Starting phenix.real_space_refine on Wed Feb 4 10:47:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i3k_52595/02_2026/9i3k_52595_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i3k_52595/02_2026/9i3k_52595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i3k_52595/02_2026/9i3k_52595_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i3k_52595/02_2026/9i3k_52595_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i3k_52595/02_2026/9i3k_52595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i3k_52595/02_2026/9i3k_52595.map" } resolution = 2.87 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= 0.001 sd= 0.026 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 95 5.16 5 C 6865 2.51 5 N 1630 2.21 5 O 1760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10350 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2070 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 8, 'TRANS': 263} Chain: "B" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2070 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 8, 'TRANS': 263} Chain: "C" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2070 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 8, 'TRANS': 263} Chain: "D" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2070 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 8, 'TRANS': 263} Chain: "E" Number of atoms: 2070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2070 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 8, 'TRANS': 263} Time building chain proxies: 2.92, per 1000 atoms: 0.28 Number of scatterers: 10350 At special positions: 0 Unit cell: (95.2798, 95.2798, 69.2406, 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 95 16.00 O 1760 8.00 N 1630 7.00 C 6865 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 597.8 milliseconds 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 0 sheets defined 90.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 11 through 28 Processing helix chain 'A' and resid 30 through 56 Processing helix chain 'A' and resid 63 through 85 removed outlier: 4.388A pdb=" N LEU A 77 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N GLY A 78 " --> pdb=" O CYS A 74 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 95 removed outlier: 3.511A pdb=" N LEU A 95 " --> pdb=" O SER A 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 95' Processing helix chain 'A' and resid 96 through 102 Processing helix chain 'A' and resid 106 through 135 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.705A pdb=" N VAL A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 185 removed outlier: 3.549A pdb=" N TYR A 183 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY A 185 " --> pdb=" O MET A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.685A pdb=" N ILE A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 removed outlier: 3.809A pdb=" N VAL A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 227 removed outlier: 3.574A pdb=" N PHE A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 228 through 236 removed outlier: 3.541A pdb=" N TRP A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 246 through 254 Processing helix chain 'A' and resid 254 through 269 Processing helix chain 'A' and resid 270 through 280 removed outlier: 3.846A pdb=" N ARG A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 28 Processing helix chain 'B' and resid 30 through 56 Processing helix chain 'B' and resid 63 through 86 removed outlier: 4.360A pdb=" N LEU B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N GLY B 78 " --> pdb=" O CYS B 74 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU B 79 " --> pdb=" O PHE B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 removed outlier: 3.516A pdb=" N VAL B 94 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 95 " --> pdb=" O SER B 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 95' Processing helix chain 'B' and resid 96 through 102 Processing helix chain 'B' and resid 106 through 135 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 143 through 156 Processing helix chain 'B' and resid 160 through 185 removed outlier: 3.729A pdb=" N SER B 184 " --> pdb=" O TRP B 180 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY B 185 " --> pdb=" O MET B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 194 removed outlier: 3.568A pdb=" N ILE B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.592A pdb=" N PHE B 202 " --> pdb=" O PRO B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 227 Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.638A pdb=" N SER B 243 " --> pdb=" O GLU B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 254 Processing helix chain 'B' and resid 254 through 269 Processing helix chain 'B' and resid 270 through 279 Processing helix chain 'C' and resid 11 through 28 Processing helix chain 'C' and resid 30 through 56 Processing helix chain 'C' and resid 63 through 86 removed outlier: 4.453A pdb=" N LEU C 77 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLY C 78 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C 79 " --> pdb=" O PHE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 96 through 102 Processing helix chain 'C' and resid 106 through 135 Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 143 through 157 removed outlier: 3.634A pdb=" N LYS C 156 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 185 removed outlier: 3.526A pdb=" N TYR C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY C 185 " --> pdb=" O MET C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.715A pdb=" N MET C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 removed outlier: 3.594A pdb=" N VAL C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 227 removed outlier: 3.591A pdb=" N PHE C 215 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Proline residue: C 218 - end of helix Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 246 through 254 Processing helix chain 'C' and resid 254 through 269 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.713A pdb=" N ARG C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 28 Processing helix chain 'D' and resid 30 through 56 Processing helix chain 'D' and resid 63 through 86 removed outlier: 4.376A pdb=" N LEU D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLY D 78 " --> pdb=" O CYS D 74 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU D 79 " --> pdb=" O PHE D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 96 through 102 removed outlier: 3.529A pdb=" N LYS D 100 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 135 Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.812A pdb=" N MET D 139 " --> pdb=" O GLY D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 157 removed outlier: 3.765A pdb=" N VAL D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 185 removed outlier: 3.935A pdb=" N SER D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY D 185 " --> pdb=" O MET D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 194 removed outlier: 3.553A pdb=" N ILE D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 209 through 227 removed outlier: 3.516A pdb=" N PHE D 215 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Proline residue: D 218 - end of helix Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 238 through 243 removed outlier: 3.541A pdb=" N SER D 243 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 254 Processing helix chain 'D' and resid 254 through 269 Processing helix chain 'D' and resid 270 through 279 Processing helix chain 'E' and resid 11 through 28 Processing helix chain 'E' and resid 30 through 56 Processing helix chain 'E' and resid 63 through 86 removed outlier: 4.494A pdb=" N LEU E 77 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N GLY E 78 " --> pdb=" O CYS E 74 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU E 79 " --> pdb=" O PHE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 94 Processing helix chain 'E' and resid 96 through 102 Processing helix chain 'E' and resid 106 through 136 Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 143 through 157 removed outlier: 3.675A pdb=" N LYS E 156 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 183 removed outlier: 3.538A pdb=" N TYR E 183 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 194 Processing helix chain 'E' and resid 195 through 205 Processing helix chain 'E' and resid 209 through 227 Proline residue: E 218 - end of helix Processing helix chain 'E' and resid 228 through 236 removed outlier: 3.707A pdb=" N TRP E 232 " --> pdb=" O SER E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 243 removed outlier: 3.652A pdb=" N SER E 243 " --> pdb=" O GLU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 254 Processing helix chain 'E' and resid 254 through 269 Processing helix chain 'E' and resid 270 through 279 829 hydrogen bonds defined for protein. 2421 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: 1.68 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3086 1.34 - 1.46: 2269 1.46 - 1.58: 5095 1.58 - 1.70: 0 1.70 - 1.82: 165 Bond restraints: 10615 Sorted by residual: bond pdb=" CB LYS D 100 " pdb=" CG LYS D 100 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.23e+00 bond pdb=" CB GLU E 230 " pdb=" CG GLU E 230 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CB PHE C 49 " pdb=" CG PHE C 49 " ideal model delta sigma weight residual 1.502 1.524 -0.022 2.30e-02 1.89e+03 9.19e-01 bond pdb=" CB GLU E 208 " pdb=" CG GLU E 208 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.42e-01 bond pdb=" CB PHE B 250 " pdb=" CG PHE B 250 " ideal model delta sigma weight residual 1.502 1.521 -0.019 2.30e-02 1.89e+03 6.63e-01 ... (remaining 10610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 14335 2.42 - 4.85: 100 4.85 - 7.27: 19 7.27 - 9.69: 5 9.69 - 12.12: 1 Bond angle restraints: 14460 Sorted by residual: angle pdb=" CB MET D 174 " pdb=" CG MET D 174 " pdb=" SD MET D 174 " ideal model delta sigma weight residual 112.70 124.82 -12.12 3.00e+00 1.11e-01 1.63e+01 angle pdb=" CA LYS D 100 " pdb=" CB LYS D 100 " pdb=" CG LYS D 100 " ideal model delta sigma weight residual 114.10 121.90 -7.80 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CB LYS D 100 " pdb=" CG LYS D 100 " pdb=" CD LYS D 100 " ideal model delta sigma weight residual 111.30 119.88 -8.58 2.30e+00 1.89e-01 1.39e+01 angle pdb=" N ILE C 96 " pdb=" CA ILE C 96 " pdb=" C ILE C 96 " ideal model delta sigma weight residual 113.07 108.09 4.98 1.36e+00 5.41e-01 1.34e+01 angle pdb=" CA GLU E 230 " pdb=" CB GLU E 230 " pdb=" CG GLU E 230 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 ... (remaining 14455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5251 17.54 - 35.08: 585 35.08 - 52.63: 144 52.63 - 70.17: 33 70.17 - 87.71: 17 Dihedral angle restraints: 6030 sinusoidal: 2175 harmonic: 3855 Sorted by residual: dihedral pdb=" CA MET A 214 " pdb=" C MET A 214 " pdb=" N PHE A 215 " pdb=" CA PHE A 215 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA LEU E 89 " pdb=" C LEU E 89 " pdb=" N PHE E 90 " pdb=" CA PHE E 90 " ideal model delta harmonic sigma weight residual 180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA LEU D 268 " pdb=" C LEU D 268 " pdb=" N LEU D 269 " pdb=" CA LEU D 269 " ideal model delta harmonic sigma weight residual 180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1263 0.043 - 0.086: 402 0.086 - 0.130: 57 0.130 - 0.173: 2 0.173 - 0.216: 1 Chirality restraints: 1725 Sorted by residual: chirality pdb=" CB ILE B 277 " pdb=" CA ILE B 277 " pdb=" CG1 ILE B 277 " pdb=" CG2 ILE B 277 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA MET C 216 " pdb=" N MET C 216 " pdb=" C MET C 216 " pdb=" CB MET C 216 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CG LEU B 10 " pdb=" CB LEU B 10 " pdb=" CD1 LEU B 10 " pdb=" CD2 LEU B 10 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 1722 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 278 " 0.011 2.00e-02 2.50e+03 1.68e-02 5.62e+00 pdb=" CG TYR B 278 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 278 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 278 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR B 278 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 278 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 278 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 278 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 172 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.74e+00 pdb=" CG ASN D 172 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN D 172 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN D 172 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 62 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO C 63 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 63 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 63 " 0.023 5.00e-02 4.00e+02 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 4153 2.91 - 3.41: 11472 3.41 - 3.91: 18944 3.91 - 4.40: 21852 4.40 - 4.90: 35845 Nonbonded interactions: 92266 Sorted by model distance: nonbonded pdb=" ND2 ASN D 172 " pdb=" O ASN D 262 " model vdw 2.414 3.120 nonbonded pdb=" O THR C 59 " pdb=" OG1 THR C 59 " model vdw 2.479 3.040 nonbonded pdb=" N GLU E 230 " pdb=" OE1 GLU E 230 " model vdw 2.535 3.120 nonbonded pdb=" O ASN D 172 " pdb=" OD1 ASN D 172 " model vdw 2.569 3.040 nonbonded pdb=" N ILE C 96 " pdb=" N VAL C 97 " model vdw 2.580 2.560 ... (remaining 92261 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' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.230 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: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.270 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 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 : 0.003 0.045 10615 Z= 0.125 Angle : 0.597 12.115 14460 Z= 0.332 Chirality : 0.039 0.216 1725 Planarity : 0.004 0.041 1745 Dihedral : 16.403 87.711 3570 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 1.56 % Allowed : 21.10 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.23), residues: 1350 helix: 1.52 (0.16), residues: 1115 sheet: None (None), residues: 0 loop : 0.62 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 186 TYR 0.040 0.001 TYR B 278 PHE 0.019 0.001 PHE B 202 TRP 0.023 0.001 TRP E 180 HIS 0.006 0.001 HIS E 155 Details of bonding type rmsd covalent geometry : bond 0.00262 (10615) covalent geometry : angle 0.59723 (14460) hydrogen bonds : bond 0.14610 ( 829) hydrogen bonds : angle 5.62198 ( 2421) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.376 Fit side-chains REVERT: A 201 MET cc_start: 0.6875 (tmt) cc_final: 0.6567 (ppp) REVERT: B 45 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7655 (tp) REVERT: B 219 MET cc_start: 0.8365 (tpp) cc_final: 0.7697 (ttt) REVERT: C 17 LYS cc_start: 0.7452 (tptt) cc_final: 0.6910 (mmtt) REVERT: D 26 LYS cc_start: 0.7431 (mttt) cc_final: 0.6617 (mptt) outliers start: 17 outliers final: 9 residues processed: 196 average time/residue: 0.4465 time to fit residues: 95.4704 Evaluate side-chains 195 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 202 PHE Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 246 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 ASN C 254 ASN E 121 ASN E 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.192288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.176710 restraints weight = 10388.816| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.53 r_work: 0.4043 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3920 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10615 Z= 0.205 Angle : 0.612 9.323 14460 Z= 0.319 Chirality : 0.044 0.167 1725 Planarity : 0.005 0.041 1745 Dihedral : 5.761 59.489 1432 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 4.22 % Allowed : 17.25 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.23), residues: 1350 helix: 1.43 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : 0.26 (0.44), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 186 TYR 0.020 0.002 TYR A 25 PHE 0.021 0.002 PHE D 202 TRP 0.020 0.002 TRP E 133 HIS 0.007 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00493 (10615) covalent geometry : angle 0.61245 (14460) hydrogen bonds : bond 0.04678 ( 829) hydrogen bonds : angle 4.81504 ( 2421) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 0.242 Fit side-chains REVERT: B 45 ILE cc_start: 0.8103 (OUTLIER) cc_final: 0.7800 (tp) REVERT: B 155 HIS cc_start: 0.6519 (OUTLIER) cc_final: 0.5675 (p90) REVERT: C 17 LYS cc_start: 0.7315 (tptt) cc_final: 0.6811 (mmmt) REVERT: C 151 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6408 (mt0) REVERT: D 26 LYS cc_start: 0.7516 (mttt) cc_final: 0.6540 (mptt) REVERT: E 96 ILE cc_start: 0.7717 (pt) cc_final: 0.7500 (pt) REVERT: E 195 MET cc_start: 0.7722 (mtp) cc_final: 0.7396 (mtm) REVERT: E 202 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6493 (t80) outliers start: 46 outliers final: 17 residues processed: 226 average time/residue: 0.3948 time to fit residues: 97.6836 Evaluate side-chains 211 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 246 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 23 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 131 optimal weight: 0.0980 chunk 59 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN B 30 HIS B 121 ASN B 155 HIS ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN E 121 ASN E 159 HIS E 244 HIS E 262 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.198377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.183080 restraints weight = 10336.897| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 1.52 r_work: 0.4126 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4006 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10615 Z= 0.107 Angle : 0.501 8.704 14460 Z= 0.259 Chirality : 0.038 0.128 1725 Planarity : 0.004 0.042 1745 Dihedral : 5.321 59.320 1428 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 3.67 % Allowed : 18.44 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.23), residues: 1350 helix: 1.71 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : 0.57 (0.44), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 186 TYR 0.018 0.001 TYR E 25 PHE 0.018 0.001 PHE D 49 TRP 0.022 0.001 TRP E 180 HIS 0.008 0.001 HIS E 159 Details of bonding type rmsd covalent geometry : bond 0.00227 (10615) covalent geometry : angle 0.50064 (14460) hydrogen bonds : bond 0.03531 ( 829) hydrogen bonds : angle 4.46742 ( 2421) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: B 32 LEU cc_start: 0.7752 (mm) cc_final: 0.7533 (tp) REVERT: B 45 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7684 (tp) REVERT: B 79 LEU cc_start: 0.7842 (mm) cc_final: 0.7371 (tp) REVERT: C 17 LYS cc_start: 0.7284 (tptt) cc_final: 0.6861 (mmtt) REVERT: C 202 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7084 (t80) REVERT: D 26 LYS cc_start: 0.7504 (mttt) cc_final: 0.6561 (mptt) REVERT: E 33 LYS cc_start: 0.7648 (tttm) cc_final: 0.7439 (mtpm) REVERT: E 49 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7779 (t80) REVERT: E 202 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6766 (t80) outliers start: 40 outliers final: 17 residues processed: 218 average time/residue: 0.3635 time to fit residues: 87.0468 Evaluate side-chains 203 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 47 ILE Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 246 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 73 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 ASN E 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.199355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.183925 restraints weight = 10363.999| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 1.55 r_work: 0.4135 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10615 Z= 0.106 Angle : 0.497 9.454 14460 Z= 0.255 Chirality : 0.038 0.146 1725 Planarity : 0.004 0.044 1745 Dihedral : 5.230 59.438 1428 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 4.31 % Allowed : 18.35 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.23), residues: 1350 helix: 1.77 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : 0.83 (0.44), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 186 TYR 0.015 0.001 TYR E 25 PHE 0.032 0.001 PHE A 75 TRP 0.020 0.001 TRP E 180 HIS 0.006 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00233 (10615) covalent geometry : angle 0.49697 (14460) hydrogen bonds : bond 0.03322 ( 829) hydrogen bonds : angle 4.37045 ( 2421) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 53 ILE cc_start: 0.7785 (OUTLIER) cc_final: 0.7299 (mp) REVERT: B 32 LEU cc_start: 0.7778 (mm) cc_final: 0.7541 (tp) REVERT: B 45 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7689 (tp) REVERT: B 79 LEU cc_start: 0.7872 (mm) cc_final: 0.7390 (tp) REVERT: B 186 ARG cc_start: 0.8323 (mmt90) cc_final: 0.8004 (mmm160) REVERT: C 17 LYS cc_start: 0.7322 (tptt) cc_final: 0.6873 (mmtt) REVERT: C 151 GLN cc_start: 0.6689 (OUTLIER) cc_final: 0.6419 (mt0) REVERT: C 202 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7293 (t80) REVERT: D 26 LYS cc_start: 0.7496 (mttt) cc_final: 0.6545 (mptt) REVERT: D 208 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7095 (mm-30) REVERT: D 270 VAL cc_start: 0.7054 (t) cc_final: 0.6837 (p) REVERT: E 96 ILE cc_start: 0.7642 (pt) cc_final: 0.7414 (pt) REVERT: E 202 PHE cc_start: 0.7274 (OUTLIER) cc_final: 0.6826 (t80) outliers start: 47 outliers final: 19 residues processed: 230 average time/residue: 0.3795 time to fit residues: 95.8381 Evaluate side-chains 214 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 276 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 31 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 40 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 73 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 121 ASN E 244 HIS E 262 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.198066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.182924 restraints weight = 10383.788| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 1.51 r_work: 0.4124 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4005 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10615 Z= 0.118 Angle : 0.529 12.025 14460 Z= 0.266 Chirality : 0.039 0.158 1725 Planarity : 0.004 0.044 1745 Dihedral : 5.227 59.559 1428 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 3.67 % Allowed : 19.36 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.23), residues: 1350 helix: 1.79 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : 0.61 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 186 TYR 0.017 0.001 TYR E 25 PHE 0.023 0.001 PHE A 75 TRP 0.019 0.001 TRP E 180 HIS 0.005 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00271 (10615) covalent geometry : angle 0.52878 (14460) hydrogen bonds : bond 0.03392 ( 829) hydrogen bonds : angle 4.38239 ( 2421) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.230 Fit side-chains revert: symmetry clash REVERT: B 32 LEU cc_start: 0.7811 (mm) cc_final: 0.7581 (tp) REVERT: B 45 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7699 (tp) REVERT: B 79 LEU cc_start: 0.7944 (mm) cc_final: 0.7461 (tp) REVERT: B 155 HIS cc_start: 0.6626 (OUTLIER) cc_final: 0.5641 (p-80) REVERT: B 186 ARG cc_start: 0.8375 (mmt90) cc_final: 0.7993 (mmm160) REVERT: C 17 LYS cc_start: 0.7333 (tptt) cc_final: 0.6864 (mmtt) REVERT: C 151 GLN cc_start: 0.6780 (OUTLIER) cc_final: 0.6428 (mt0) REVERT: C 202 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7266 (t80) REVERT: D 26 LYS cc_start: 0.7520 (mttt) cc_final: 0.6579 (mptt) REVERT: D 193 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6816 (t80) REVERT: D 208 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7117 (mm-30) REVERT: D 248 MET cc_start: 0.7946 (tpp) cc_final: 0.7243 (ttp) REVERT: D 270 VAL cc_start: 0.7019 (t) cc_final: 0.6787 (p) REVERT: E 96 ILE cc_start: 0.7645 (pt) cc_final: 0.7410 (pt) REVERT: E 202 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6784 (t80) outliers start: 40 outliers final: 20 residues processed: 220 average time/residue: 0.3489 time to fit residues: 84.1614 Evaluate side-chains 215 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 276 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 28 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 102 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN E 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.197277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.181945 restraints weight = 10554.958| |-----------------------------------------------------------------------------| r_work (start): 0.4196 rms_B_bonded: 1.53 r_work: 0.4111 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3991 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10615 Z= 0.122 Angle : 0.533 10.874 14460 Z= 0.270 Chirality : 0.039 0.151 1725 Planarity : 0.004 0.044 1745 Dihedral : 5.194 58.315 1427 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 4.31 % Allowed : 20.09 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.23), residues: 1350 helix: 1.79 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : 0.62 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 186 TYR 0.017 0.001 TYR E 25 PHE 0.023 0.002 PHE D 49 TRP 0.022 0.001 TRP E 180 HIS 0.007 0.001 HIS D 30 Details of bonding type rmsd covalent geometry : bond 0.00285 (10615) covalent geometry : angle 0.53256 (14460) hydrogen bonds : bond 0.03435 ( 829) hydrogen bonds : angle 4.38575 ( 2421) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: B 32 LEU cc_start: 0.7823 (mm) cc_final: 0.7585 (tp) REVERT: B 45 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7696 (tp) REVERT: B 79 LEU cc_start: 0.7977 (mm) cc_final: 0.7483 (tp) REVERT: B 155 HIS cc_start: 0.6638 (OUTLIER) cc_final: 0.5583 (p-80) REVERT: B 186 ARG cc_start: 0.8397 (mmt90) cc_final: 0.8017 (mmm160) REVERT: B 189 MET cc_start: 0.8469 (mtm) cc_final: 0.8230 (mtp) REVERT: C 17 LYS cc_start: 0.7358 (tptt) cc_final: 0.6886 (mmtm) REVERT: C 202 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.7281 (t80) REVERT: D 26 LYS cc_start: 0.7521 (mttt) cc_final: 0.6576 (mptt) REVERT: D 66 MET cc_start: 0.8819 (mmp) cc_final: 0.8602 (mmp) REVERT: D 193 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.6450 (t80) REVERT: D 208 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7090 (mm-30) REVERT: D 270 VAL cc_start: 0.7014 (t) cc_final: 0.6798 (p) REVERT: E 96 ILE cc_start: 0.7641 (pt) cc_final: 0.7377 (pt) REVERT: E 172 ASN cc_start: 0.7540 (OUTLIER) cc_final: 0.7289 (t0) REVERT: E 202 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6738 (t80) outliers start: 47 outliers final: 23 residues processed: 225 average time/residue: 0.3569 time to fit residues: 88.3006 Evaluate side-chains 219 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 172 ASN Chi-restraints excluded: chain E residue 173 LEU Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 276 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 82 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 8 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN E 172 ASN E 244 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.195523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.180264 restraints weight = 10386.968| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 1.51 r_work: 0.4096 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3976 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10615 Z= 0.143 Angle : 0.560 11.622 14460 Z= 0.285 Chirality : 0.040 0.161 1725 Planarity : 0.004 0.043 1745 Dihedral : 5.234 57.810 1427 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 4.40 % Allowed : 21.10 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.23), residues: 1350 helix: 1.71 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : 0.72 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 186 TYR 0.018 0.001 TYR E 25 PHE 0.030 0.002 PHE D 49 TRP 0.022 0.001 TRP E 180 HIS 0.006 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00339 (10615) covalent geometry : angle 0.55975 (14460) hydrogen bonds : bond 0.03640 ( 829) hydrogen bonds : angle 4.43827 ( 2421) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 198 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: B 32 LEU cc_start: 0.7826 (mm) cc_final: 0.7595 (tp) REVERT: B 45 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7710 (tp) REVERT: B 79 LEU cc_start: 0.8001 (mm) cc_final: 0.7492 (tp) REVERT: B 155 HIS cc_start: 0.6641 (OUTLIER) cc_final: 0.5608 (p-80) REVERT: B 189 MET cc_start: 0.8487 (mtm) cc_final: 0.8275 (mtp) REVERT: C 17 LYS cc_start: 0.7358 (tptt) cc_final: 0.6910 (mmtm) REVERT: C 76 SER cc_start: 0.8720 (t) cc_final: 0.8457 (p) REVERT: C 151 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6728 (mp10) REVERT: C 202 PHE cc_start: 0.8185 (OUTLIER) cc_final: 0.7280 (t80) REVERT: D 26 LYS cc_start: 0.7536 (mttt) cc_final: 0.6594 (mptt) REVERT: D 66 MET cc_start: 0.8804 (mmp) cc_final: 0.8596 (mmp) REVERT: D 193 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6354 (t80) REVERT: D 208 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7016 (mm-30) REVERT: D 270 VAL cc_start: 0.7042 (t) cc_final: 0.6801 (p) REVERT: E 49 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7705 (t80) REVERT: E 96 ILE cc_start: 0.7658 (pt) cc_final: 0.7399 (pt) REVERT: E 172 ASN cc_start: 0.7618 (OUTLIER) cc_final: 0.7310 (t0) REVERT: E 202 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6682 (t80) outliers start: 48 outliers final: 21 residues processed: 222 average time/residue: 0.3838 time to fit residues: 93.4455 Evaluate side-chains 223 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 172 ASN Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 276 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 19 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN E 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.195930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.180670 restraints weight = 10502.976| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 1.52 r_work: 0.4101 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3982 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10615 Z= 0.134 Angle : 0.557 11.361 14460 Z= 0.283 Chirality : 0.040 0.165 1725 Planarity : 0.004 0.043 1745 Dihedral : 5.247 56.983 1427 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Rotamer: Outliers : 4.50 % Allowed : 21.19 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.26 (0.23), residues: 1350 helix: 1.72 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : 0.61 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 186 TYR 0.019 0.001 TYR E 25 PHE 0.033 0.002 PHE D 49 TRP 0.026 0.001 TRP E 180 HIS 0.006 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00316 (10615) covalent geometry : angle 0.55660 (14460) hydrogen bonds : bond 0.03571 ( 829) hydrogen bonds : angle 4.42879 ( 2421) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 193 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: B 32 LEU cc_start: 0.7818 (mm) cc_final: 0.7591 (tp) REVERT: B 45 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7706 (tp) REVERT: B 79 LEU cc_start: 0.7985 (mm) cc_final: 0.7475 (tp) REVERT: B 155 HIS cc_start: 0.6646 (OUTLIER) cc_final: 0.5633 (p-80) REVERT: B 189 MET cc_start: 0.8498 (mtm) cc_final: 0.8289 (mtp) REVERT: C 17 LYS cc_start: 0.7345 (tptt) cc_final: 0.6871 (mmtm) REVERT: C 76 SER cc_start: 0.8728 (t) cc_final: 0.8456 (p) REVERT: C 151 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6206 (mt0) REVERT: C 202 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7270 (t80) REVERT: D 26 LYS cc_start: 0.7534 (mttt) cc_final: 0.6600 (mptt) REVERT: D 100 LYS cc_start: 0.7663 (tppt) cc_final: 0.6601 (ttpt) REVERT: D 193 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6248 (t80) REVERT: D 194 ILE cc_start: 0.8021 (tp) cc_final: 0.7469 (tp) REVERT: D 208 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7008 (mm-30) REVERT: D 270 VAL cc_start: 0.7033 (t) cc_final: 0.6800 (p) REVERT: E 49 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7695 (t80) REVERT: E 96 ILE cc_start: 0.7639 (pt) cc_final: 0.7387 (pt) REVERT: E 172 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7255 (t0) REVERT: E 195 MET cc_start: 0.7584 (mtp) cc_final: 0.7281 (mtt) REVERT: E 202 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6674 (t80) REVERT: E 242 PHE cc_start: 0.7280 (m-80) cc_final: 0.7060 (m-80) outliers start: 49 outliers final: 22 residues processed: 222 average time/residue: 0.3602 time to fit residues: 87.9505 Evaluate side-chains 219 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 189 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 151 GLN Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 172 ASN Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 276 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 72 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.0870 chunk 52 optimal weight: 5.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN E 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.194246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.179080 restraints weight = 10448.559| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 1.51 r_work: 0.4083 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3966 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10615 Z= 0.157 Angle : 0.585 12.543 14460 Z= 0.297 Chirality : 0.041 0.174 1725 Planarity : 0.004 0.043 1745 Dihedral : 5.319 57.347 1427 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.94 % Allowed : 21.74 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.12 (0.23), residues: 1350 helix: 1.61 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : 0.68 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 186 TYR 0.020 0.001 TYR E 25 PHE 0.041 0.002 PHE D 49 TRP 0.033 0.001 TRP E 180 HIS 0.006 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00376 (10615) covalent geometry : angle 0.58528 (14460) hydrogen bonds : bond 0.03772 ( 829) hydrogen bonds : angle 4.49795 ( 2421) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: B 32 LEU cc_start: 0.7855 (mm) cc_final: 0.7629 (tp) REVERT: B 45 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7715 (tp) REVERT: B 79 LEU cc_start: 0.8002 (mm) cc_final: 0.7473 (tp) REVERT: B 155 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.5548 (p-80) REVERT: B 189 MET cc_start: 0.8489 (mtm) cc_final: 0.8258 (mtt) REVERT: C 17 LYS cc_start: 0.7351 (tptt) cc_final: 0.6872 (mmtm) REVERT: C 76 SER cc_start: 0.8740 (t) cc_final: 0.8471 (p) REVERT: C 202 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7319 (t80) REVERT: D 26 LYS cc_start: 0.7541 (mttt) cc_final: 0.6603 (mptt) REVERT: D 193 PHE cc_start: 0.6853 (OUTLIER) cc_final: 0.6221 (t80) REVERT: D 194 ILE cc_start: 0.8019 (tp) cc_final: 0.7474 (tp) REVERT: E 49 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7645 (t80) REVERT: E 96 ILE cc_start: 0.7665 (pt) cc_final: 0.7415 (pt) REVERT: E 172 ASN cc_start: 0.7573 (OUTLIER) cc_final: 0.7304 (t0) REVERT: E 195 MET cc_start: 0.7590 (mtp) cc_final: 0.7291 (mtt) REVERT: E 202 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6607 (t80) outliers start: 43 outliers final: 23 residues processed: 224 average time/residue: 0.3957 time to fit residues: 97.2517 Evaluate side-chains 220 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 172 ASN Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 26 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.194113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.178983 restraints weight = 10384.715| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 1.50 r_work: 0.4080 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3962 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10615 Z= 0.153 Angle : 0.599 12.072 14460 Z= 0.303 Chirality : 0.041 0.185 1725 Planarity : 0.004 0.043 1745 Dihedral : 5.366 57.323 1427 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 3.30 % Allowed : 22.02 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.09 (0.23), residues: 1350 helix: 1.62 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : 0.51 (0.45), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 186 TYR 0.020 0.001 TYR E 25 PHE 0.043 0.002 PHE D 49 TRP 0.040 0.001 TRP E 180 HIS 0.006 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00364 (10615) covalent geometry : angle 0.59930 (14460) hydrogen bonds : bond 0.03749 ( 829) hydrogen bonds : angle 4.51553 ( 2421) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2700 Ramachandran restraints generated. 1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: B 32 LEU cc_start: 0.7849 (mm) cc_final: 0.7627 (tp) REVERT: B 45 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7718 (tp) REVERT: B 79 LEU cc_start: 0.7988 (mm) cc_final: 0.7459 (tp) REVERT: B 155 HIS cc_start: 0.6615 (OUTLIER) cc_final: 0.5561 (p-80) REVERT: C 17 LYS cc_start: 0.7335 (tptt) cc_final: 0.6859 (mmtm) REVERT: C 76 SER cc_start: 0.8703 (t) cc_final: 0.8429 (p) REVERT: C 202 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7313 (t80) REVERT: D 26 LYS cc_start: 0.7539 (mttt) cc_final: 0.6594 (mptt) REVERT: D 100 LYS cc_start: 0.7663 (tppt) cc_final: 0.6591 (ttpt) REVERT: D 193 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.6081 (t80) REVERT: D 194 ILE cc_start: 0.7979 (tp) cc_final: 0.7431 (tp) REVERT: E 49 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7663 (t80) REVERT: E 96 ILE cc_start: 0.7641 (pt) cc_final: 0.7392 (pt) REVERT: E 195 MET cc_start: 0.7575 (mtp) cc_final: 0.7270 (mtt) REVERT: E 202 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.6550 (t80) outliers start: 36 outliers final: 23 residues processed: 217 average time/residue: 0.3685 time to fit residues: 87.5169 Evaluate side-chains 220 residues out of total 1090 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 202 PHE Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 184 SER Chi-restraints excluded: chain C residue 202 PHE Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 104 ARG Chi-restraints excluded: chain D residue 155 HIS Chi-restraints excluded: chain D residue 193 PHE Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 246 THR Chi-restraints excluded: chain E residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 172 ASN E 244 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.192126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.176765 restraints weight = 10536.502| |-----------------------------------------------------------------------------| r_work (start): 0.4139 rms_B_bonded: 1.53 r_work: 0.4053 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3933 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 10615 Z= 0.176 Angle : 0.634 12.952 14460 Z= 0.319 Chirality : 0.043 0.206 1725 Planarity : 0.004 0.042 1745 Dihedral : 5.479 57.820 1427 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.58 % Allowed : 22.02 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.23), residues: 1350 helix: 1.50 (0.15), residues: 1130 sheet: None (None), residues: 0 loop : 0.55 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 186 TYR 0.021 0.001 TYR E 25 PHE 0.041 0.002 PHE D 49 TRP 0.048 0.001 TRP E 180 HIS 0.007 0.001 HIS D 155 Details of bonding type rmsd covalent geometry : bond 0.00427 (10615) covalent geometry : angle 0.63351 (14460) hydrogen bonds : bond 0.04000 ( 829) hydrogen bonds : angle 4.62183 ( 2421) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2782.76 seconds wall clock time: 48 minutes 17.22 seconds (2897.22 seconds total)