdw 2.570 3.040 nonbonded pdb=" O GLY A 127 " pdb=" OH TYR B 248 " model vdw 2.631 3.040 nonbonded pdb=" O GLY B 127 " pdb=" OH TYR C 248 " model vdw 2.658 3.040 nonbonded pdb=" OE1 GLN B 229 " pdb=" OG SER B 240 " model vdw 2.665 3.040 ... (remaining 26307 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.140 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 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 : 0.012 0.038 3312 Z= 0.685 Angle : 1.928 9.079 4503 Z= 1.265 Chirality : 0.107 0.561 540 Planarity : 0.011 0.043 558 Dihedral : 13.263 74.511 1206 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 50.00 % 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: -2.89 (0.33), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.25), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS C 239 PHE 0.053 0.012 PHE A 171 TYR 0.066 0.015 TYR A 250 ARG 0.007 0.002 ARG C 247 Details of bonding type rmsd hydrogen bonds : bond 0.13200 ( 56) hydrogen bonds : angle 9.14220 ( 168) SS BOND : bond 0.00704 ( 3) SS BOND : angle 1.61876 ( 6) covalent geometry : bond 0.01198 ( 3309) covalent geometry : angle 1.92867 ( 4497) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7553 (mttt) cc_final: 0.7236 (mttm) REVERT: A 145 ASN cc_start: 0.7161 (m-40) cc_final: 0.6885 (m-40) REVERT: B 140 ARG cc_start: 0.6423 (mtt-85) cc_final: 0.6198 (mmm-85) REVERT: B 173 LYS cc_start: 0.7358 (tttt) cc_final: 0.7007 (tttt) REVERT: B 196 ASP cc_start: 0.7314 (t0) cc_final: 0.6969 (t0) REVERT: B 202 VAL cc_start: 0.8110 (t) cc_final: 0.7900 (t) REVERT: B 205 GLU cc_start: 0.6530 (mt-10) cc_final: 0.5932 (mt-10) REVERT: C 140 ARG cc_start: 0.6769 (mtt-85) cc_final: 0.6345 (mmm-85) REVERT: C 159 SER cc_start: 0.8232 (t) cc_final: 0.8013 (m) REVERT: C 173 LYS cc_start: 0.7555 (tttt) cc_final: 0.7220 (tttt) REVERT: C 196 ASP cc_start: 0.7459 (t0) cc_final: 0.7004 (t0) REVERT: C 205 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6126 (mt-10) REVERT: C 210 MET cc_start: 0.7267 (mtt) cc_final: 0.7044 (mtp) REVERT: C 246 GLU cc_start: 0.7185 (mt-10) cc_final: 0.5886 (mp0) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 1.1387 time to fit residues: 139.3316 Evaluate side-chains 86 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN B 164 ASN B 194 GLN C 194 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.157570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.138203 restraints weight = 3041.485| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.40 r_work: 0.3702 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 3312 Z= 0.149 Angle : 0.682 8.227 4503 Z= 0.372 Chirality : 0.055 0.129 540 Planarity : 0.003 0.014 558 Dihedral : 7.145 22.262 447 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.12 % Allowed : 10.85 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.75 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 239 PHE 0.014 0.003 PHE B 213 TYR 0.016 0.002 TYR A 248 ARG 0.003 0.000 ARG A 247 Details of bonding type rmsd hydrogen bonds : bond 0.02853 ( 56) hydrogen bonds : angle 6.73410 ( 168) SS BOND : bond 0.00110 ( 3) SS BOND : angle 0.33391 ( 6) covalent geometry : bond 0.00351 ( 3309) covalent geometry : angle 0.68189 ( 4497) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8307 (mp) cc_final: 0.7999 (mt) REVERT: A 178 LYS cc_start: 0.6772 (tttt) cc_final: 0.6430 (mttp) REVERT: A 180 ARG cc_start: 0.6654 (ttm-80) cc_final: 0.6079 (mmt-90) REVERT: A 205 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6208 (tt0) REVERT: B 140 ARG cc_start: 0.6584 (mtt-85) cc_final: 0.6175 (mmm-85) REVERT: B 161 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7499 (mt-10) REVERT: B 205 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6274 (mm-30) REVERT: B 207 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6130 (mmm) REVERT: C 140 ARG cc_start: 0.6795 (mtt-85) cc_final: 0.6426 (mmm-85) REVERT: C 145 ASN cc_start: 0.7260 (m-40) cc_final: 0.6948 (m110) REVERT: C 161 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7362 (mt-10) REVERT: C 162 VAL cc_start: 0.8300 (t) cc_final: 0.7892 (m) REVERT: C 191 ASP cc_start: 0.7753 (t0) cc_final: 0.7552 (t70) REVERT: C 205 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6439 (mt-10) REVERT: C 246 GLU cc_start: 0.7597 (mt-10) cc_final: 0.6211 (mp0) outliers start: 8 outliers final: 1 residues processed: 97 average time/residue: 1.4900 time to fit residues: 147.9479 Evaluate side-chains 90 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain B residue 207 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 36 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.152509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.132780 restraints weight = 3084.490| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.42 r_work: 0.3657 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 3312 Z= 0.203 Angle : 0.709 7.657 4503 Z= 0.392 Chirality : 0.055 0.148 540 Planarity : 0.003 0.020 558 Dihedral : 7.079 25.002 447 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 3.17 % Allowed : 12.96 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.84 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 239 PHE 0.015 0.003 PHE A 237 TYR 0.017 0.002 TYR A 248 ARG 0.005 0.001 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.02991 ( 56) hydrogen bonds : angle 6.26618 ( 168) SS BOND : bond 0.00219 ( 3) SS BOND : angle 0.73782 ( 6) covalent geometry : bond 0.00495 ( 3309) covalent geometry : angle 0.70871 ( 4497) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.8048 (t) cc_final: 0.7591 (m) REVERT: A 171 PHE cc_start: 0.7855 (m-80) cc_final: 0.7643 (m-80) REVERT: A 178 LYS cc_start: 0.6776 (tttt) cc_final: 0.6408 (mttp) REVERT: A 180 ARG cc_start: 0.6781 (ttm-80) cc_final: 0.6078 (mmt-90) REVERT: A 205 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6313 (tt0) REVERT: B 140 ARG cc_start: 0.6557 (mtt-85) cc_final: 0.6091 (mmm-85) REVERT: B 161 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7539 (mt-10) REVERT: B 205 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6427 (mm-30) REVERT: B 207 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6230 (mmm) REVERT: C 140 ARG cc_start: 0.6953 (mtt-85) cc_final: 0.6610 (mmm-85) REVERT: C 145 ASN cc_start: 0.7318 (m-40) cc_final: 0.7080 (m110) REVERT: C 161 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7434 (mt-10) REVERT: C 173 LYS cc_start: 0.7854 (tttt) cc_final: 0.7412 (tttt) REVERT: C 205 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6621 (mt-10) REVERT: C 246 GLU cc_start: 0.7761 (mt-10) cc_final: 0.6359 (mp0) outliers start: 12 outliers final: 4 residues processed: 97 average time/residue: 1.2995 time to fit residues: 129.0431 Evaluate side-chains 93 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 193 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.152465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.132890 restraints weight = 3128.609| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.40 r_work: 0.3649 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 3312 Z= 0.201 Angle : 0.680 6.903 4503 Z= 0.375 Chirality : 0.054 0.141 540 Planarity : 0.003 0.021 558 Dihedral : 6.978 24.194 447 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.91 % Allowed : 15.34 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.91 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.014 0.003 PHE A 237 TYR 0.015 0.002 TYR B 248 ARG 0.005 0.001 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.02835 ( 56) hydrogen bonds : angle 6.23973 ( 168) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.65525 ( 6) covalent geometry : bond 0.00487 ( 3309) covalent geometry : angle 0.68036 ( 4497) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7775 (mttt) cc_final: 0.7457 (mppt) REVERT: A 162 VAL cc_start: 0.8026 (t) cc_final: 0.7553 (m) REVERT: A 180 ARG cc_start: 0.6747 (ttm-80) cc_final: 0.6071 (mmt-90) REVERT: A 186 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7962 (mt) REVERT: A 193 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7829 (mtpp) REVERT: A 205 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6329 (tt0) REVERT: B 140 ARG cc_start: 0.6535 (mtt-85) cc_final: 0.6115 (mmm-85) REVERT: B 162 VAL cc_start: 0.7995 (t) cc_final: 0.7476 (m) REVERT: B 205 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6457 (mm-30) REVERT: B 207 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6295 (mmm) REVERT: C 140 ARG cc_start: 0.7038 (mtt-85) cc_final: 0.6669 (mmm-85) REVERT: C 145 ASN cc_start: 0.7398 (m-40) cc_final: 0.7130 (m110) REVERT: C 161 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7429 (mt-10) REVERT: C 162 VAL cc_start: 0.8218 (t) cc_final: 0.7616 (m) REVERT: C 173 LYS cc_start: 0.7906 (tttt) cc_final: 0.7471 (tttt) REVERT: C 205 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6704 (mt-10) REVERT: C 246 GLU cc_start: 0.7715 (mt-10) cc_final: 0.6364 (mp0) outliers start: 11 outliers final: 3 residues processed: 95 average time/residue: 1.5119 time to fit residues: 146.7905 Evaluate side-chains 95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 193 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.153376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.134908 restraints weight = 3131.749| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.39 r_work: 0.3678 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3312 Z= 0.182 Angle : 0.658 6.121 4503 Z= 0.365 Chirality : 0.054 0.137 540 Planarity : 0.003 0.019 558 Dihedral : 6.902 24.309 447 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.44 % Allowed : 15.87 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.97 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.013 0.003 PHE A 237 TYR 0.014 0.002 TYR B 248 ARG 0.005 0.001 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.02635 ( 56) hydrogen bonds : angle 6.11621 ( 168) SS BOND : bond 0.00224 ( 3) SS BOND : angle 0.60936 ( 6) covalent geometry : bond 0.00439 ( 3309) covalent geometry : angle 0.65838 ( 4497) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 139 LYS cc_start: 0.7734 (mttt) cc_final: 0.7418 (mppt) REVERT: A 162 VAL cc_start: 0.7977 (t) cc_final: 0.7515 (m) REVERT: A 180 ARG cc_start: 0.6769 (ttm-80) cc_final: 0.6016 (mmt-90) REVERT: A 186 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7987 (mt) REVERT: A 193 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7819 (mtpp) REVERT: A 205 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6307 (tt0) REVERT: B 140 ARG cc_start: 0.6539 (mtt-85) cc_final: 0.6108 (mmm-85) REVERT: B 162 VAL cc_start: 0.7960 (t) cc_final: 0.7479 (m) REVERT: B 205 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6440 (mm-30) REVERT: B 207 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6204 (mmm) REVERT: C 140 ARG cc_start: 0.7011 (mtt-85) cc_final: 0.6654 (mmm-85) REVERT: C 145 ASN cc_start: 0.7358 (m-40) cc_final: 0.7060 (m110) REVERT: C 161 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7419 (mt-10) REVERT: C 162 VAL cc_start: 0.8216 (t) cc_final: 0.7613 (m) REVERT: C 173 LYS cc_start: 0.7855 (tttt) cc_final: 0.7459 (tttt) REVERT: C 205 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6748 (mt-10) REVERT: C 246 GLU cc_start: 0.7663 (mt-10) cc_final: 0.6318 (mp0) outliers start: 13 outliers final: 3 residues processed: 96 average time/residue: 1.3480 time to fit residues: 132.5162 Evaluate side-chains 95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 193 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.154991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136469 restraints weight = 3175.481| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.42 r_work: 0.3703 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3312 Z= 0.148 Angle : 0.613 5.353 4503 Z= 0.341 Chirality : 0.053 0.131 540 Planarity : 0.002 0.018 558 Dihedral : 6.725 22.989 447 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.91 % Allowed : 16.67 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.94 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.012 0.002 PHE A 237 TYR 0.013 0.002 TYR A 248 ARG 0.006 0.001 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.02477 ( 56) hydrogen bonds : angle 5.96748 ( 168) SS BOND : bond 0.00198 ( 3) SS BOND : angle 0.46836 ( 6) covalent geometry : bond 0.00362 ( 3309) covalent geometry : angle 0.61281 ( 4497) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.7983 (t) cc_final: 0.7518 (m) REVERT: A 180 ARG cc_start: 0.6740 (ttm-80) cc_final: 0.6013 (mmt-90) REVERT: A 186 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7914 (mt) REVERT: A 193 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7740 (mtpp) REVERT: A 196 ASP cc_start: 0.7298 (t0) cc_final: 0.7018 (t70) REVERT: A 205 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6272 (tt0) REVERT: B 140 ARG cc_start: 0.6531 (mtt-85) cc_final: 0.6096 (mmm-85) REVERT: B 162 VAL cc_start: 0.7960 (t) cc_final: 0.7473 (m) REVERT: B 205 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6434 (mm-30) REVERT: B 207 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6153 (mmm) REVERT: B 231 THR cc_start: 0.6329 (OUTLIER) cc_final: 0.6111 (p) REVERT: C 139 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7014 (mptt) REVERT: C 140 ARG cc_start: 0.6958 (mtt-85) cc_final: 0.6623 (mmm-85) REVERT: C 145 ASN cc_start: 0.7271 (m-40) cc_final: 0.7007 (m110) REVERT: C 161 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7414 (mt-10) REVERT: C 162 VAL cc_start: 0.8193 (t) cc_final: 0.7582 (m) REVERT: C 173 LYS cc_start: 0.7839 (tttt) cc_final: 0.7453 (tttt) REVERT: C 205 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6660 (mt-10) REVERT: C 246 GLU cc_start: 0.7590 (mt-10) cc_final: 0.6243 (mp0) outliers start: 11 outliers final: 2 residues processed: 95 average time/residue: 1.3688 time to fit residues: 133.0266 Evaluate side-chains 95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 193 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.151852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.132004 restraints weight = 3134.501| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.41 r_work: 0.3640 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 3312 Z= 0.241 Angle : 0.714 6.116 4503 Z= 0.399 Chirality : 0.055 0.157 540 Planarity : 0.003 0.020 558 Dihedral : 7.038 25.179 447 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.65 % Allowed : 19.05 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.95 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 222 PHE 0.016 0.003 PHE A 237 TYR 0.016 0.002 TYR B 143 ARG 0.005 0.001 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.02926 ( 56) hydrogen bonds : angle 6.08811 ( 168) SS BOND : bond 0.00241 ( 3) SS BOND : angle 0.80428 ( 6) covalent geometry : bond 0.00584 ( 3309) covalent geometry : angle 0.71398 ( 4497) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.8009 (t) cc_final: 0.7543 (m) REVERT: A 180 ARG cc_start: 0.6856 (ttm-80) cc_final: 0.6082 (mmt-90) REVERT: A 186 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7957 (mt) REVERT: A 193 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7859 (mtpp) REVERT: A 205 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6423 (tt0) REVERT: B 140 ARG cc_start: 0.6627 (mtt-85) cc_final: 0.6203 (mmm-85) REVERT: B 162 VAL cc_start: 0.7954 (t) cc_final: 0.7461 (m) REVERT: B 207 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6253 (mmm) REVERT: B 231 THR cc_start: 0.6514 (OUTLIER) cc_final: 0.6302 (p) REVERT: C 140 ARG cc_start: 0.7026 (mtt-85) cc_final: 0.6692 (mmm-85) REVERT: C 161 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7454 (mt-10) REVERT: C 162 VAL cc_start: 0.8200 (t) cc_final: 0.7605 (m) REVERT: C 205 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6724 (mt-10) outliers start: 10 outliers final: 3 residues processed: 96 average time/residue: 1.3932 time to fit residues: 136.7743 Evaluate side-chains 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 193 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 0.2980 chunk 5 optimal weight: 10.0000 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 34 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.157216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137606 restraints weight = 3060.422| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.40 r_work: 0.3720 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3312 Z= 0.121 Angle : 0.589 5.320 4503 Z= 0.330 Chirality : 0.052 0.134 540 Planarity : 0.002 0.019 558 Dihedral : 6.680 23.252 447 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.65 % Allowed : 20.63 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.91 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 239 PHE 0.010 0.002 PHE A 237 TYR 0.012 0.001 TYR A 248 ARG 0.006 0.001 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.02319 ( 56) hydrogen bonds : angle 5.88077 ( 168) SS BOND : bond 0.00166 ( 3) SS BOND : angle 0.32855 ( 6) covalent geometry : bond 0.00291 ( 3309) covalent geometry : angle 0.58907 ( 4497) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.7993 (t) cc_final: 0.7528 (m) REVERT: A 180 ARG cc_start: 0.6839 (ttm-80) cc_final: 0.6109 (mmt-90) REVERT: A 186 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7897 (mt) REVERT: A 193 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7788 (mtpp) REVERT: A 196 ASP cc_start: 0.7317 (t0) cc_final: 0.7018 (t70) REVERT: A 205 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6423 (tt0) REVERT: B 140 ARG cc_start: 0.6574 (mtt-85) cc_final: 0.6170 (mmm-85) REVERT: B 162 VAL cc_start: 0.7953 (t) cc_final: 0.7488 (m) REVERT: B 171 PHE cc_start: 0.7800 (m-80) cc_final: 0.7427 (m-80) REVERT: B 207 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6118 (mmm) REVERT: B 231 THR cc_start: 0.6320 (OUTLIER) cc_final: 0.5972 (p) REVERT: C 140 ARG cc_start: 0.6864 (mtt-85) cc_final: 0.6578 (mmm-85) REVERT: C 161 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7475 (mt-10) REVERT: C 162 VAL cc_start: 0.8196 (t) cc_final: 0.7596 (m) REVERT: C 205 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6760 (mt-10) REVERT: C 231 THR cc_start: 0.6508 (OUTLIER) cc_final: 0.6165 (p) REVERT: C 246 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6310 (mp0) outliers start: 10 outliers final: 3 residues processed: 97 average time/residue: 1.3083 time to fit residues: 130.0751 Evaluate side-chains 97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 4 optimal weight: 0.5980 chunk 35 optimal weight: 9.9990 chunk 22 optimal weight: 1.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.152536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.132649 restraints weight = 3148.860| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.42 r_work: 0.3659 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 3312 Z= 0.212 Angle : 0.682 5.588 4503 Z= 0.383 Chirality : 0.054 0.144 540 Planarity : 0.003 0.017 558 Dihedral : 6.995 25.594 447 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.38 % Allowed : 21.69 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.92 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.016 0.003 PHE A 237 TYR 0.014 0.002 TYR B 143 ARG 0.006 0.001 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.02824 ( 56) hydrogen bonds : angle 5.98761 ( 168) SS BOND : bond 0.00210 ( 3) SS BOND : angle 0.73255 ( 6) covalent geometry : bond 0.00503 ( 3309) covalent geometry : angle 0.68147 ( 4497) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.8073 (t) cc_final: 0.7608 (m) REVERT: A 180 ARG cc_start: 0.6877 (ttm-80) cc_final: 0.6103 (mmt-90) REVERT: A 186 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7972 (mt) REVERT: A 193 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7778 (mtpp) REVERT: A 196 ASP cc_start: 0.7379 (t0) cc_final: 0.7091 (t70) REVERT: A 205 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6413 (tt0) REVERT: B 140 ARG cc_start: 0.6567 (mtt-85) cc_final: 0.6143 (mmm-85) REVERT: B 162 VAL cc_start: 0.7931 (t) cc_final: 0.7461 (m) REVERT: B 171 PHE cc_start: 0.7811 (m-80) cc_final: 0.7413 (m-80) REVERT: B 207 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.6260 (mmm) REVERT: B 210 MET cc_start: 0.7831 (mtp) cc_final: 0.7305 (mtp) REVERT: B 231 THR cc_start: 0.6309 (OUTLIER) cc_final: 0.5998 (p) REVERT: C 140 ARG cc_start: 0.6991 (mtt-85) cc_final: 0.6665 (mmm-85) REVERT: C 161 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7467 (mt-10) REVERT: C 162 VAL cc_start: 0.8228 (t) cc_final: 0.7626 (m) REVERT: C 205 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6781 (mt-10) REVERT: C 231 THR cc_start: 0.6718 (OUTLIER) cc_final: 0.6373 (p) REVERT: C 246 GLU cc_start: 0.7706 (mt-10) cc_final: 0.6410 (mp0) outliers start: 9 outliers final: 3 residues processed: 96 average time/residue: 1.4507 time to fit residues: 142.4747 Evaluate side-chains 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 overall best weight: 4.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.151403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.131778 restraints weight = 3090.094| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.40 r_work: 0.3647 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 3312 Z= 0.237 Angle : 0.722 6.247 4503 Z= 0.406 Chirality : 0.055 0.152 540 Planarity : 0.003 0.022 558 Dihedral : 7.157 25.962 447 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 2.12 % Allowed : 22.49 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.99 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 222 PHE 0.016 0.004 PHE A 237 TYR 0.015 0.002 TYR B 143 ARG 0.006 0.001 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 56) hydrogen bonds : angle 6.06070 ( 168) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.81512 ( 6) covalent geometry : bond 0.00563 ( 3309) covalent geometry : angle 0.72215 ( 4497) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.8088 (t) cc_final: 0.7610 (m) REVERT: A 180 ARG cc_start: 0.6874 (ttm-80) cc_final: 0.6099 (mmt-90) REVERT: A 186 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7964 (mt) REVERT: A 193 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7772 (mtpp) REVERT: A 196 ASP cc_start: 0.7370 (t0) cc_final: 0.7082 (t70) REVERT: A 205 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6414 (tt0) REVERT: B 140 ARG cc_start: 0.6589 (mtt-85) cc_final: 0.6173 (mmm-85) REVERT: B 162 VAL cc_start: 0.7933 (t) cc_final: 0.7458 (m) REVERT: B 171 PHE cc_start: 0.7826 (m-80) cc_final: 0.7446 (m-80) REVERT: B 207 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6225 (mmm) REVERT: B 210 MET cc_start: 0.7808 (mtp) cc_final: 0.7306 (mtp) REVERT: B 231 THR cc_start: 0.6346 (OUTLIER) cc_final: 0.5995 (p) REVERT: C 140 ARG cc_start: 0.7033 (mtt-85) cc_final: 0.6704 (mmm-85) REVERT: C 161 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7458 (mt-10) REVERT: C 162 VAL cc_start: 0.8214 (t) cc_final: 0.7610 (m) REVERT: C 205 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6753 (mt-10) REVERT: C 231 THR cc_start: 0.6624 (OUTLIER) cc_final: 0.6326 (p) REVERT: C 246 GLU cc_start: 0.7697 (mt-10) cc_final: 0.6383 (mp0) outliers start: 8 outliers final: 3 residues processed: 93 average time/residue: 1.4703 time to fit residues: 139.9630 Evaluate side-chains 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.0570 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.157250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.138047 restraints weight = 3046.162| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.39 r_work: 0.3730 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3640 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3312 Z= 0.118 Angle : 0.598 6.497 4503 Z= 0.337 Chirality : 0.053 0.130 540 Planarity : 0.002 0.022 558 Dihedral : 6.829 25.485 447 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.65 % Allowed : 22.49 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % 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: -2.92 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 239 PHE 0.010 0.002 PHE B 213 TYR 0.012 0.001 TYR C 157 ARG 0.006 0.001 ARG B 180 Details of bonding type rmsd hydrogen bonds : bond 0.02257 ( 56) hydrogen bonds : angle 5.82188 ( 168) SS BOND : bond 0.00211 ( 3) SS BOND : angle 0.33377 ( 6) covalent geometry : bond 0.00276 ( 3309) covalent geometry : angle 0.59864 ( 4497) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3582.86 seconds wall clock time: 61 minutes 53.43 seconds (3713.43 seconds total)