Starting phenix.real_space_refine on Tue Mar 3 11:28:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qwm_14189/03_2026/7qwm_14189.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qwm_14189/03_2026/7qwm_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 { model { file = "/net/cci-nas-00/data/ceres_data/7qwm_14189/03_2026/7qwm_14189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qwm_14189/03_2026/7qwm_14189.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qwm_14189/03_2026/7qwm_14189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qwm_14189/03_2026/7qwm_14189.map" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.95, per 1000 atoms: 0.29 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: 0.26 Conformation dependent library (CDL) restraints added in 129.2 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: 0.12 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: 0.45 Time building geometry restraints manager: 0.33 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: 2.370 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.290 Find NCS groups from input model: 0.040 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.890 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (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 ARG 0.007 0.002 ARG C 247 TYR 0.066 0.015 TYR A 250 PHE 0.053 0.012 PHE A 171 HIS 0.009 0.003 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.01198 ( 3309) covalent geometry : angle 1.92867 ( 4497) SS BOND : bond 0.00704 ( 3) SS BOND : angle 1.61876 ( 6) hydrogen bonds : bond 0.13200 ( 56) hydrogen bonds : angle 9.14220 ( 168) *********************** 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 : 0.134 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: 0.6900 (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: 0.7268 (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: 0.5290 time to fit residues: 64.6572 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 : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.163506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.144246 restraints weight = 3065.587| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.41 r_work: 0.3760 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3312 Z= 0.119 Angle : 0.641 7.497 4503 Z= 0.349 Chirality : 0.054 0.126 540 Planarity : 0.002 0.013 558 Dihedral : 6.948 21.071 447 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.85 % Allowed : 11.38 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (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 ARG 0.003 0.000 ARG A 247 TYR 0.013 0.001 TYR A 209 PHE 0.013 0.002 PHE B 213 HIS 0.010 0.002 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 3309) covalent geometry : angle 0.64093 ( 4497) SS BOND : bond 0.00057 ( 3) SS BOND : angle 0.13208 ( 6) hydrogen bonds : bond 0.02790 ( 56) hydrogen bonds : angle 6.77481 ( 168) *********************** 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 106 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8293 (mp) cc_final: 0.8028 (mt) REVERT: A 171 PHE cc_start: 0.7852 (m-80) cc_final: 0.7643 (m-80) REVERT: A 178 LYS cc_start: 0.6756 (tttt) cc_final: 0.6440 (mttp) REVERT: A 180 ARG cc_start: 0.6641 (ttm-80) cc_final: 0.6064 (mmt-90) REVERT: A 205 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6589 (mt-10) REVERT: B 140 ARG cc_start: 0.6621 (mtt-85) cc_final: 0.6222 (mmm-85) REVERT: B 161 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7363 (mt-10) REVERT: B 191 ASP cc_start: 0.7611 (t0) cc_final: 0.7383 (t0) REVERT: B 205 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6281 (mm-30) REVERT: B 207 MET cc_start: 0.6741 (mmt) cc_final: 0.6062 (mmm) REVERT: B 220 LYS cc_start: 0.8239 (mtmm) cc_final: 0.8027 (mtpt) REVERT: C 140 ARG cc_start: 0.6648 (mtt-85) cc_final: 0.6292 (mmm-85) REVERT: C 145 ASN cc_start: 0.7108 (m-40) cc_final: 0.6794 (m110) REVERT: C 161 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7326 (mt-10) REVERT: C 162 VAL cc_start: 0.8259 (t) cc_final: 0.7953 (m) REVERT: C 191 ASP cc_start: 0.7697 (t0) cc_final: 0.7473 (t70) REVERT: C 205 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6420 (mt-10) REVERT: C 246 GLU cc_start: 0.7390 (mt-10) cc_final: 0.5982 (mp0) outliers start: 7 outliers final: 0 residues processed: 101 average time/residue: 0.5506 time to fit residues: 57.0256 Evaluate side-chains 95 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 0.0060 chunk 30 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 11 optimal weight: 0.0470 chunk 28 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.133522 restraints weight = 3114.097| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.42 r_work: 0.3659 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 3312 Z= 0.205 Angle : 0.709 7.232 4503 Z= 0.389 Chirality : 0.056 0.149 540 Planarity : 0.003 0.019 558 Dihedral : 7.019 24.767 447 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 180 TYR 0.018 0.002 TYR A 248 PHE 0.016 0.003 PHE A 237 HIS 0.006 0.002 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 3309) covalent geometry : angle 0.70924 ( 4497) SS BOND : bond 0.00231 ( 3) SS BOND : angle 0.69885 ( 6) hydrogen bonds : bond 0.02929 ( 56) hydrogen bonds : angle 6.29492 ( 168) *********************** 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 103 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.8037 (t) cc_final: 0.7584 (m) REVERT: A 171 PHE cc_start: 0.7870 (m-80) cc_final: 0.7565 (m-80) REVERT: A 178 LYS cc_start: 0.6792 (tttt) cc_final: 0.6415 (mttp) REVERT: A 180 ARG cc_start: 0.6711 (ttm-80) cc_final: 0.6035 (mmt-90) REVERT: A 205 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6276 (tt0) REVERT: B 140 ARG cc_start: 0.6646 (mtt-85) cc_final: 0.6219 (mmm-85) REVERT: B 205 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6404 (mm-30) REVERT: B 207 MET cc_start: 0.6980 (OUTLIER) cc_final: 0.6265 (mmm) REVERT: C 140 ARG cc_start: 0.6899 (mtt-85) cc_final: 0.6527 (mmm-85) REVERT: C 145 ASN cc_start: 0.7304 (m-40) cc_final: 0.7056 (m110) REVERT: C 161 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7434 (mt-10) REVERT: C 173 LYS cc_start: 0.7874 (tttt) cc_final: 0.7418 (tttt) REVERT: C 205 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6557 (mt-10) REVERT: C 246 GLU cc_start: 0.7756 (mt-10) cc_final: 0.6352 (mp0) outliers start: 12 outliers final: 4 residues processed: 97 average time/residue: 0.6191 time to fit residues: 61.4525 Evaluate side-chains 92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 193 LYS Chi-restraints excluded: chain C residue 227 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.157760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.138083 restraints weight = 3085.005| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.43 r_work: 0.3719 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3312 Z= 0.120 Angle : 0.585 5.975 4503 Z= 0.320 Chirality : 0.052 0.134 540 Planarity : 0.002 0.015 558 Dihedral : 6.578 21.790 447 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.91 % Allowed : 14.55 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 180 TYR 0.012 0.001 TYR A 248 PHE 0.011 0.002 PHE A 237 HIS 0.006 0.002 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3309) covalent geometry : angle 0.58566 ( 4497) SS BOND : bond 0.00173 ( 3) SS BOND : angle 0.35024 ( 6) hydrogen bonds : bond 0.02328 ( 56) hydrogen bonds : angle 6.05304 ( 168) *********************** 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 100 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.134 Fit side-chains revert: symmetry clash REVERT: A 150 LEU cc_start: 0.8314 (mp) cc_final: 0.7993 (mt) REVERT: A 171 PHE cc_start: 0.7828 (m-80) cc_final: 0.7540 (m-80) REVERT: A 180 ARG cc_start: 0.6708 (ttm-80) cc_final: 0.6081 (mmt-90) REVERT: A 193 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7648 (mtpp) REVERT: A 205 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6250 (tt0) REVERT: A 220 LYS cc_start: 0.8404 (mtmm) cc_final: 0.8182 (mppt) REVERT: B 140 ARG cc_start: 0.6503 (mtt-85) cc_final: 0.6057 (mmm-85) REVERT: B 162 VAL cc_start: 0.8011 (t) cc_final: 0.7556 (m) REVERT: B 205 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6456 (mm-30) REVERT: B 207 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6240 (mmm) REVERT: C 140 ARG cc_start: 0.6811 (mtt-85) cc_final: 0.6474 (mmm-85) REVERT: C 145 ASN cc_start: 0.7348 (m-40) cc_final: 0.7074 (m110) REVERT: C 161 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7448 (mt-10) REVERT: C 162 VAL cc_start: 0.8334 (t) cc_final: 0.7740 (m) REVERT: C 205 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6714 (mt-10) REVERT: C 246 GLU cc_start: 0.7724 (mt-10) cc_final: 0.6354 (mp0) outliers start: 11 outliers final: 2 residues processed: 95 average time/residue: 0.6104 time to fit residues: 59.3553 Evaluate side-chains 92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET 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 12 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.151541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.131878 restraints weight = 3114.113| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 1.41 r_work: 0.3651 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: 0.7952 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 3312 Z= 0.213 Angle : 0.699 6.669 4503 Z= 0.386 Chirality : 0.055 0.151 540 Planarity : 0.003 0.018 558 Dihedral : 6.894 24.702 447 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 2.65 % Allowed : 16.14 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 180 TYR 0.015 0.002 TYR B 143 PHE 0.015 0.003 PHE A 237 HIS 0.005 0.002 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 3309) covalent geometry : angle 0.69883 ( 4497) SS BOND : bond 0.00216 ( 3) SS BOND : angle 0.77820 ( 6) hydrogen bonds : bond 0.02856 ( 56) hydrogen bonds : angle 6.08436 ( 168) *********************** 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 98 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.128 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.8040 (t) cc_final: 0.7559 (m) REVERT: A 180 ARG cc_start: 0.6798 (ttm-80) cc_final: 0.6068 (mmt-90) REVERT: A 193 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7652 (mtpp) REVERT: A 205 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6271 (tt0) REVERT: B 140 ARG cc_start: 0.6557 (mtt-85) cc_final: 0.6127 (mmm-85) REVERT: B 162 VAL cc_start: 0.7981 (t) cc_final: 0.7476 (m) REVERT: B 205 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6456 (mm-30) REVERT: B 207 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6287 (mmm) REVERT: C 140 ARG cc_start: 0.6985 (mtt-85) cc_final: 0.6637 (mmm-85) REVERT: C 145 ASN cc_start: 0.7416 (m-40) cc_final: 0.7137 (m110) REVERT: C 161 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7397 (mt-10) REVERT: C 162 VAL cc_start: 0.8231 (t) cc_final: 0.7620 (m) REVERT: C 173 LYS cc_start: 0.7924 (tttt) cc_final: 0.7474 (tttt) REVERT: C 205 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6669 (mt-10) REVERT: C 246 GLU cc_start: 0.7735 (mt-10) cc_final: 0.6357 (mp0) outliers start: 10 outliers final: 3 residues processed: 92 average time/residue: 0.6806 time to fit residues: 63.9498 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 : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 227 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 8 optimal weight: 0.0870 chunk 30 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 0.0570 chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.2680 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.159494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.141326 restraints weight = 3117.786| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.43 r_work: 0.3766 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3312 Z= 0.106 Angle : 0.556 4.689 4503 Z= 0.308 Chirality : 0.052 0.127 540 Planarity : 0.002 0.019 558 Dihedral : 6.444 22.113 447 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.17 % Allowed : 15.87 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 180 TYR 0.010 0.001 TYR A 248 PHE 0.011 0.002 PHE A 237 HIS 0.006 0.002 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 3309) covalent geometry : angle 0.55587 ( 4497) SS BOND : bond 0.00161 ( 3) SS BOND : angle 0.23671 ( 6) hydrogen bonds : bond 0.02039 ( 56) hydrogen bonds : angle 5.68642 ( 168) *********************** 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 102 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.7988 (t) cc_final: 0.7538 (m) REVERT: A 180 ARG cc_start: 0.6711 (ttm-80) cc_final: 0.6041 (mmt-90) REVERT: A 186 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7945 (mt) REVERT: A 193 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7503 (mtpp) REVERT: A 205 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6292 (tt0) REVERT: B 140 ARG cc_start: 0.6544 (mtt-85) cc_final: 0.6139 (mmm-85) REVERT: B 162 VAL cc_start: 0.8019 (t) cc_final: 0.7494 (m) REVERT: B 205 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6422 (mm-30) REVERT: B 207 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6089 (mmm) REVERT: C 140 ARG cc_start: 0.6761 (mtt-85) cc_final: 0.6469 (mmm-85) REVERT: C 145 ASN cc_start: 0.7188 (m-40) cc_final: 0.6883 (m110) REVERT: C 161 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7407 (mt-10) REVERT: C 173 LYS cc_start: 0.7840 (tttt) cc_final: 0.7443 (tttt) REVERT: C 205 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6759 (mt-10) REVERT: C 246 GLU cc_start: 0.7535 (mt-10) cc_final: 0.6254 (mp0) outliers start: 12 outliers final: 0 residues processed: 95 average time/residue: 0.6319 time to fit residues: 61.4420 Evaluate side-chains 92 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 207 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 37 optimal weight: 0.0570 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 2.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.157179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138667 restraints weight = 3167.796| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.46 r_work: 0.3740 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3312 Z= 0.140 Angle : 0.604 6.267 4503 Z= 0.335 Chirality : 0.052 0.127 540 Planarity : 0.003 0.025 558 Dihedral : 6.522 23.493 447 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.38 % Allowed : 17.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 247 TYR 0.013 0.002 TYR A 248 PHE 0.012 0.002 PHE A 237 HIS 0.005 0.002 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3309) covalent geometry : angle 0.60457 ( 4497) SS BOND : bond 0.00149 ( 3) SS BOND : angle 0.48088 ( 6) hydrogen bonds : bond 0.02294 ( 56) hydrogen bonds : angle 5.60874 ( 168) *********************** 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 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.7988 (t) cc_final: 0.7532 (m) REVERT: A 180 ARG cc_start: 0.6778 (ttm-80) cc_final: 0.6049 (mmt-90) REVERT: A 186 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7927 (mt) REVERT: A 193 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7624 (mtpp) REVERT: A 196 ASP cc_start: 0.7466 (p0) cc_final: 0.7147 (p0) REVERT: A 205 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6242 (tt0) REVERT: B 140 ARG cc_start: 0.6553 (mtt-85) cc_final: 0.6129 (mmm-85) REVERT: B 162 VAL cc_start: 0.7934 (t) cc_final: 0.7455 (m) REVERT: B 205 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6450 (mm-30) REVERT: B 207 MET cc_start: 0.6719 (OUTLIER) cc_final: 0.6066 (mmm) REVERT: C 140 ARG cc_start: 0.6861 (mtt-85) cc_final: 0.6534 (mmm-85) REVERT: C 145 ASN cc_start: 0.7339 (m-40) cc_final: 0.7036 (m110) REVERT: C 161 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7425 (mt-10) REVERT: C 162 VAL cc_start: 0.8195 (t) cc_final: 0.7567 (m) REVERT: C 173 LYS cc_start: 0.7843 (tttt) cc_final: 0.7442 (tttt) REVERT: C 205 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6767 (mt-10) REVERT: C 231 THR cc_start: 0.6453 (OUTLIER) cc_final: 0.6166 (p) REVERT: C 246 GLU cc_start: 0.7587 (mt-10) cc_final: 0.6291 (mp0) outliers start: 9 outliers final: 1 residues processed: 92 average time/residue: 0.6364 time to fit residues: 59.8936 Evaluate side-chains 91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.156184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.137756 restraints weight = 3132.946| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.41 r_work: 0.3737 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3312 Z= 0.148 Angle : 0.617 7.010 4503 Z= 0.343 Chirality : 0.053 0.130 540 Planarity : 0.003 0.027 558 Dihedral : 6.594 23.807 447 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.85 % Allowed : 17.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 247 TYR 0.013 0.002 TYR A 248 PHE 0.012 0.002 PHE A 237 HIS 0.005 0.002 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 3309) covalent geometry : angle 0.61677 ( 4497) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.50290 ( 6) hydrogen bonds : bond 0.02396 ( 56) hydrogen bonds : angle 5.61256 ( 168) *********************** 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 94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.144 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.8022 (t) cc_final: 0.7578 (m) REVERT: A 180 ARG cc_start: 0.6777 (ttm-80) cc_final: 0.6056 (mmt-90) REVERT: A 186 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7931 (mt) REVERT: A 193 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7530 (mtpp) REVERT: A 196 ASP cc_start: 0.7606 (p0) cc_final: 0.7326 (p0) REVERT: A 205 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6240 (tt0) REVERT: B 140 ARG cc_start: 0.6553 (mtt-85) cc_final: 0.6140 (mmm-85) REVERT: B 162 VAL cc_start: 0.7906 (t) cc_final: 0.7408 (m) REVERT: B 205 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6474 (mm-30) REVERT: B 207 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6020 (mmm) REVERT: C 140 ARG cc_start: 0.6855 (mtt-85) cc_final: 0.6566 (mmm-85) REVERT: C 145 ASN cc_start: 0.7318 (m-40) cc_final: 0.7022 (m110) REVERT: C 161 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7434 (mt-10) REVERT: C 173 LYS cc_start: 0.7871 (tttt) cc_final: 0.7495 (tttt) REVERT: C 193 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7797 (mtpp) REVERT: C 205 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6798 (mt-10) REVERT: C 231 THR cc_start: 0.6447 (OUTLIER) cc_final: 0.6143 (p) REVERT: C 246 GLU cc_start: 0.7647 (mt-10) cc_final: 0.6328 (mp0) outliers start: 7 outliers final: 1 residues processed: 92 average time/residue: 0.6506 time to fit residues: 61.1936 Evaluate side-chains 91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 31 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.152236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.131900 restraints weight = 3202.905| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.44 r_work: 0.3687 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 3312 Z= 0.190 Angle : 0.663 5.558 4503 Z= 0.370 Chirality : 0.054 0.141 540 Planarity : 0.003 0.028 558 Dihedral : 6.809 24.493 447 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.38 % Allowed : 17.99 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.34), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 247 TYR 0.015 0.002 TYR B 143 PHE 0.015 0.003 PHE A 237 HIS 0.005 0.002 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 3309) covalent geometry : angle 0.66270 ( 4497) SS BOND : bond 0.00176 ( 3) SS BOND : angle 0.72109 ( 6) hydrogen bonds : bond 0.02571 ( 56) hydrogen bonds : angle 5.68086 ( 168) *********************** 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 96 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.8046 (t) cc_final: 0.7585 (m) REVERT: A 180 ARG cc_start: 0.6834 (ttm-80) cc_final: 0.6098 (mmt-90) REVERT: A 186 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7992 (mt) REVERT: A 193 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7719 (mtpp) REVERT: A 196 ASP cc_start: 0.7731 (p0) cc_final: 0.7459 (p0) REVERT: A 205 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6351 (tt0) REVERT: B 140 ARG cc_start: 0.6648 (mtt-85) cc_final: 0.6242 (mmm-85) REVERT: B 162 VAL cc_start: 0.7902 (t) cc_final: 0.7414 (m) REVERT: B 205 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6599 (mm-30) REVERT: B 207 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6165 (mmm) REVERT: C 140 ARG cc_start: 0.6970 (mtt-85) cc_final: 0.6654 (mmm-85) REVERT: C 145 ASN cc_start: 0.7383 (m-40) cc_final: 0.7096 (m110) REVERT: C 161 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7445 (mt-10) REVERT: C 162 VAL cc_start: 0.8216 (t) cc_final: 0.7601 (m) REVERT: C 205 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6851 (mt-10) REVERT: C 231 THR cc_start: 0.6624 (OUTLIER) cc_final: 0.6326 (p) REVERT: C 246 GLU cc_start: 0.7733 (mt-10) cc_final: 0.6377 (mp0) outliers start: 9 outliers final: 1 residues processed: 92 average time/residue: 0.6255 time to fit residues: 58.8030 Evaluate side-chains 91 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.121 ------------------------------------------------------------------------------- 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 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4023 r_free = 0.4023 target = 0.158214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.138583 restraints weight = 3090.027| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.41 r_work: 0.3743 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3653 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3312 Z= 0.117 Angle : 0.593 6.719 4503 Z= 0.332 Chirality : 0.052 0.130 540 Planarity : 0.002 0.024 558 Dihedral : 6.657 24.558 447 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.32 % Allowed : 19.31 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 180 TYR 0.011 0.001 TYR B 248 PHE 0.010 0.002 PHE A 237 HIS 0.005 0.002 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3309) covalent geometry : angle 0.59303 ( 4497) SS BOND : bond 0.00153 ( 3) SS BOND : angle 0.39204 ( 6) hydrogen bonds : bond 0.02179 ( 56) hydrogen bonds : angle 5.51016 ( 168) ********************** 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 89 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 162 VAL cc_start: 0.8028 (t) cc_final: 0.7584 (m) REVERT: A 180 ARG cc_start: 0.6803 (ttm-80) cc_final: 0.6100 (mmt180) REVERT: A 186 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7930 (mt) REVERT: A 193 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7652 (mtpp) REVERT: A 196 ASP cc_start: 0.7691 (p0) cc_final: 0.7405 (p0) REVERT: A 205 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6284 (tt0) REVERT: B 140 ARG cc_start: 0.6631 (mtt-85) cc_final: 0.6235 (mmm-85) REVERT: B 162 VAL cc_start: 0.7948 (t) cc_final: 0.7452 (m) REVERT: B 171 PHE cc_start: 0.7775 (m-80) cc_final: 0.7379 (m-80) REVERT: B 205 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6467 (mm-30) REVERT: B 207 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6164 (mmm) REVERT: C 140 ARG cc_start: 0.6877 (mtt-85) cc_final: 0.6604 (mmm-85) REVERT: C 145 ASN cc_start: 0.7159 (m-40) cc_final: 0.6902 (m110) REVERT: C 161 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7484 (mt-10) REVERT: C 205 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6717 (mt-10) REVERT: C 246 GLU cc_start: 0.7658 (mt-10) cc_final: 0.6324 (mp0) outliers start: 5 outliers final: 1 residues processed: 88 average time/residue: 0.6630 time to fit residues: 59.6302 Evaluate side-chains 87 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 0.0970 chunk 5 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 0.0030 chunk 16 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.166744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.147135 restraints weight = 3066.152| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.42 r_work: 0.3849 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3312 Z= 0.085 Angle : 0.527 5.182 4503 Z= 0.295 Chirality : 0.051 0.125 540 Planarity : 0.002 0.027 558 Dihedral : 6.211 23.567 447 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.59 % Allowed : 19.05 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 50.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.35), residues: 399 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 180 TYR 0.008 0.001 TYR B 248 PHE 0.007 0.001 PHE A 237 HIS 0.005 0.002 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 3309) covalent geometry : angle 0.52713 ( 4497) SS BOND : bond 0.00108 ( 3) SS BOND : angle 0.13165 ( 6) hydrogen bonds : bond 0.01659 ( 56) hydrogen bonds : angle 5.03634 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1679.79 seconds wall clock time: 29 minutes 18.64 seconds (1758.64 seconds total)