Starting phenix.real_space_refine on Sun Aug 24 21:42:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9om6_70608/08_2025/9om6_70608.cif Found real_map, /net/cci-nas-00/data/ceres_data/9om6_70608/08_2025/9om6_70608.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9om6_70608/08_2025/9om6_70608.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9om6_70608/08_2025/9om6_70608.map" model { file = "/net/cci-nas-00/data/ceres_data/9om6_70608/08_2025/9om6_70608.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9om6_70608/08_2025/9om6_70608.cif" } resolution = 4.14 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= 0.002 sd= 0.039 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: 5 Type Number sf(0) Gaussians S 90 5.16 5 C 7068 2.51 5 N 1888 2.21 5 O 2284 1.98 5 H 11063 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22393 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 1111 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "B" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1100 Classifications: {'peptide': 68} Link IDs: {'TRANS': 67} Chain: "C" Number of atoms: 1099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1099 Classifications: {'peptide': 70} Link IDs: {'TRANS': 69} Chain: "D" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1062 Classifications: {'peptide': 67} Link IDs: {'TRANS': 66} Chain: "E" Number of atoms: 4503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 4503 Classifications: {'peptide': 289} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 285} Chain: "F" Number of atoms: 4485 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 287, 4467 Classifications: {'peptide': 287} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 283} Conformer: "B" Number of residues, atoms: 287, 4467 Classifications: {'peptide': 287} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 283} bond proxies already assigned to first conformer: 4488 Chain: "G" Number of atoms: 4503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 4503 Classifications: {'peptide': 289} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 285} Chain: "H" Number of atoms: 4467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4467 Classifications: {'peptide': 287} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN F 179 " occ=0.71 ... (32 atoms not shown) pdb="HE22BGLN F 179 " occ=0.29 Time building chain proxies: 4.46, per 1000 atoms: 0.20 Number of scatterers: 22393 At special positions: 0 Unit cell: (121.656, 122.752, 110.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 O 2284 8.00 N 1888 7.00 C 7068 6.00 H 11063 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 656.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2744 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 0 sheets defined 92.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 191 through 258 removed outlier: 4.209A pdb=" N MET A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 258 Processing helix chain 'C' and resid 18 through 86 removed outlier: 4.004A pdb=" N ASP C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU C 52 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 53 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 83 removed outlier: 3.686A pdb=" N ARG D 45 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU D 58 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 83 " --> pdb=" O THR D 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 29 Processing helix chain 'E' and resid 33 through 55 removed outlier: 4.263A pdb=" N LYS E 37 " --> pdb=" O GLY E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 73 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 78 through 94 removed outlier: 4.386A pdb=" N LYS E 94 " --> pdb=" O ASN E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 removed outlier: 3.723A pdb=" N ASN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 135 removed outlier: 4.055A pdb=" N ALA E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 155 Processing helix chain 'E' and resid 157 through 176 removed outlier: 3.679A pdb=" N ALA E 161 " --> pdb=" O SER E 157 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN E 174 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU E 175 " --> pdb=" O TYR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 194 removed outlier: 4.444A pdb=" N ALA E 181 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA E 192 " --> pdb=" O VAL E 188 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 200 Processing helix chain 'E' and resid 201 through 217 removed outlier: 4.153A pdb=" N TYR E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE E 216 " --> pdb=" O CYS E 212 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP E 217 " --> pdb=" O HIS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 232 Processing helix chain 'E' and resid 232 through 237 removed outlier: 4.200A pdb=" N SER E 236 " --> pdb=" O PHE E 232 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP E 237 " --> pdb=" O PRO E 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 232 through 237' Processing helix chain 'E' and resid 239 through 254 removed outlier: 3.884A pdb=" N LEU E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS E 245 " --> pdb=" O CYS E 241 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 268 removed outlier: 3.549A pdb=" N TYR E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 286 removed outlier: 3.520A pdb=" N THR E 277 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR E 286 " --> pdb=" O ARG E 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 32 Processing helix chain 'F' and resid 35 through 55 Processing helix chain 'F' and resid 57 through 75 Processing helix chain 'F' and resid 78 through 94 removed outlier: 4.409A pdb=" N LYS F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 115 removed outlier: 3.712A pdb=" N ASN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 135 Processing helix chain 'F' and resid 137 through 155 removed outlier: 3.779A pdb=" N ALA F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 175 removed outlier: 3.505A pdb=" N ASN F 162 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS F 164 " --> pdb=" O SER F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 192 Processing helix chain 'F' and resid 197 through 200 removed outlier: 3.908A pdb=" N TYR F 200 " --> pdb=" O LEU F 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 197 through 200' Processing helix chain 'F' and resid 201 through 214 removed outlier: 4.094A pdb=" N TYR F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE F 206 " --> pdb=" O ALA F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 232 Processing helix chain 'F' and resid 233 through 237 removed outlier: 3.992A pdb=" N SER F 236 " --> pdb=" O PRO F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 253 removed outlier: 4.228A pdb=" N LYS F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 270 Processing helix chain 'F' and resid 273 through 285 Processing helix chain 'G' and resid 1 through 31 removed outlier: 4.036A pdb=" N SER G 29 " --> pdb=" O GLN G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 55 Processing helix chain 'G' and resid 58 through 74 Processing helix chain 'G' and resid 78 through 93 Processing helix chain 'G' and resid 96 through 115 Processing helix chain 'G' and resid 117 through 134 removed outlier: 3.743A pdb=" N GLU G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 155 removed outlier: 3.674A pdb=" N GLU G 155 " --> pdb=" O TYR G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 175 Processing helix chain 'G' and resid 178 through 190 Processing helix chain 'G' and resid 202 through 217 removed outlier: 3.606A pdb=" N PHE G 206 " --> pdb=" O ALA G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 232 Processing helix chain 'G' and resid 233 through 237 Processing helix chain 'G' and resid 238 through 253 removed outlier: 3.844A pdb=" N GLU G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 270 removed outlier: 3.568A pdb=" N TYR G 259 " --> pdb=" O ASN G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 286 removed outlier: 3.570A pdb=" N MET G 279 " --> pdb=" O TRP G 275 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR G 286 " --> pdb=" O ARG G 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 26 Processing helix chain 'H' and resid 27 through 30 Processing helix chain 'H' and resid 34 through 56 Processing helix chain 'H' and resid 57 through 73 Processing helix chain 'H' and resid 77 through 94 removed outlier: 4.284A pdb=" N LYS H 94 " --> pdb=" O ASN H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 115 removed outlier: 3.614A pdb=" N ILE H 101 " --> pdb=" O PRO H 97 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN H 102 " --> pdb=" O GLN H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 135 removed outlier: 3.582A pdb=" N ALA H 120 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 155 removed outlier: 3.847A pdb=" N GLU H 155 " --> pdb=" O TYR H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 175 removed outlier: 3.594A pdb=" N ALA H 161 " --> pdb=" O SER H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 190 removed outlier: 3.715A pdb=" N ALA H 181 " --> pdb=" O GLN H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 217 removed outlier: 3.939A pdb=" N TYR H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE H 216 " --> pdb=" O CYS H 212 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP H 217 " --> pdb=" O HIS H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 232 removed outlier: 3.809A pdb=" N LYS H 222 " --> pdb=" O MET H 218 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU H 223 " --> pdb=" O LEU H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 236 removed outlier: 4.210A pdb=" N SER H 236 " --> pdb=" O PRO H 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 233 through 236' Processing helix chain 'H' and resid 238 through 252 removed outlier: 3.655A pdb=" N LYS H 242 " --> pdb=" O SER H 238 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU H 252 " --> pdb=" O LEU H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 268 removed outlier: 3.916A pdb=" N TYR H 259 " --> pdb=" O ASN H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 285 removed outlier: 3.598A pdb=" N LYS H 285 " --> pdb=" O LEU H 281 " (cutoff:3.500A) 978 hydrogen bonds defined for protein. 2919 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: 4.47 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11032 1.03 - 1.23: 48 1.23 - 1.42: 4781 1.42 - 1.62: 6493 1.62 - 1.81: 148 Bond restraints: 22502 Sorted by residual: bond pdb=" SG CYS E 241 " pdb=" HG CYS E 241 " ideal model delta sigma weight residual 1.200 0.977 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C ASP D 51 " pdb=" N GLU D 52 " ideal model delta sigma weight residual 1.335 1.252 0.083 1.31e-02 5.83e+03 3.99e+01 bond pdb=" C MET G 193 " pdb=" N ASP G 194 " ideal model delta sigma weight residual 1.331 1.243 0.089 1.44e-02 4.82e+03 3.79e+01 bond pdb=" C ASN E 102 " pdb=" N CYS E 103 " ideal model delta sigma weight residual 1.335 1.414 -0.079 1.36e-02 5.41e+03 3.37e+01 bond pdb=" C ASP E 204 " pdb=" N TYR E 205 " ideal model delta sigma weight residual 1.334 1.397 -0.063 1.27e-02 6.20e+03 2.46e+01 ... (remaining 22497 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 40397 2.50 - 4.99: 182 4.99 - 7.49: 8 7.49 - 9.99: 2 9.99 - 12.48: 1 Bond angle restraints: 40590 Sorted by residual: angle pdb=" N GLU E 240 " pdb=" CA GLU E 240 " pdb=" C GLU E 240 " ideal model delta sigma weight residual 111.33 105.52 5.81 1.21e+00 6.83e-01 2.30e+01 angle pdb=" CA LYS F 20 " pdb=" C LYS F 20 " pdb=" O LYS F 20 " ideal model delta sigma weight residual 121.00 116.04 4.96 1.05e+00 9.07e-01 2.23e+01 angle pdb=" CA VAL D 48 " pdb=" C VAL D 48 " pdb=" O VAL D 48 " ideal model delta sigma weight residual 120.95 116.28 4.67 1.04e+00 9.25e-01 2.01e+01 angle pdb=" CA ASP E 194 " pdb=" C ASP E 194 " pdb=" O ASP E 194 " ideal model delta sigma weight residual 120.80 116.36 4.44 1.05e+00 9.07e-01 1.79e+01 angle pdb=" N LEU G 197 " pdb=" CA LEU G 197 " pdb=" C LEU G 197 " ideal model delta sigma weight residual 113.43 108.15 5.28 1.26e+00 6.30e-01 1.75e+01 ... (remaining 40585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 9727 17.88 - 35.77: 606 35.77 - 53.65: 175 53.65 - 71.53: 41 71.53 - 89.42: 2 Dihedral angle restraints: 10551 sinusoidal: 5652 harmonic: 4899 Sorted by residual: dihedral pdb=" CA GLU H 176 " pdb=" C GLU H 176 " pdb=" N GLN H 177 " pdb=" CA GLN H 177 " ideal model delta harmonic sigma weight residual 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLN H 177 " pdb=" C GLN H 177 " pdb=" N TYR H 178 " pdb=" CA TYR H 178 " ideal model delta harmonic sigma weight residual 180.00 -161.55 -18.45 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ALA H 10 " pdb=" C ALA H 10 " pdb=" N MET H 11 " pdb=" CA MET H 11 " ideal model delta harmonic sigma weight residual 180.00 161.98 18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 10548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1303 0.033 - 0.067: 272 0.067 - 0.100: 81 0.100 - 0.134: 15 0.134 - 0.167: 5 Chirality restraints: 1676 Sorted by residual: chirality pdb=" CA GLU E 240 " pdb=" N GLU E 240 " pdb=" C GLU E 240 " pdb=" CB GLU E 240 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CA TYR E 200 " pdb=" N TYR E 200 " pdb=" C TYR E 200 " pdb=" CB TYR E 200 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA LEU G 198 " pdb=" N LEU G 198 " pdb=" C LEU G 198 " pdb=" CB LEU G 198 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 1673 not shown) Planarity restraints: 3396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO E 233 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C PRO E 233 " -0.055 2.00e-02 2.50e+03 pdb=" O PRO E 233 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA E 234 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 191 " 0.016 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" N ALA E 192 " -0.050 2.00e-02 2.50e+03 pdb=" CA ALA E 192 " 0.013 2.00e-02 2.50e+03 pdb=" H ALA E 192 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 200 " 0.014 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" N SER E 201 " -0.044 2.00e-02 2.50e+03 pdb=" CA SER E 201 " 0.011 2.00e-02 2.50e+03 pdb=" H SER E 201 " 0.019 2.00e-02 2.50e+03 ... (remaining 3393 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 256 2.04 - 2.68: 34560 2.68 - 3.32: 64743 3.32 - 3.96: 75056 3.96 - 4.60: 118419 Nonbonded interactions: 293034 Sorted by model distance: nonbonded pdb=" HD3 ARG C 45 " pdb=" HB2 PRO G 196 " model vdw 1.403 2.440 nonbonded pdb="HG23 VAL A 244 " pdb=" HE2 MET D 71 " model vdw 1.451 2.440 nonbonded pdb=" OE1 GLU C 52 " pdb=" H GLU C 52 " model vdw 1.571 2.450 nonbonded pdb=" OE1 GLU G 99 " pdb=" H GLU G 99 " model vdw 1.583 2.450 nonbonded pdb=" OE1 GLU F 99 " pdb=" H GLU F 99 " model vdw 1.595 2.450 ... (remaining 293029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 191 through 258) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 17 through 83) selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 0 through 178 or resid 181 through 286)) selection = (chain 'F' and (resid 0 through 178 or resid 181 through 286)) selection = (chain 'G' and (resid 0 through 178 or resid 181 through 286)) selection = (chain 'H' and (resid 0 through 178 or resid 181 through 286)) } 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=0.29 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.540 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: 0.090 Extract box with map and model: 0.340 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 20.050 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.004 0.089 11439 Z= 0.258 Angle : 0.602 7.909 15353 Z= 0.391 Chirality : 0.033 0.167 1676 Planarity : 0.004 0.088 1988 Dihedral : 13.215 89.416 4292 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.40 % Favored : 96.38 % Rotamer: Outliers : 1.43 % Allowed : 4.88 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.22), residues: 1413 helix: 1.63 (0.15), residues: 1207 sheet: None (None), residues: 0 loop : -2.70 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 45 TYR 0.021 0.001 TYR E 200 PHE 0.012 0.001 PHE E 65 TRP 0.010 0.001 TRP H 275 HIS 0.005 0.001 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.00403 (11439) covalent geometry : angle 0.60194 (15353) hydrogen bonds : bond 0.10082 ( 978) hydrogen bonds : angle 5.50175 ( 2919) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 372 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.8708 (tp30) cc_final: 0.8301 (mm-30) REVERT: A 224 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8219 (tm-30) REVERT: A 234 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8654 (tm-30) REVERT: A 245 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8970 (tm-30) REVERT: B 239 HIS cc_start: 0.8482 (t70) cc_final: 0.8228 (t70) REVERT: B 253 LYS cc_start: 0.8785 (mmpt) cc_final: 0.8251 (tptm) REVERT: C 30 ARG cc_start: 0.8734 (tpp-160) cc_final: 0.8255 (tpp80) REVERT: C 31 ARG cc_start: 0.7767 (ptt180) cc_final: 0.6596 (mtt-85) REVERT: C 34 GLN cc_start: 0.8685 (pt0) cc_final: 0.8148 (pt0) REVERT: D 58 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7755 (tm-30) REVERT: D 62 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8543 (mm-30) REVERT: E 42 CYS cc_start: 0.9188 (m) cc_final: 0.8948 (t) REVERT: E 131 TYR cc_start: 0.7288 (t80) cc_final: 0.7077 (t80) REVERT: F 51 MET cc_start: 0.9080 (ppp) cc_final: 0.8855 (ppp) REVERT: F 87 ASP cc_start: 0.8737 (t0) cc_final: 0.8504 (t70) REVERT: F 129 GLU cc_start: 0.9195 (tp30) cc_final: 0.8738 (tp30) REVERT: F 132 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8834 (tm-30) REVERT: F 146 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7006 (tm-30) REVERT: F 150 ASP cc_start: 0.7756 (m-30) cc_final: 0.7337 (m-30) REVERT: F 265 GLU cc_start: 0.9153 (tt0) cc_final: 0.8942 (tm-30) REVERT: G 146 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8369 (tm-30) REVERT: G 228 TYR cc_start: 0.8751 (m-80) cc_final: 0.7848 (m-80) REVERT: H 146 GLU cc_start: 0.9388 (mm-30) cc_final: 0.8936 (mm-30) REVERT: H 200 TYR cc_start: 0.8769 (m-80) cc_final: 0.8285 (m-80) REVERT: H 241 CYS cc_start: 0.8971 (t) cc_final: 0.8579 (t) REVERT: H 249 GLU cc_start: 0.8959 (pt0) cc_final: 0.8562 (pt0) REVERT: H 259 TYR cc_start: 0.8879 (p90) cc_final: 0.8676 (p90) outliers start: 17 outliers final: 6 residues processed: 381 average time/residue: 0.2416 time to fit residues: 125.6260 Evaluate side-chains 312 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 306 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 HIS F 50 ASN H 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.102605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.076013 restraints weight = 127163.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080254 restraints weight = 55928.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.083102 restraints weight = 32836.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084983 restraints weight = 22841.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086191 restraints weight = 17865.207| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11439 Z= 0.181 Angle : 0.527 4.344 15353 Z= 0.319 Chirality : 0.031 0.120 1676 Planarity : 0.003 0.039 1988 Dihedral : 4.325 20.127 1528 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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 aren not related in a simple way. whole: 1.67 (0.22), residues: 1413 helix: 1.63 (0.14), residues: 1241 sheet: None (None), residues: 0 loop : -2.75 (0.45), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 19 TYR 0.016 0.001 TYR F 152 PHE 0.026 0.002 PHE E 52 TRP 0.010 0.001 TRP H 275 HIS 0.004 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00344 (11439) covalent geometry : angle 0.52702 (15353) hydrogen bonds : bond 0.05549 ( 978) hydrogen bonds : angle 5.02303 ( 2919) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 373 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8777 (mt) cc_final: 0.8504 (mt) REVERT: A 206 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7402 (tm-30) REVERT: A 224 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8561 (tm-30) REVERT: A 228 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8272 (mm-30) REVERT: A 234 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8849 (tm-30) REVERT: B 207 ASN cc_start: 0.9352 (m-40) cc_final: 0.9132 (m-40) REVERT: B 211 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8739 (mm-30) REVERT: B 250 ASP cc_start: 0.9253 (t0) cc_final: 0.8886 (t0) REVERT: B 253 LYS cc_start: 0.8888 (mmpt) cc_final: 0.8218 (tptt) REVERT: C 30 ARG cc_start: 0.8759 (tpp-160) cc_final: 0.8538 (tpp80) REVERT: C 31 ARG cc_start: 0.7967 (ptt180) cc_final: 0.6752 (mtt-85) REVERT: C 41 ASP cc_start: 0.8978 (m-30) cc_final: 0.8767 (m-30) REVERT: C 61 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8749 (tm-30) REVERT: D 58 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8267 (tm-30) REVERT: D 62 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8778 (mm-30) REVERT: E 1 MET cc_start: 0.7232 (ptp) cc_final: 0.6960 (ptp) REVERT: E 7 GLN cc_start: 0.8880 (tp-100) cc_final: 0.8501 (tp-100) REVERT: E 42 CYS cc_start: 0.9209 (m) cc_final: 0.8954 (t) REVERT: E 114 MET cc_start: 0.8996 (mmp) cc_final: 0.8775 (mmm) REVERT: E 191 SER cc_start: 0.9287 (t) cc_final: 0.9076 (m) REVERT: F 87 ASP cc_start: 0.8887 (t0) cc_final: 0.8641 (t70) REVERT: F 129 GLU cc_start: 0.9293 (tp30) cc_final: 0.8838 (tp30) REVERT: F 132 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8762 (tm-30) REVERT: F 146 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7097 (tm-30) REVERT: G 9 GLU cc_start: 0.9109 (pt0) cc_final: 0.8885 (pt0) REVERT: G 129 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8940 (tm-30) REVERT: G 146 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8482 (tm-30) REVERT: G 183 ASP cc_start: 0.9185 (t0) cc_final: 0.8919 (t70) REVERT: H 146 GLU cc_start: 0.9429 (mm-30) cc_final: 0.8956 (mm-30) REVERT: H 241 CYS cc_start: 0.8961 (t) cc_final: 0.8516 (t) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 0.2259 time to fit residues: 117.5458 Evaluate side-chains 321 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 66 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 chunk 120 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 ASN H 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.104818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.077766 restraints weight = 131445.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.082196 restraints weight = 56055.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085165 restraints weight = 32358.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.087121 restraints weight = 22264.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.088379 restraints weight = 17268.981| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11439 Z= 0.131 Angle : 0.480 5.171 15353 Z= 0.281 Chirality : 0.030 0.110 1676 Planarity : 0.003 0.038 1988 Dihedral : 4.117 18.354 1528 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % 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 aren not related in a simple way. whole: 2.28 (0.22), residues: 1413 helix: 2.04 (0.14), residues: 1242 sheet: None (None), residues: 0 loop : -2.62 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 19 TYR 0.034 0.001 TYR B 235 PHE 0.017 0.001 PHE E 52 TRP 0.011 0.001 TRP H 275 HIS 0.006 0.001 HIS F 124 Details of bonding type rmsd covalent geometry : bond 0.00250 (11439) covalent geometry : angle 0.48029 (15353) hydrogen bonds : bond 0.05208 ( 978) hydrogen bonds : angle 4.57938 ( 2919) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.9274 (mm) cc_final: 0.9066 (mm) REVERT: A 205 LEU cc_start: 0.8774 (mt) cc_final: 0.8515 (mt) REVERT: A 206 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7313 (tm-30) REVERT: A 211 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8722 (mm-30) REVERT: A 224 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8494 (tm-30) REVERT: A 228 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8270 (mm-30) REVERT: A 234 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8837 (tm-30) REVERT: A 245 GLU cc_start: 0.9336 (tm-30) cc_final: 0.9087 (tm-30) REVERT: B 239 HIS cc_start: 0.8652 (t70) cc_final: 0.8353 (t70) REVERT: B 253 LYS cc_start: 0.8938 (mmpt) cc_final: 0.8253 (tptt) REVERT: C 30 ARG cc_start: 0.8711 (tpp-160) cc_final: 0.8456 (tpp80) REVERT: C 31 ARG cc_start: 0.7894 (ptt180) cc_final: 0.6738 (mtt-85) REVERT: C 38 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8739 (mm-30) REVERT: C 41 ASP cc_start: 0.9022 (m-30) cc_final: 0.8777 (m-30) REVERT: C 61 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8718 (tm-30) REVERT: D 58 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8187 (tm-30) REVERT: D 62 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8741 (mm-30) REVERT: E 7 GLN cc_start: 0.8870 (tp-100) cc_final: 0.8581 (tp-100) REVERT: E 42 CYS cc_start: 0.9204 (m) cc_final: 0.8891 (t) REVERT: E 191 SER cc_start: 0.9237 (t) cc_final: 0.9026 (m) REVERT: E 245 LYS cc_start: 0.9037 (mttt) cc_final: 0.8765 (ptpt) REVERT: F 51 MET cc_start: 0.9035 (ppp) cc_final: 0.8795 (ppp) REVERT: F 129 GLU cc_start: 0.9223 (tp30) cc_final: 0.8778 (tp30) REVERT: F 132 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8795 (tm-30) REVERT: F 146 GLU cc_start: 0.7821 (tm-30) cc_final: 0.6981 (tm-30) REVERT: F 150 ASP cc_start: 0.7924 (m-30) cc_final: 0.7384 (m-30) REVERT: G 146 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8449 (tm-30) REVERT: G 183 ASP cc_start: 0.9112 (t0) cc_final: 0.8857 (t70) REVERT: H 146 GLU cc_start: 0.9408 (mm-30) cc_final: 0.8913 (mm-30) REVERT: H 241 CYS cc_start: 0.8939 (t) cc_final: 0.8453 (t) outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.2441 time to fit residues: 125.2990 Evaluate side-chains 318 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 5 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 HIS F 50 ASN H 50 ASN H 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.109058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.081687 restraints weight = 117734.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.085998 restraints weight = 53430.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.088880 restraints weight = 31676.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.090774 restraints weight = 22076.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.092037 restraints weight = 17240.187| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11439 Z= 0.144 Angle : 0.486 5.128 15353 Z= 0.290 Chirality : 0.030 0.125 1676 Planarity : 0.003 0.032 1988 Dihedral : 4.074 19.068 1528 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 0.08 % Allowed : 1.18 % Favored : 98.74 % 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 aren not related in a simple way. whole: 2.35 (0.22), residues: 1413 helix: 2.08 (0.14), residues: 1242 sheet: None (None), residues: 0 loop : -2.53 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 116 TYR 0.021 0.001 TYR G 111 PHE 0.011 0.001 PHE E 52 TRP 0.012 0.001 TRP H 275 HIS 0.005 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00269 (11439) covalent geometry : angle 0.48619 (15353) hydrogen bonds : bond 0.05149 ( 978) hydrogen bonds : angle 4.59779 ( 2919) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8748 (mt) cc_final: 0.8488 (mt) REVERT: A 206 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7423 (tm-30) REVERT: A 211 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8705 (mm-30) REVERT: A 224 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8472 (tm-30) REVERT: A 228 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8237 (mm-30) REVERT: A 234 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8826 (tm-30) REVERT: A 245 GLU cc_start: 0.9354 (tm-30) cc_final: 0.9092 (tm-30) REVERT: B 245 GLU cc_start: 0.9313 (mm-30) cc_final: 0.9094 (mm-30) REVERT: B 253 LYS cc_start: 0.8951 (mmpt) cc_final: 0.8340 (tptm) REVERT: C 30 ARG cc_start: 0.8673 (tpp-160) cc_final: 0.8435 (tpp80) REVERT: C 31 ARG cc_start: 0.7893 (ptt180) cc_final: 0.6759 (mtt-85) REVERT: C 41 ASP cc_start: 0.9076 (m-30) cc_final: 0.8824 (m-30) REVERT: C 61 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8734 (tm-30) REVERT: D 58 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8192 (tm-30) REVERT: D 62 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8696 (mm-30) REVERT: E 1 MET cc_start: 0.7274 (ptp) cc_final: 0.6908 (ptp) REVERT: E 42 CYS cc_start: 0.9214 (m) cc_final: 0.8950 (t) REVERT: E 191 SER cc_start: 0.9312 (t) cc_final: 0.9074 (m) REVERT: F 51 MET cc_start: 0.9015 (ppp) cc_final: 0.8771 (ppp) REVERT: F 87 ASP cc_start: 0.9411 (m-30) cc_final: 0.9189 (m-30) REVERT: F 129 GLU cc_start: 0.9225 (tp30) cc_final: 0.8766 (tp30) REVERT: F 132 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8712 (tm-30) REVERT: F 146 GLU cc_start: 0.7815 (tm-30) cc_final: 0.6982 (tm-30) REVERT: F 150 ASP cc_start: 0.7906 (m-30) cc_final: 0.7357 (m-30) REVERT: G 9 GLU cc_start: 0.9094 (pt0) cc_final: 0.8860 (pt0) REVERT: G 129 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8964 (tm-30) REVERT: G 146 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8429 (tm-30) REVERT: G 183 ASP cc_start: 0.9116 (t0) cc_final: 0.8846 (t70) REVERT: H 37 LYS cc_start: 0.8467 (tptp) cc_final: 0.8225 (mmmt) REVERT: H 142 ILE cc_start: 0.9192 (mm) cc_final: 0.8954 (mm) REVERT: H 146 GLU cc_start: 0.9405 (mm-30) cc_final: 0.8904 (mm-30) REVERT: H 200 TYR cc_start: 0.8818 (m-80) cc_final: 0.8449 (m-80) REVERT: H 241 CYS cc_start: 0.8892 (t) cc_final: 0.8403 (t) outliers start: 1 outliers final: 1 residues processed: 359 average time/residue: 0.2682 time to fit residues: 133.8003 Evaluate side-chains 320 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 10 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 ASN H 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.104831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.077506 restraints weight = 136381.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.082031 restraints weight = 58500.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.085070 restraints weight = 33682.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.087069 restraints weight = 22958.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.088385 restraints weight = 17686.220| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11439 Z= 0.135 Angle : 0.471 5.222 15353 Z= 0.279 Chirality : 0.030 0.112 1676 Planarity : 0.003 0.029 1988 Dihedral : 4.014 18.732 1528 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % Rotamer: Outliers : 0.08 % Allowed : 2.94 % Favored : 96.97 % 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 aren not related in a simple way. whole: 2.58 (0.22), residues: 1413 helix: 2.23 (0.14), residues: 1243 sheet: None (None), residues: 0 loop : -2.46 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.025 0.001 TYR G 111 PHE 0.020 0.001 PHE H 214 TRP 0.013 0.001 TRP H 275 HIS 0.005 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00255 (11439) covalent geometry : angle 0.47126 (15353) hydrogen bonds : bond 0.05017 ( 978) hydrogen bonds : angle 4.45782 ( 2919) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8743 (mt) cc_final: 0.8486 (mt) REVERT: A 206 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7362 (tm-30) REVERT: A 211 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8752 (mm-30) REVERT: A 224 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8460 (tm-30) REVERT: A 228 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8216 (mm-30) REVERT: A 234 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8814 (tm-30) REVERT: A 245 GLU cc_start: 0.9393 (tm-30) cc_final: 0.9160 (tm-30) REVERT: B 245 GLU cc_start: 0.9288 (mm-30) cc_final: 0.9077 (mm-30) REVERT: B 253 LYS cc_start: 0.9003 (mmpt) cc_final: 0.8383 (tptp) REVERT: C 30 ARG cc_start: 0.8699 (tpp-160) cc_final: 0.8459 (tpp80) REVERT: C 31 ARG cc_start: 0.7879 (ptt180) cc_final: 0.6783 (mtt-85) REVERT: C 37 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8830 (mm-30) REVERT: C 41 ASP cc_start: 0.9082 (m-30) cc_final: 0.8824 (m-30) REVERT: C 61 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8761 (tm-30) REVERT: D 58 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8196 (tm-30) REVERT: D 62 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8680 (mm-30) REVERT: E 1 MET cc_start: 0.7166 (ptp) cc_final: 0.6841 (ptp) REVERT: E 42 CYS cc_start: 0.9205 (m) cc_final: 0.8925 (t) REVERT: F 87 ASP cc_start: 0.9378 (m-30) cc_final: 0.9176 (m-30) REVERT: F 129 GLU cc_start: 0.9192 (tp30) cc_final: 0.8681 (tp30) REVERT: F 132 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8712 (tm-30) REVERT: F 133 THR cc_start: 0.8586 (t) cc_final: 0.8371 (t) REVERT: F 146 GLU cc_start: 0.7781 (tm-30) cc_final: 0.6928 (tm-30) REVERT: F 150 ASP cc_start: 0.7905 (m-30) cc_final: 0.7365 (m-30) REVERT: G 9 GLU cc_start: 0.9057 (pt0) cc_final: 0.8829 (pt0) REVERT: G 146 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8451 (tm-30) REVERT: G 183 ASP cc_start: 0.9042 (t0) cc_final: 0.8795 (t70) REVERT: H 142 ILE cc_start: 0.9209 (mm) cc_final: 0.8987 (mm) REVERT: H 146 GLU cc_start: 0.9393 (mm-30) cc_final: 0.8916 (mm-30) REVERT: H 200 TYR cc_start: 0.8851 (m-80) cc_final: 0.8576 (m-80) outliers start: 1 outliers final: 1 residues processed: 364 average time/residue: 0.2694 time to fit residues: 135.1355 Evaluate side-chains 315 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 86 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 124 HIS F 7 GLN F 50 ASN H 23 ASN H 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.100870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074158 restraints weight = 126011.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.078341 restraints weight = 56666.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.081125 restraints weight = 33582.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082968 restraints weight = 23499.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.084146 restraints weight = 18418.888| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11439 Z= 0.230 Angle : 0.569 6.372 15353 Z= 0.350 Chirality : 0.032 0.122 1676 Planarity : 0.003 0.035 1988 Dihedral : 4.321 21.503 1528 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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 aren not related in a simple way. whole: 1.70 (0.21), residues: 1413 helix: 1.63 (0.14), residues: 1242 sheet: None (None), residues: 0 loop : -2.54 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 271 TYR 0.025 0.002 TYR F 131 PHE 0.018 0.002 PHE H 214 TRP 0.010 0.001 TRP H 275 HIS 0.005 0.001 HIS H 251 Details of bonding type rmsd covalent geometry : bond 0.00434 (11439) covalent geometry : angle 0.56899 (15353) hydrogen bonds : bond 0.05686 ( 978) hydrogen bonds : angle 5.06018 ( 2919) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8893 (mt) cc_final: 0.8601 (mt) REVERT: A 206 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 211 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8747 (mm-30) REVERT: A 215 MET cc_start: 0.9293 (ttm) cc_final: 0.9041 (ttm) REVERT: A 224 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8498 (tm-30) REVERT: A 228 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8309 (mm-30) REVERT: A 234 GLU cc_start: 0.9079 (tm-30) cc_final: 0.8835 (tm-30) REVERT: A 245 GLU cc_start: 0.9411 (tm-30) cc_final: 0.9191 (tm-30) REVERT: B 231 ASP cc_start: 0.9116 (t70) cc_final: 0.8862 (t0) REVERT: B 236 ASN cc_start: 0.8833 (m110) cc_final: 0.8630 (m110) REVERT: B 253 LYS cc_start: 0.8987 (mmpt) cc_final: 0.8344 (tptp) REVERT: C 30 ARG cc_start: 0.8733 (tpp-160) cc_final: 0.8519 (tpp80) REVERT: C 31 ARG cc_start: 0.7979 (ptt180) cc_final: 0.6749 (mtt-85) REVERT: C 41 ASP cc_start: 0.9065 (m-30) cc_final: 0.8835 (m-30) REVERT: C 51 ASP cc_start: 0.9654 (m-30) cc_final: 0.9365 (m-30) REVERT: C 61 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8676 (tm-30) REVERT: D 58 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8319 (tm-30) REVERT: D 62 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8708 (mm-30) REVERT: E 1 MET cc_start: 0.7276 (ptp) cc_final: 0.6960 (ptp) REVERT: E 7 GLN cc_start: 0.8777 (tp-100) cc_final: 0.8310 (tp-100) REVERT: F 87 ASP cc_start: 0.9401 (m-30) cc_final: 0.9198 (m-30) REVERT: F 129 GLU cc_start: 0.9246 (tp30) cc_final: 0.8665 (tp30) REVERT: F 132 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8669 (tm-30) REVERT: F 133 THR cc_start: 0.8636 (t) cc_final: 0.8327 (t) REVERT: F 146 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7004 (tm-30) REVERT: F 150 ASP cc_start: 0.7934 (m-30) cc_final: 0.7341 (m-30) REVERT: G 9 GLU cc_start: 0.9069 (pt0) cc_final: 0.8827 (pt0) REVERT: G 87 ASP cc_start: 0.9017 (t70) cc_final: 0.8629 (t70) REVERT: G 129 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8765 (tm-30) REVERT: G 146 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8467 (tm-30) REVERT: G 183 ASP cc_start: 0.9146 (t0) cc_final: 0.8920 (t70) REVERT: H 146 GLU cc_start: 0.9456 (mm-30) cc_final: 0.8955 (mm-30) REVERT: H 264 LYS cc_start: 0.9176 (mmtp) cc_final: 0.8756 (mmmt) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.2694 time to fit residues: 129.6519 Evaluate side-chains 301 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 126 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 ASN H 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.101911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.074834 restraints weight = 136947.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.079223 restraints weight = 58503.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.082134 restraints weight = 33785.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.084048 restraints weight = 23207.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085296 restraints weight = 18007.808| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11439 Z= 0.171 Angle : 0.520 5.760 15353 Z= 0.312 Chirality : 0.031 0.129 1676 Planarity : 0.003 0.044 1988 Dihedral : 4.237 19.732 1528 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.05 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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 aren not related in a simple way. whole: 1.94 (0.22), residues: 1413 helix: 1.82 (0.14), residues: 1237 sheet: None (None), residues: 0 loop : -2.60 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 271 TYR 0.021 0.001 TYR B 235 PHE 0.018 0.001 PHE H 214 TRP 0.012 0.001 TRP H 275 HIS 0.004 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00326 (11439) covalent geometry : angle 0.52023 (15353) hydrogen bonds : bond 0.05322 ( 978) hydrogen bonds : angle 4.80784 ( 2919) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8871 (mt) cc_final: 0.8582 (mt) REVERT: A 206 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 211 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8684 (mm-30) REVERT: A 215 MET cc_start: 0.9261 (ttm) cc_final: 0.8999 (ttm) REVERT: A 224 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8487 (tm-30) REVERT: A 228 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8322 (mm-30) REVERT: A 234 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8885 (tm-30) REVERT: A 245 GLU cc_start: 0.9420 (tm-30) cc_final: 0.9189 (tm-30) REVERT: B 253 LYS cc_start: 0.8958 (mmpt) cc_final: 0.8302 (tptp) REVERT: C 30 ARG cc_start: 0.8730 (tpp-160) cc_final: 0.8499 (tpp80) REVERT: C 31 ARG cc_start: 0.7980 (ptt180) cc_final: 0.6784 (mtt-85) REVERT: C 51 ASP cc_start: 0.9650 (m-30) cc_final: 0.9402 (m-30) REVERT: C 61 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8756 (tm-30) REVERT: D 58 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8293 (tm-30) REVERT: D 62 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8699 (mm-30) REVERT: E 1 MET cc_start: 0.7231 (ptp) cc_final: 0.6909 (ptp) REVERT: E 7 GLN cc_start: 0.8776 (tp-100) cc_final: 0.8376 (tp-100) REVERT: E 42 CYS cc_start: 0.9243 (m) cc_final: 0.9003 (t) REVERT: F 129 GLU cc_start: 0.9227 (tp30) cc_final: 0.8716 (tp30) REVERT: F 132 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8665 (tm-30) REVERT: F 133 THR cc_start: 0.8630 (t) cc_final: 0.8405 (t) REVERT: F 146 GLU cc_start: 0.7706 (tm-30) cc_final: 0.6865 (tm-30) REVERT: F 150 ASP cc_start: 0.7965 (m-30) cc_final: 0.7361 (m-30) REVERT: G 9 GLU cc_start: 0.9102 (pt0) cc_final: 0.8842 (pt0) REVERT: G 146 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8451 (tm-30) REVERT: G 183 ASP cc_start: 0.9122 (t0) cc_final: 0.8905 (t70) REVERT: H 146 GLU cc_start: 0.9410 (mm-30) cc_final: 0.8919 (mm-30) REVERT: H 200 TYR cc_start: 0.8982 (m-80) cc_final: 0.8750 (m-80) REVERT: H 264 LYS cc_start: 0.9175 (mmtp) cc_final: 0.8735 (mmmt) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.2651 time to fit residues: 128.1018 Evaluate side-chains 298 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 43 optimal weight: 0.3980 chunk 128 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 116 optimal weight: 0.0170 chunk 103 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 ASN G 213 HIS H 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.104038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.076640 restraints weight = 135186.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.081121 restraints weight = 58101.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.084103 restraints weight = 33550.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.086069 restraints weight = 23059.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.087328 restraints weight = 17867.020| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11439 Z= 0.132 Angle : 0.509 8.708 15353 Z= 0.294 Chirality : 0.030 0.143 1676 Planarity : 0.003 0.029 1988 Dihedral : 4.095 19.032 1528 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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 aren not related in a simple way. whole: 2.46 (0.22), residues: 1413 helix: 2.16 (0.14), residues: 1239 sheet: None (None), residues: 0 loop : -2.47 (0.45), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 19 TYR 0.024 0.002 TYR B 235 PHE 0.019 0.001 PHE H 214 TRP 0.016 0.001 TRP H 275 HIS 0.003 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00258 (11439) covalent geometry : angle 0.50939 (15353) hydrogen bonds : bond 0.04995 ( 978) hydrogen bonds : angle 4.48301 ( 2919) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8766 (mt) cc_final: 0.8485 (mt) REVERT: A 206 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7365 (tm-30) REVERT: A 211 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8709 (mm-30) REVERT: A 215 MET cc_start: 0.9272 (ttm) cc_final: 0.9004 (ttm) REVERT: A 228 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8433 (mm-30) REVERT: A 234 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8278 (tm-30) REVERT: A 238 GLU cc_start: 0.9391 (mm-30) cc_final: 0.8798 (mm-30) REVERT: A 245 GLU cc_start: 0.9439 (tm-30) cc_final: 0.9226 (tm-30) REVERT: B 253 LYS cc_start: 0.8961 (mmpt) cc_final: 0.8303 (tptp) REVERT: C 31 ARG cc_start: 0.7924 (ptt180) cc_final: 0.6801 (mtt-85) REVERT: C 51 ASP cc_start: 0.9639 (m-30) cc_final: 0.9388 (m-30) REVERT: C 61 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8736 (tm-30) REVERT: D 58 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8233 (tm-30) REVERT: D 62 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8669 (mm-30) REVERT: D 70 ASP cc_start: 0.9177 (t0) cc_final: 0.8765 (t0) REVERT: D 73 GLU cc_start: 0.8360 (pp20) cc_final: 0.8127 (pp20) REVERT: E 1 MET cc_start: 0.7176 (ptp) cc_final: 0.6852 (ptp) REVERT: E 7 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8379 (tp-100) REVERT: E 42 CYS cc_start: 0.9187 (m) cc_final: 0.8952 (t) REVERT: F 87 ASP cc_start: 0.9379 (m-30) cc_final: 0.9162 (m-30) REVERT: F 129 GLU cc_start: 0.9231 (tp30) cc_final: 0.8739 (tp30) REVERT: F 132 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8698 (tm-30) REVERT: F 146 GLU cc_start: 0.7680 (tm-30) cc_final: 0.6785 (tm-30) REVERT: F 150 ASP cc_start: 0.8107 (m-30) cc_final: 0.7480 (m-30) REVERT: G 9 GLU cc_start: 0.9118 (pt0) cc_final: 0.8875 (pt0) REVERT: G 129 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8816 (tm-30) REVERT: G 146 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8453 (tm-30) REVERT: G 183 ASP cc_start: 0.9082 (t0) cc_final: 0.8854 (t70) REVERT: H 142 ILE cc_start: 0.9141 (mm) cc_final: 0.8925 (mm) REVERT: H 146 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8844 (mm-30) REVERT: H 200 TYR cc_start: 0.8945 (m-80) cc_final: 0.8730 (m-80) REVERT: H 264 LYS cc_start: 0.9171 (mmtp) cc_final: 0.8713 (mmmt) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.2756 time to fit residues: 134.3378 Evaluate side-chains 304 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 135 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 GLN F 50 ASN H 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.101210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.074349 restraints weight = 130960.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.078592 restraints weight = 57454.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.081431 restraints weight = 33721.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.083291 restraints weight = 23404.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.084513 restraints weight = 18294.399| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11439 Z= 0.203 Angle : 0.560 6.066 15353 Z= 0.340 Chirality : 0.032 0.132 1676 Planarity : 0.003 0.033 1988 Dihedral : 4.218 20.182 1528 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.76 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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 aren not related in a simple way. whole: 1.87 (0.22), residues: 1413 helix: 1.73 (0.14), residues: 1248 sheet: None (None), residues: 0 loop : -2.53 (0.44), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 19 TYR 0.023 0.002 TYR G 111 PHE 0.025 0.002 PHE H 214 TRP 0.014 0.001 TRP H 275 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00389 (11439) covalent geometry : angle 0.56017 (15353) hydrogen bonds : bond 0.05411 ( 978) hydrogen bonds : angle 4.86332 ( 2919) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8868 (mt) cc_final: 0.8567 (mt) REVERT: A 206 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7533 (tm-30) REVERT: A 211 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8775 (mm-30) REVERT: A 215 MET cc_start: 0.9250 (ttm) cc_final: 0.9048 (ttm) REVERT: A 224 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8464 (tm-30) REVERT: A 228 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8293 (mm-30) REVERT: A 234 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8899 (tm-30) REVERT: A 245 GLU cc_start: 0.9403 (tm-30) cc_final: 0.9168 (tm-30) REVERT: A 246 ARG cc_start: 0.8925 (ttm170) cc_final: 0.8128 (tpt-90) REVERT: B 253 LYS cc_start: 0.8998 (mmpt) cc_final: 0.8337 (tptp) REVERT: C 31 ARG cc_start: 0.7913 (ptt180) cc_final: 0.6734 (mtt-85) REVERT: C 45 ARG cc_start: 0.8909 (tpp80) cc_final: 0.8460 (ttt90) REVERT: C 51 ASP cc_start: 0.9633 (m-30) cc_final: 0.9340 (m-30) REVERT: C 61 GLU cc_start: 0.8955 (tm-30) cc_final: 0.8734 (tm-30) REVERT: D 58 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8350 (tm-30) REVERT: D 62 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8769 (mm-30) REVERT: E 1 MET cc_start: 0.7208 (ptp) cc_final: 0.6891 (ptp) REVERT: E 7 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8387 (tp-100) REVERT: E 42 CYS cc_start: 0.9270 (m) cc_final: 0.8986 (t) REVERT: F 129 GLU cc_start: 0.9236 (tp30) cc_final: 0.8769 (tp30) REVERT: F 132 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8707 (tm-30) REVERT: F 146 GLU cc_start: 0.7696 (tm-30) cc_final: 0.6846 (tm-30) REVERT: F 150 ASP cc_start: 0.7974 (m-30) cc_final: 0.7369 (m-30) REVERT: G 9 GLU cc_start: 0.9125 (pt0) cc_final: 0.8867 (pt0) REVERT: G 129 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8842 (tm-30) REVERT: G 146 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8444 (tm-30) REVERT: G 183 ASP cc_start: 0.9116 (t0) cc_final: 0.8881 (t70) REVERT: H 142 ILE cc_start: 0.9208 (mm) cc_final: 0.8974 (mm) REVERT: H 146 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8809 (mm-30) REVERT: H 244 MET cc_start: 0.9096 (tpt) cc_final: 0.8844 (tpp) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.2264 time to fit residues: 107.8311 Evaluate side-chains 294 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 127 optimal weight: 0.0010 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 ASN H 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.103609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.076717 restraints weight = 123590.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.081044 restraints weight = 55015.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.083904 restraints weight = 32334.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.085822 restraints weight = 22491.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087054 restraints weight = 17529.899| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11439 Z= 0.134 Angle : 0.529 6.180 15353 Z= 0.304 Chirality : 0.031 0.130 1676 Planarity : 0.003 0.069 1988 Dihedral : 4.121 19.632 1528 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.70 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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 aren not related in a simple way. whole: 2.31 (0.22), residues: 1413 helix: 2.05 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : -2.46 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 116 TYR 0.021 0.002 TYR A 235 PHE 0.023 0.001 PHE H 65 TRP 0.017 0.001 TRP H 275 HIS 0.005 0.001 HIS G 213 Details of bonding type rmsd covalent geometry : bond 0.00260 (11439) covalent geometry : angle 0.52867 (15353) hydrogen bonds : bond 0.05039 ( 978) hydrogen bonds : angle 4.51312 ( 2919) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2826 Ramachandran restraints generated. 1413 Oldfield, 0 Emsley, 1413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 LEU cc_start: 0.8801 (mt) cc_final: 0.8500 (mt) REVERT: A 206 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7357 (tm-30) REVERT: A 211 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8661 (mm-30) REVERT: A 215 MET cc_start: 0.9237 (ttm) cc_final: 0.8962 (ttm) REVERT: A 216 PHE cc_start: 0.8652 (m-80) cc_final: 0.8438 (m-80) REVERT: A 224 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8446 (tm-30) REVERT: A 228 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8227 (mm-30) REVERT: A 234 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8871 (tm-30) REVERT: A 245 GLU cc_start: 0.9440 (tm-30) cc_final: 0.9219 (tm-30) REVERT: A 246 ARG cc_start: 0.8984 (ttm170) cc_final: 0.8620 (ttp-170) REVERT: B 216 PHE cc_start: 0.8416 (m-80) cc_final: 0.8059 (m-80) REVERT: B 253 LYS cc_start: 0.8947 (mmpt) cc_final: 0.8272 (tptp) REVERT: C 31 ARG cc_start: 0.7907 (ptt180) cc_final: 0.6774 (mtt-85) REVERT: C 51 ASP cc_start: 0.9629 (m-30) cc_final: 0.9327 (m-30) REVERT: C 61 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8748 (tm-30) REVERT: D 58 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8215 (tm-30) REVERT: D 62 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8645 (mm-30) REVERT: E 1 MET cc_start: 0.7164 (ptp) cc_final: 0.6845 (ptp) REVERT: E 7 GLN cc_start: 0.8831 (tp-100) cc_final: 0.8442 (tp-100) REVERT: E 42 CYS cc_start: 0.9225 (m) cc_final: 0.8953 (t) REVERT: F 87 ASP cc_start: 0.9374 (m-30) cc_final: 0.9154 (m-30) REVERT: F 129 GLU cc_start: 0.9223 (tp30) cc_final: 0.8868 (tp30) REVERT: F 132 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8671 (tm-30) REVERT: F 146 GLU cc_start: 0.7621 (tm-30) cc_final: 0.6700 (tm-30) REVERT: F 150 ASP cc_start: 0.7928 (m-30) cc_final: 0.7269 (m-30) REVERT: G 9 GLU cc_start: 0.9094 (pt0) cc_final: 0.8843 (pt0) REVERT: G 87 ASP cc_start: 0.9006 (t70) cc_final: 0.8586 (t70) REVERT: G 146 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8431 (tm-30) REVERT: G 183 ASP cc_start: 0.9128 (t0) cc_final: 0.8878 (t70) REVERT: H 87 ASP cc_start: 0.9380 (t0) cc_final: 0.8913 (t0) REVERT: H 142 ILE cc_start: 0.9157 (mm) cc_final: 0.8952 (mm) REVERT: H 146 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8832 (mm-30) REVERT: H 193 MET cc_start: 0.8642 (mmm) cc_final: 0.8355 (mmm) REVERT: H 200 TYR cc_start: 0.8984 (m-80) cc_final: 0.8739 (m-80) REVERT: H 264 LYS cc_start: 0.9172 (mmtp) cc_final: 0.8757 (mmmt) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2243 time to fit residues: 109.6685 Evaluate side-chains 305 residues out of total 1186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 305 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 72 optimal weight: 1.9990 chunk 49 optimal weight: 0.0270 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 7 GLN F 50 ASN H 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.103783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.076728 restraints weight = 128644.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.081113 restraints weight = 55966.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.084029 restraints weight = 32564.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.085919 restraints weight = 22468.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.087176 restraints weight = 17531.077| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3397 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11439 Z= 0.134 Angle : 0.526 6.502 15353 Z= 0.305 Chirality : 0.030 0.130 1676 Planarity : 0.003 0.029 1988 Dihedral : 4.050 18.178 1528 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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 aren not related in a simple way. whole: 2.45 (0.22), residues: 1413 helix: 2.14 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : -2.40 (0.45), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 271 TYR 0.020 0.001 TYR H 151 PHE 0.020 0.001 PHE H 214 TRP 0.017 0.001 TRP H 275 HIS 0.004 0.001 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00263 (11439) covalent geometry : angle 0.52638 (15353) hydrogen bonds : bond 0.04987 ( 978) hydrogen bonds : angle 4.44245 ( 2919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5381.97 seconds wall clock time: 92 minutes 13.28 seconds (5533.28 seconds total)