Starting phenix.real_space_refine on Sat Aug 23 03:48:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z21_39742/08_2025/8z21_39742_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z21_39742/08_2025/8z21_39742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z21_39742/08_2025/8z21_39742_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z21_39742/08_2025/8z21_39742_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z21_39742/08_2025/8z21_39742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z21_39742/08_2025/8z21_39742.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 Fe 8 7.16 5 S 78 5.16 5 C 6166 2.51 5 N 1612 2.21 5 O 1681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 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: 9545 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2317 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 18, 'TRANS': 283} Chain: "B" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2122 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain: "C" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2522 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 304} Chain: "D" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2568 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 303} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6773 SG CYS C 312 49.149 77.344 98.500 1.00 84.77 S ATOM 6669 SG CYS C 299 51.625 72.772 95.247 1.00 66.92 S ATOM 6720 SG CYS C 305 46.639 71.081 99.619 1.00 91.90 S ATOM 6900 SG CYS C 329 52.616 72.637 101.846 1.00 72.46 S ATOM 9359 SG CYS D 311 48.007 16.034 99.068 1.00 92.38 S ATOM 9489 SG CYS D 328 45.189 21.006 102.325 1.00 85.43 S ATOM 9260 SG CYS D 298 46.073 20.461 95.422 1.00 83.21 S ATOM 9313 SG CYS D 304 51.137 22.235 99.659 1.00 96.18 S Time building chain proxies: 1.86, per 1000 atoms: 0.19 Number of scatterers: 9545 At special positions: 0 Unit cell: (95.16, 92.04, 121.68, 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) Fe 8 26.01 S 78 16.00 O 1681 8.00 N 1612 7.00 C 6166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 379.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 401 " pdb="FE2 SF4 C 401 " - pdb=" SG CYS C 299 " pdb="FE4 SF4 C 401 " - pdb=" SG CYS C 329 " pdb="FE1 SF4 C 401 " - pdb=" SG CYS C 312 " pdb="FE3 SF4 C 401 " - pdb=" SG CYS C 305 " pdb=" SF4 D 401 " pdb="FE3 SF4 D 401 " - pdb=" SG CYS D 298 " pdb="FE4 SF4 D 401 " - pdb=" SG CYS D 304 " pdb="FE1 SF4 D 401 " - pdb=" SG CYS D 311 " pdb="FE2 SF4 D 401 " - pdb=" SG CYS D 328 " Number of angles added : 24 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2278 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 5 sheets defined 62.3% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 2 through 29 removed outlier: 3.525A pdb=" N LEU A 6 " --> pdb=" O LEU A 2 " (cutoff:3.500A) Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 33 through 37 Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.765A pdb=" N ASN A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 52 " --> pdb=" O ASN A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 72 Processing helix chain 'A' and resid 85 through 121 Proline residue: A 95 - end of helix Processing helix chain 'A' and resid 125 through 141 removed outlier: 3.963A pdb=" N VAL A 139 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 155 Proline residue: A 148 - end of helix Processing helix chain 'A' and resid 170 through 202 removed outlier: 5.119A pdb=" N LEU A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 4.912A pdb=" N ALA A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 224 through 235 Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 235 through 255 removed outlier: 4.063A pdb=" N MET A 248 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 269 Processing helix chain 'A' and resid 271 through 301 Processing helix chain 'B' and resid 24 through 36 Processing helix chain 'B' and resid 36 through 60 Proline residue: B 57 - end of helix Processing helix chain 'B' and resid 68 through 72 removed outlier: 4.011A pdb=" N MET B 72 " --> pdb=" O TRP B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 129 Processing helix chain 'B' and resid 130 through 145 removed outlier: 4.073A pdb=" N VAL B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 161 Processing helix chain 'B' and resid 163 through 175 removed outlier: 3.508A pdb=" N SER B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 Processing helix chain 'B' and resid 193 through 202 removed outlier: 3.756A pdb=" N GLU B 197 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 214 through 243 removed outlier: 4.400A pdb=" N GLY B 220 " --> pdb=" O PRO B 216 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) Proline residue: B 231 - end of helix Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.544A pdb=" N SER B 252 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 removed outlier: 3.523A pdb=" N ASP B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 298 Proline residue: B 275 - end of helix Processing helix chain 'C' and resid 11 through 15 Processing helix chain 'C' and resid 61 through 71 removed outlier: 3.715A pdb=" N ALA C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 112 through 117 removed outlier: 3.611A pdb=" N SER C 116 " --> pdb=" O ASP C 112 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 117' Processing helix chain 'C' and resid 122 through 135 removed outlier: 4.728A pdb=" N VAL C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 3.520A pdb=" N PHE C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 162 Processing helix chain 'C' and resid 163 through 164 No H-bonds generated for 'chain 'C' and resid 163 through 164' Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 170 through 184 Processing helix chain 'C' and resid 200 through 219 removed outlier: 4.065A pdb=" N ARG C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 removed outlier: 4.147A pdb=" N GLY C 234 " --> pdb=" O VAL C 230 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 259 Processing helix chain 'C' and resid 262 through 272 Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'D' and resid 62 through 71 Processing helix chain 'D' and resid 95 through 101 removed outlier: 3.737A pdb=" N VAL D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 132 Proline residue: D 127 - end of helix Processing helix chain 'D' and resid 136 through 152 Processing helix chain 'D' and resid 154 through 160 removed outlier: 4.606A pdb=" N ASN D 159 " --> pdb=" O ASN D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 165 Processing helix chain 'D' and resid 167 through 180 Processing helix chain 'D' and resid 196 through 215 Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.546A pdb=" N HIS D 230 " --> pdb=" O ALA D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 255 removed outlier: 3.859A pdb=" N TYR D 253 " --> pdb=" O TYR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 268 Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.868A pdb=" N LYS D 313 " --> pdb=" O PRO D 309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 46 removed outlier: 6.618A pdb=" N ALA C 38 " --> pdb=" O THR C 28 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N THR C 28 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN C 40 " --> pdb=" O ARG C 26 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG C 26 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU C 42 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL C 22 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR C 84 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASP C 24 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER C 82 " --> pdb=" O ASP C 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 108 through 109 removed outlier: 6.385A pdb=" N LEU C 52 " --> pdb=" O MET C 224 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR C 226 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE C 54 " --> pdb=" O THR C 226 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL C 239 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR C 250 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL C 241 " --> pdb=" O MET C 248 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 35 through 48 removed outlier: 6.636A pdb=" N VAL D 19 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASP D 41 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU D 17 " --> pdb=" O ASP D 41 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL D 43 " --> pdb=" O ALA D 15 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA D 15 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU D 45 " --> pdb=" O GLU D 13 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU D 13 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU D 47 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU D 17 " --> pdb=" O ASP D 78 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP D 78 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 103 through 106 removed outlier: 6.388A pdb=" N LEU D 53 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA D 222 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL D 55 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR D 52 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU D 236 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY D 54 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N MET D 238 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL D 56 " --> pdb=" O MET D 238 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 245 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR D 239 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ALA D 243 " --> pdb=" O TYR D 239 " (cutoff:3.500A) 543 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.16 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 4008 1.43 - 1.65: 5601 1.65 - 1.86: 125 1.86 - 2.08: 0 2.08 - 2.29: 24 Bond restraints: 9758 Sorted by residual: bond pdb=" CZ ARG D 68 " pdb=" NH2 ARG D 68 " ideal model delta sigma weight residual 1.330 1.228 0.102 1.30e-02 5.92e+03 6.15e+01 bond pdb=" CZ ARG C 254 " pdb=" NH2 ARG C 254 " ideal model delta sigma weight residual 1.330 1.229 0.101 1.30e-02 5.92e+03 5.99e+01 bond pdb=" CA ALA B 41 " pdb=" CB ALA B 41 " ideal model delta sigma weight residual 1.529 1.415 0.114 1.55e-02 4.16e+03 5.44e+01 bond pdb=" CZ ARG C 254 " pdb=" NH1 ARG C 254 " ideal model delta sigma weight residual 1.323 1.221 0.102 1.40e-02 5.10e+03 5.31e+01 bond pdb=" CZ ARG D 68 " pdb=" NH1 ARG D 68 " ideal model delta sigma weight residual 1.323 1.221 0.102 1.40e-02 5.10e+03 5.30e+01 ... (remaining 9753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 10300 2.20 - 4.39: 2672 4.39 - 6.59: 227 6.59 - 8.79: 48 8.79 - 10.98: 8 Bond angle restraints: 13255 Sorted by residual: angle pdb=" CA PHE B 168 " pdb=" CB PHE B 168 " pdb=" CG PHE B 168 " ideal model delta sigma weight residual 113.80 122.44 -8.64 1.00e+00 1.00e+00 7.47e+01 angle pdb=" CA PHE B 284 " pdb=" CB PHE B 284 " pdb=" CG PHE B 284 " ideal model delta sigma weight residual 113.80 121.53 -7.73 1.00e+00 1.00e+00 5.98e+01 angle pdb=" CA PHE A 240 " pdb=" CB PHE A 240 " pdb=" CG PHE A 240 " ideal model delta sigma weight residual 113.80 120.74 -6.94 1.00e+00 1.00e+00 4.82e+01 angle pdb=" C GLY B 130 " pdb=" N GLY B 131 " pdb=" CA GLY B 131 " ideal model delta sigma weight residual 119.98 127.65 -7.67 1.11e+00 8.12e-01 4.77e+01 angle pdb=" CA ASP B 298 " pdb=" CB ASP B 298 " pdb=" CG ASP B 298 " ideal model delta sigma weight residual 112.60 119.49 -6.89 1.00e+00 1.00e+00 4.74e+01 ... (remaining 13250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 5468 16.67 - 33.34: 336 33.34 - 50.01: 56 50.01 - 66.68: 14 66.68 - 83.35: 8 Dihedral angle restraints: 5882 sinusoidal: 2344 harmonic: 3538 Sorted by residual: dihedral pdb=" CA LEU D 216 " pdb=" C LEU D 216 " pdb=" N SER D 217 " pdb=" CA SER D 217 " ideal model delta harmonic sigma weight residual 180.00 151.41 28.59 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA ALA A 120 " pdb=" C ALA A 120 " pdb=" N LEU A 121 " pdb=" CA LEU A 121 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA TRP A 166 " pdb=" C TRP A 166 " pdb=" N ASN A 167 " pdb=" CA ASN A 167 " ideal model delta harmonic sigma weight residual 180.00 152.98 27.02 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 5879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1339 0.147 - 0.293: 155 0.293 - 0.440: 14 0.440 - 0.586: 29 0.586 - 0.733: 10 Chirality restraints: 1547 Sorted by residual: chirality pdb=" CG LEU B 219 " pdb=" CB LEU B 219 " pdb=" CD1 LEU B 219 " pdb=" CD2 LEU B 219 " both_signs ideal model delta sigma weight residual False -2.59 -1.86 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CG LEU B 113 " pdb=" CB LEU B 113 " pdb=" CD1 LEU B 113 " pdb=" CD2 LEU B 113 " both_signs ideal model delta sigma weight residual False -2.59 -1.88 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CB VAL B 45 " pdb=" CA VAL B 45 " pdb=" CG1 VAL B 45 " pdb=" CG2 VAL B 45 " both_signs ideal model delta sigma weight residual False -2.63 -1.92 -0.71 2.00e-01 2.50e+01 1.26e+01 ... (remaining 1544 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 260 " -0.185 2.00e-02 2.50e+03 1.10e-01 2.43e+02 pdb=" CG TYR D 260 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR D 260 " 0.073 2.00e-02 2.50e+03 pdb=" CD2 TYR D 260 " 0.094 2.00e-02 2.50e+03 pdb=" CE1 TYR D 260 " 0.080 2.00e-02 2.50e+03 pdb=" CE2 TYR D 260 " 0.071 2.00e-02 2.50e+03 pdb=" CZ TYR D 260 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR D 260 " -0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 169 " 0.168 2.00e-02 2.50e+03 1.05e-01 1.94e+02 pdb=" CG PHE C 169 " -0.108 2.00e-02 2.50e+03 pdb=" CD1 PHE C 169 " -0.114 2.00e-02 2.50e+03 pdb=" CD2 PHE C 169 " -0.095 2.00e-02 2.50e+03 pdb=" CE1 PHE C 169 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE C 169 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 169 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 185 " 0.159 2.00e-02 2.50e+03 8.34e-02 1.39e+02 pdb=" CG TYR A 185 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR A 185 " -0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR A 185 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR A 185 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR A 185 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR A 185 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 185 " 0.112 2.00e-02 2.50e+03 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 4560 3.01 - 3.49: 9941 3.49 - 3.96: 15207 3.96 - 4.43: 16599 4.43 - 4.90: 28443 Nonbonded interactions: 74750 Sorted by model distance: nonbonded pdb=" OG SER A 78 " pdb=" OD2 ASP A 271 " model vdw 2.544 3.040 nonbonded pdb=" OE2 GLU C 57 " pdb=" OG SER D 198 " model vdw 2.549 3.040 nonbonded pdb=" OE2 GLU B 237 " pdb=" OG SER B 253 " model vdw 2.556 3.040 nonbonded pdb=" N ASP A 83 " pdb=" OD1 ASP A 83 " model vdw 2.566 3.120 nonbonded pdb=" OG SER C 170 " pdb=" OE2 GLU D 287 " model vdw 2.566 3.040 ... (remaining 74745 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.770 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.280 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.016 0.235 9766 Z= 0.901 Angle : 1.895 13.199 13279 Z= 1.265 Chirality : 0.131 0.733 1547 Planarity : 0.013 0.110 1676 Dihedral : 12.026 83.348 3604 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 0.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 2.11 % 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: -0.98 (0.22), residues: 1227 helix: -0.70 (0.18), residues: 687 sheet: 0.43 (0.67), residues: 60 loop : -0.44 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 234 TYR 0.188 0.021 TYR D 260 PHE 0.168 0.011 PHE C 169 TRP 0.094 0.017 TRP D 83 HIS 0.010 0.002 HIS B 213 Details of bonding type rmsd covalent geometry : bond 0.01556 ( 9758) covalent geometry : angle 1.87464 (13255) hydrogen bonds : bond 0.17682 ( 543) hydrogen bonds : angle 7.27494 ( 1563) metal coordination : bond 0.17631 ( 8) metal coordination : angle 6.82078 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.327 Fit side-chains REVERT: A 132 MET cc_start: 0.7411 (mmp) cc_final: 0.7201 (mmt) REVERT: A 196 SER cc_start: 0.8569 (t) cc_final: 0.8322 (p) REVERT: B 65 ASP cc_start: 0.7516 (t0) cc_final: 0.7165 (t0) REVERT: B 124 SER cc_start: 0.8605 (m) cc_final: 0.8229 (p) REVERT: B 182 ILE cc_start: 0.8135 (tp) cc_final: 0.7931 (tp) REVERT: B 247 THR cc_start: 0.7999 (p) cc_final: 0.7791 (p) REVERT: C 95 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7256 (mt-10) REVERT: C 162 MET cc_start: 0.8155 (mmm) cc_final: 0.7383 (mmm) REVERT: C 248 MET cc_start: 0.7943 (mmp) cc_final: 0.7342 (mmt) REVERT: D 9 LYS cc_start: 0.8476 (mtpp) cc_final: 0.8239 (mtpp) REVERT: D 91 MET cc_start: 0.6973 (mtm) cc_final: 0.6759 (mtm) REVERT: D 95 GLU cc_start: 0.6895 (pt0) cc_final: 0.6504 (pt0) REVERT: D 150 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8083 (ttmm) REVERT: D 199 ILE cc_start: 0.8284 (mm) cc_final: 0.8065 (mt) REVERT: D 238 MET cc_start: 0.8430 (mtp) cc_final: 0.8194 (mtm) REVERT: D 330 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7626 (mtpp) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1216 time to fit residues: 42.8242 Evaluate side-chains 237 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.4980 chunk 117 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN B 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.119856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107988 restraints weight = 13871.160| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.05 r_work: 0.3235 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9766 Z= 0.167 Angle : 0.683 11.354 13279 Z= 0.330 Chirality : 0.045 0.157 1547 Planarity : 0.004 0.046 1676 Dihedral : 5.350 31.332 1328 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.55 % Allowed : 6.67 % Favored : 91.79 % 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: 0.37 (0.24), residues: 1227 helix: 0.74 (0.19), residues: 706 sheet: -0.62 (0.57), residues: 77 loop : -0.22 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 129 TYR 0.025 0.002 TYR A 185 PHE 0.023 0.002 PHE B 239 TRP 0.012 0.001 TRP B 254 HIS 0.004 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9758) covalent geometry : angle 0.63678 (13255) hydrogen bonds : bond 0.04396 ( 543) hydrogen bonds : angle 4.98260 ( 1563) metal coordination : bond 0.01281 ( 8) metal coordination : angle 5.86810 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 281 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.7884 (mmm) cc_final: 0.7614 (mmm) REVERT: A 132 MET cc_start: 0.7539 (mmp) cc_final: 0.7172 (mmt) REVERT: A 152 MET cc_start: 0.7988 (ttt) cc_final: 0.7739 (ttt) REVERT: A 196 SER cc_start: 0.8529 (t) cc_final: 0.8286 (p) REVERT: A 222 ARG cc_start: 0.8388 (tpt170) cc_final: 0.8142 (tpt170) REVERT: B 34 MET cc_start: 0.8348 (mmm) cc_final: 0.8145 (mpp) REVERT: B 65 ASP cc_start: 0.8141 (t0) cc_final: 0.7826 (t0) REVERT: B 113 LEU cc_start: 0.8172 (mt) cc_final: 0.7963 (mp) REVERT: B 121 LEU cc_start: 0.8044 (tt) cc_final: 0.7494 (mp) REVERT: B 124 SER cc_start: 0.8540 (m) cc_final: 0.8123 (p) REVERT: B 125 LEU cc_start: 0.8434 (mm) cc_final: 0.8201 (mm) REVERT: B 173 MET cc_start: 0.8450 (mmm) cc_final: 0.8199 (mmm) REVERT: B 182 ILE cc_start: 0.8016 (tp) cc_final: 0.7811 (tp) REVERT: B 294 ARG cc_start: 0.7857 (ttm-80) cc_final: 0.7586 (ttm-80) REVERT: C 145 GLU cc_start: 0.7830 (tp30) cc_final: 0.7529 (tp30) REVERT: C 188 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7906 (mmtp) REVERT: C 238 LYS cc_start: 0.7904 (mttp) cc_final: 0.7685 (mtpp) REVERT: C 248 MET cc_start: 0.8116 (mmp) cc_final: 0.7469 (mmt) REVERT: C 295 LEU cc_start: 0.8237 (tp) cc_final: 0.8032 (tp) REVERT: C 331 LYS cc_start: 0.8178 (tptp) cc_final: 0.7919 (tptp) REVERT: D 9 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8362 (mtpp) REVERT: D 91 MET cc_start: 0.7313 (mtm) cc_final: 0.6719 (mtm) REVERT: D 95 GLU cc_start: 0.7215 (pt0) cc_final: 0.6653 (pt0) REVERT: D 189 ASP cc_start: 0.7567 (t0) cc_final: 0.7361 (t0) REVERT: D 238 MET cc_start: 0.8567 (mtp) cc_final: 0.8301 (mtm) REVERT: D 268 VAL cc_start: 0.7962 (t) cc_final: 0.7759 (p) REVERT: D 299 VAL cc_start: 0.8469 (p) cc_final: 0.8262 (t) REVERT: D 329 LEU cc_start: 0.8577 (mm) cc_final: 0.8258 (mp) outliers start: 16 outliers final: 10 residues processed: 286 average time/residue: 0.1135 time to fit residues: 42.3364 Evaluate side-chains 273 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 263 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 193 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 0.9980 chunk 89 optimal weight: 0.0870 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 117 optimal weight: 0.0000 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 GLN D 230 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109422 restraints weight = 13658.141| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.08 r_work: 0.3247 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9766 Z= 0.133 Angle : 0.605 9.111 13279 Z= 0.287 Chirality : 0.043 0.158 1547 Planarity : 0.004 0.047 1676 Dihedral : 4.791 25.820 1328 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.64 % Allowed : 9.08 % Favored : 89.28 % 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: 0.80 (0.24), residues: 1227 helix: 1.24 (0.20), residues: 706 sheet: -0.91 (0.55), residues: 83 loop : -0.19 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 327 TYR 0.021 0.001 TYR A 185 PHE 0.024 0.002 PHE B 239 TRP 0.008 0.001 TRP A 166 HIS 0.004 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9758) covalent geometry : angle 0.56177 (13255) hydrogen bonds : bond 0.03996 ( 543) hydrogen bonds : angle 4.59274 ( 1563) metal coordination : bond 0.00306 ( 8) metal coordination : angle 5.31674 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 263 time to evaluate : 0.266 Fit side-chains REVERT: A 46 MET cc_start: 0.7783 (mmm) cc_final: 0.7446 (mmm) REVERT: A 132 MET cc_start: 0.7619 (mmp) cc_final: 0.7256 (mmt) REVERT: A 152 MET cc_start: 0.7876 (ttt) cc_final: 0.7520 (ttt) REVERT: A 196 SER cc_start: 0.8550 (t) cc_final: 0.8279 (p) REVERT: B 34 MET cc_start: 0.8388 (mmm) cc_final: 0.8180 (mpp) REVERT: B 65 ASP cc_start: 0.8233 (t0) cc_final: 0.7907 (t0) REVERT: B 80 SER cc_start: 0.9047 (m) cc_final: 0.8840 (p) REVERT: B 121 LEU cc_start: 0.8018 (tt) cc_final: 0.7498 (mp) REVERT: B 124 SER cc_start: 0.8543 (m) cc_final: 0.8179 (p) REVERT: B 125 LEU cc_start: 0.8422 (mm) cc_final: 0.8210 (mm) REVERT: B 182 ILE cc_start: 0.8064 (tp) cc_final: 0.7841 (tp) REVERT: B 233 MET cc_start: 0.8496 (mmp) cc_final: 0.8094 (mmt) REVERT: C 21 ASN cc_start: 0.7813 (t0) cc_final: 0.7601 (t0) REVERT: C 161 ARG cc_start: 0.8377 (mmt90) cc_final: 0.7918 (mmm-85) REVERT: C 164 MET cc_start: 0.8584 (mtt) cc_final: 0.8355 (mtp) REVERT: C 168 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7809 (mm-30) REVERT: C 208 MET cc_start: 0.8257 (mmm) cc_final: 0.8021 (mmt) REVERT: C 225 ILE cc_start: 0.8161 (mm) cc_final: 0.7882 (mt) REVERT: C 248 MET cc_start: 0.8114 (mmp) cc_final: 0.7508 (mmt) REVERT: C 288 ASN cc_start: 0.8628 (m-40) cc_final: 0.8420 (m-40) REVERT: D 9 LYS cc_start: 0.8638 (mtpp) cc_final: 0.8368 (mtpp) REVERT: D 18 LYS cc_start: 0.8711 (mttt) cc_final: 0.8511 (mttp) REVERT: D 51 GLU cc_start: 0.7864 (tt0) cc_final: 0.7655 (tt0) REVERT: D 91 MET cc_start: 0.7341 (mtm) cc_final: 0.6809 (mtm) REVERT: D 95 GLU cc_start: 0.7212 (pt0) cc_final: 0.6709 (pt0) REVERT: D 329 LEU cc_start: 0.8582 (mm) cc_final: 0.8300 (mp) REVERT: D 331 VAL cc_start: 0.8858 (p) cc_final: 0.8582 (m) outliers start: 17 outliers final: 8 residues processed: 268 average time/residue: 0.0906 time to fit residues: 34.0681 Evaluate side-chains 257 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 249 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 193 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 83 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN D 230 HIS D 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107867 restraints weight = 13885.638| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.04 r_work: 0.3224 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9766 Z= 0.181 Angle : 0.627 11.632 13279 Z= 0.291 Chirality : 0.044 0.162 1547 Planarity : 0.004 0.049 1676 Dihedral : 4.675 23.210 1328 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.22 % Allowed : 11.59 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.88 (0.24), residues: 1227 helix: 1.36 (0.20), residues: 707 sheet: -1.17 (0.55), residues: 83 loop : -0.23 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 246 TYR 0.024 0.002 TYR B 64 PHE 0.027 0.002 PHE B 168 TRP 0.007 0.001 TRP A 166 HIS 0.005 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 9758) covalent geometry : angle 0.58399 (13255) hydrogen bonds : bond 0.03986 ( 543) hydrogen bonds : angle 4.50843 ( 1563) metal coordination : bond 0.00591 ( 8) metal coordination : angle 5.37566 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.7859 (mmm) cc_final: 0.7509 (mmm) REVERT: A 132 MET cc_start: 0.7637 (mmp) cc_final: 0.7322 (mmp) REVERT: A 152 MET cc_start: 0.7914 (ttt) cc_final: 0.7558 (ttt) REVERT: A 196 SER cc_start: 0.8559 (t) cc_final: 0.8261 (p) REVERT: B 65 ASP cc_start: 0.8232 (t0) cc_final: 0.7901 (t0) REVERT: B 80 SER cc_start: 0.9095 (m) cc_final: 0.8801 (p) REVERT: B 121 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7470 (mp) REVERT: B 124 SER cc_start: 0.8555 (m) cc_final: 0.8172 (p) REVERT: B 125 LEU cc_start: 0.8427 (mm) cc_final: 0.8198 (mm) REVERT: B 182 ILE cc_start: 0.8104 (tp) cc_final: 0.7874 (tp) REVERT: C 21 ASN cc_start: 0.7805 (t0) cc_final: 0.7601 (t0) REVERT: C 133 LEU cc_start: 0.8011 (tp) cc_final: 0.7807 (tt) REVERT: C 161 ARG cc_start: 0.8355 (mmt90) cc_final: 0.8071 (mmm-85) REVERT: C 164 MET cc_start: 0.8530 (mtt) cc_final: 0.8300 (mtp) REVERT: C 208 MET cc_start: 0.8259 (mmm) cc_final: 0.7922 (mmt) REVERT: C 225 ILE cc_start: 0.8247 (mm) cc_final: 0.8001 (mt) REVERT: C 248 MET cc_start: 0.8147 (mmp) cc_final: 0.7514 (mmt) REVERT: D 9 LYS cc_start: 0.8632 (mtpp) cc_final: 0.8364 (mtpp) REVERT: D 18 LYS cc_start: 0.8717 (mttt) cc_final: 0.8509 (mttm) REVERT: D 51 GLU cc_start: 0.7932 (tt0) cc_final: 0.7696 (tt0) REVERT: D 91 MET cc_start: 0.7421 (mtm) cc_final: 0.6895 (mtm) REVERT: D 95 GLU cc_start: 0.7280 (pt0) cc_final: 0.6782 (pt0) REVERT: D 329 LEU cc_start: 0.8582 (mm) cc_final: 0.8331 (mp) REVERT: D 331 VAL cc_start: 0.8910 (p) cc_final: 0.8625 (m) outliers start: 23 outliers final: 16 residues processed: 259 average time/residue: 0.0951 time to fit residues: 34.8751 Evaluate side-chains 262 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 245 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 292 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 79 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 chunk 35 optimal weight: 0.0570 chunk 27 optimal weight: 0.0170 chunk 52 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 34 optimal weight: 0.0170 chunk 30 optimal weight: 5.9990 overall best weight: 0.1374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.119093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.106534 restraints weight = 13846.120| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.16 r_work: 0.3241 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9766 Z= 0.097 Angle : 0.575 10.086 13279 Z= 0.263 Chirality : 0.040 0.143 1547 Planarity : 0.004 0.053 1676 Dihedral : 4.340 20.614 1328 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.45 % Allowed : 13.14 % Favored : 85.41 % 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: 1.23 (0.24), residues: 1227 helix: 1.70 (0.20), residues: 709 sheet: -1.06 (0.54), residues: 86 loop : -0.17 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 212 TYR 0.023 0.001 TYR B 64 PHE 0.026 0.002 PHE A 17 TRP 0.006 0.001 TRP B 176 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 9758) covalent geometry : angle 0.53024 (13255) hydrogen bonds : bond 0.03242 ( 543) hydrogen bonds : angle 4.28581 ( 1563) metal coordination : bond 0.00361 ( 8) metal coordination : angle 5.26975 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 235 time to evaluate : 0.440 Fit side-chains REVERT: A 46 MET cc_start: 0.7904 (mmm) cc_final: 0.7231 (mmm) REVERT: A 132 MET cc_start: 0.7661 (mmp) cc_final: 0.7381 (mmp) REVERT: A 152 MET cc_start: 0.7859 (ttt) cc_final: 0.7492 (ttt) REVERT: A 196 SER cc_start: 0.8537 (t) cc_final: 0.8247 (p) REVERT: B 34 MET cc_start: 0.8404 (mmm) cc_final: 0.8117 (mpp) REVERT: B 65 ASP cc_start: 0.8216 (t0) cc_final: 0.7894 (t0) REVERT: B 80 SER cc_start: 0.9112 (m) cc_final: 0.8859 (p) REVERT: B 121 LEU cc_start: 0.7969 (tt) cc_final: 0.7583 (mp) REVERT: B 125 LEU cc_start: 0.8358 (mm) cc_final: 0.8150 (mm) REVERT: B 182 ILE cc_start: 0.7999 (tp) cc_final: 0.7767 (tp) REVERT: B 233 MET cc_start: 0.8432 (mmp) cc_final: 0.8171 (mmt) REVERT: C 70 MET cc_start: 0.8079 (mmm) cc_final: 0.7320 (mmm) REVERT: C 133 LEU cc_start: 0.7986 (tp) cc_final: 0.7781 (tt) REVERT: C 161 ARG cc_start: 0.8257 (mmt90) cc_final: 0.7947 (mmm-85) REVERT: C 164 MET cc_start: 0.8540 (mtt) cc_final: 0.8232 (mtm) REVERT: C 208 MET cc_start: 0.8231 (mmm) cc_final: 0.7988 (mmt) REVERT: C 246 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7790 (ttm110) REVERT: C 248 MET cc_start: 0.8110 (mmp) cc_final: 0.7441 (mmt) REVERT: C 327 ARG cc_start: 0.7549 (tpt-90) cc_final: 0.7284 (tpt-90) REVERT: C 335 GLU cc_start: 0.8437 (tt0) cc_final: 0.8235 (tt0) REVERT: D 9 LYS cc_start: 0.8606 (mtpp) cc_final: 0.8350 (mtpp) REVERT: D 18 LYS cc_start: 0.8640 (mttt) cc_final: 0.8427 (mttp) REVERT: D 51 GLU cc_start: 0.7933 (tt0) cc_final: 0.7634 (tt0) REVERT: D 91 MET cc_start: 0.7375 (mtm) cc_final: 0.6827 (mtm) REVERT: D 95 GLU cc_start: 0.7280 (pt0) cc_final: 0.6785 (pt0) REVERT: D 329 LEU cc_start: 0.8497 (mm) cc_final: 0.8263 (mp) REVERT: D 331 VAL cc_start: 0.8907 (p) cc_final: 0.8593 (m) outliers start: 15 outliers final: 11 residues processed: 241 average time/residue: 0.1058 time to fit residues: 35.1060 Evaluate side-chains 241 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 230 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 292 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 116 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.119245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107028 restraints weight = 13718.378| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.06 r_work: 0.3227 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9766 Z= 0.142 Angle : 0.595 11.437 13279 Z= 0.273 Chirality : 0.042 0.149 1547 Planarity : 0.004 0.048 1676 Dihedral : 4.318 20.062 1328 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.03 % Allowed : 14.01 % Favored : 83.96 % 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: 1.27 (0.24), residues: 1227 helix: 1.76 (0.20), residues: 706 sheet: -1.10 (0.53), residues: 86 loop : -0.20 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 323 TYR 0.024 0.001 TYR B 64 PHE 0.040 0.002 PHE B 168 TRP 0.007 0.001 TRP B 176 HIS 0.004 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9758) covalent geometry : angle 0.55221 (13255) hydrogen bonds : bond 0.03569 ( 543) hydrogen bonds : angle 4.29106 ( 1563) metal coordination : bond 0.00419 ( 8) metal coordination : angle 5.24430 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.406 Fit side-chains REVERT: A 46 MET cc_start: 0.7906 (mmm) cc_final: 0.7422 (mmm) REVERT: A 132 MET cc_start: 0.7638 (mmp) cc_final: 0.7395 (mmp) REVERT: A 196 SER cc_start: 0.8573 (t) cc_final: 0.8275 (p) REVERT: B 65 ASP cc_start: 0.8194 (t0) cc_final: 0.7867 (t0) REVERT: B 80 SER cc_start: 0.9099 (m) cc_final: 0.8825 (p) REVERT: B 121 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7639 (mp) REVERT: B 182 ILE cc_start: 0.8055 (tp) cc_final: 0.7827 (tp) REVERT: C 70 MET cc_start: 0.8110 (mmm) cc_final: 0.7330 (mmm) REVERT: C 133 LEU cc_start: 0.8028 (tp) cc_final: 0.7823 (tt) REVERT: C 161 ARG cc_start: 0.8305 (mmt90) cc_final: 0.8003 (mmm-85) REVERT: C 164 MET cc_start: 0.8488 (mtt) cc_final: 0.8197 (mtm) REVERT: C 208 MET cc_start: 0.8270 (mmm) cc_final: 0.8038 (mmt) REVERT: C 225 ILE cc_start: 0.8234 (mm) cc_final: 0.7997 (mt) REVERT: C 248 MET cc_start: 0.8136 (mmp) cc_final: 0.7494 (mmt) REVERT: C 335 GLU cc_start: 0.8377 (tt0) cc_final: 0.8175 (tt0) REVERT: D 9 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8340 (mtpp) REVERT: D 18 LYS cc_start: 0.8668 (mttt) cc_final: 0.8450 (mttm) REVERT: D 51 GLU cc_start: 0.7932 (tt0) cc_final: 0.7659 (tt0) REVERT: D 73 LEU cc_start: 0.8359 (mp) cc_final: 0.8154 (mp) REVERT: D 91 MET cc_start: 0.7446 (mtm) cc_final: 0.6889 (mtm) REVERT: D 95 GLU cc_start: 0.7322 (pt0) cc_final: 0.6848 (pt0) REVERT: D 147 MET cc_start: 0.7421 (tpp) cc_final: 0.7159 (tpp) REVERT: D 329 LEU cc_start: 0.8510 (mm) cc_final: 0.8279 (mp) REVERT: D 331 VAL cc_start: 0.8941 (p) cc_final: 0.8594 (m) outliers start: 21 outliers final: 16 residues processed: 246 average time/residue: 0.1054 time to fit residues: 36.3040 Evaluate side-chains 253 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 292 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 38 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 54 optimal weight: 0.0670 chunk 71 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 88 optimal weight: 0.0060 overall best weight: 0.5134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN D 108 GLN D 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.119427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107486 restraints weight = 13660.275| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.99 r_work: 0.3266 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9766 Z= 0.130 Angle : 0.595 11.883 13279 Z= 0.271 Chirality : 0.042 0.148 1547 Planarity : 0.004 0.057 1676 Dihedral : 4.291 20.489 1328 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.84 % Allowed : 14.20 % Favored : 83.96 % 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: 1.28 (0.24), residues: 1227 helix: 1.77 (0.20), residues: 703 sheet: -1.03 (0.52), residues: 97 loop : -0.17 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 246 TYR 0.020 0.001 TYR A 185 PHE 0.035 0.002 PHE B 168 TRP 0.007 0.001 TRP A 166 HIS 0.003 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9758) covalent geometry : angle 0.55192 (13255) hydrogen bonds : bond 0.03456 ( 543) hydrogen bonds : angle 4.28983 ( 1563) metal coordination : bond 0.00378 ( 8) metal coordination : angle 5.26330 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 237 time to evaluate : 0.323 Fit side-chains REVERT: A 46 MET cc_start: 0.7882 (mmm) cc_final: 0.7402 (mmm) REVERT: A 132 MET cc_start: 0.7598 (mmp) cc_final: 0.7382 (mmp) REVERT: A 152 MET cc_start: 0.7922 (ttm) cc_final: 0.7562 (tpp) REVERT: A 196 SER cc_start: 0.8562 (t) cc_final: 0.8259 (p) REVERT: A 198 ILE cc_start: 0.8552 (mm) cc_final: 0.8303 (mt) REVERT: B 65 ASP cc_start: 0.8147 (t0) cc_final: 0.7829 (t0) REVERT: B 80 SER cc_start: 0.9088 (m) cc_final: 0.8831 (p) REVERT: B 121 LEU cc_start: 0.7965 (tt) cc_final: 0.7584 (mp) REVERT: B 155 LEU cc_start: 0.8411 (tt) cc_final: 0.8194 (tt) REVERT: B 182 ILE cc_start: 0.8070 (tp) cc_final: 0.7835 (tp) REVERT: B 227 SER cc_start: 0.8559 (OUTLIER) cc_final: 0.8300 (m) REVERT: B 233 MET cc_start: 0.8619 (mmt) cc_final: 0.8344 (mmt) REVERT: B 273 LEU cc_start: 0.8145 (mt) cc_final: 0.7881 (mm) REVERT: C 70 MET cc_start: 0.8098 (mmm) cc_final: 0.7334 (mmm) REVERT: C 133 LEU cc_start: 0.8059 (tp) cc_final: 0.7843 (tt) REVERT: C 161 ARG cc_start: 0.8291 (mmt90) cc_final: 0.8011 (mmm-85) REVERT: C 164 MET cc_start: 0.8452 (mtt) cc_final: 0.8175 (mtm) REVERT: C 208 MET cc_start: 0.8268 (mmm) cc_final: 0.8041 (mmt) REVERT: C 225 ILE cc_start: 0.8261 (mm) cc_final: 0.8022 (mt) REVERT: C 248 MET cc_start: 0.8084 (mmp) cc_final: 0.7483 (mmt) REVERT: C 335 GLU cc_start: 0.8360 (tt0) cc_final: 0.8151 (tt0) REVERT: D 9 LYS cc_start: 0.8586 (mtpp) cc_final: 0.8340 (mtpp) REVERT: D 18 LYS cc_start: 0.8665 (mttt) cc_final: 0.8445 (mttm) REVERT: D 51 GLU cc_start: 0.7908 (tt0) cc_final: 0.7649 (tt0) REVERT: D 91 MET cc_start: 0.7455 (mtm) cc_final: 0.6926 (mtm) REVERT: D 95 GLU cc_start: 0.7314 (pt0) cc_final: 0.6860 (pt0) REVERT: D 108 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7445 (tp40) REVERT: D 147 MET cc_start: 0.7421 (tpp) cc_final: 0.7180 (tpp) REVERT: D 331 VAL cc_start: 0.8888 (p) cc_final: 0.8603 (m) outliers start: 19 outliers final: 14 residues processed: 244 average time/residue: 0.1056 time to fit residues: 35.1870 Evaluate side-chains 247 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 17 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 108 GLN Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 266 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 69 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 68 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 75 optimal weight: 0.0470 chunk 114 optimal weight: 0.5980 chunk 102 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.120074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.107952 restraints weight = 13730.909| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.06 r_work: 0.3235 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9766 Z= 0.109 Angle : 0.592 11.765 13279 Z= 0.267 Chirality : 0.041 0.145 1547 Planarity : 0.004 0.061 1676 Dihedral : 4.247 20.331 1328 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.74 % Allowed : 15.07 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.37 (0.24), residues: 1227 helix: 1.84 (0.20), residues: 703 sheet: -0.95 (0.53), residues: 96 loop : -0.12 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 246 TYR 0.019 0.001 TYR A 185 PHE 0.044 0.002 PHE B 168 TRP 0.006 0.001 TRP A 166 HIS 0.003 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9758) covalent geometry : angle 0.54785 (13255) hydrogen bonds : bond 0.03317 ( 543) hydrogen bonds : angle 4.27571 ( 1563) metal coordination : bond 0.00347 ( 8) metal coordination : angle 5.28549 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 227 time to evaluate : 0.381 Fit side-chains REVERT: A 46 MET cc_start: 0.7925 (mmm) cc_final: 0.7466 (mmm) REVERT: A 152 MET cc_start: 0.7964 (ttm) cc_final: 0.7265 (tpp) REVERT: A 196 SER cc_start: 0.8557 (t) cc_final: 0.8264 (p) REVERT: B 65 ASP cc_start: 0.8146 (t0) cc_final: 0.7820 (t0) REVERT: B 80 SER cc_start: 0.9088 (m) cc_final: 0.8873 (p) REVERT: B 121 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7732 (mp) REVERT: B 155 LEU cc_start: 0.8409 (tt) cc_final: 0.8149 (tt) REVERT: B 182 ILE cc_start: 0.8070 (tp) cc_final: 0.7837 (tp) REVERT: B 227 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8286 (m) REVERT: B 265 MET cc_start: 0.7889 (tpp) cc_final: 0.7564 (tpp) REVERT: B 273 LEU cc_start: 0.8104 (mt) cc_final: 0.7876 (mm) REVERT: C 70 MET cc_start: 0.8078 (mmm) cc_final: 0.7348 (mmm) REVERT: C 133 LEU cc_start: 0.8081 (tp) cc_final: 0.7872 (tt) REVERT: C 161 ARG cc_start: 0.8279 (mmt90) cc_final: 0.8014 (mmm-85) REVERT: C 164 MET cc_start: 0.8448 (mtt) cc_final: 0.8168 (mtm) REVERT: C 208 MET cc_start: 0.8274 (mmm) cc_final: 0.8050 (mmt) REVERT: C 225 ILE cc_start: 0.8225 (mm) cc_final: 0.7984 (mt) REVERT: C 248 MET cc_start: 0.8072 (mmp) cc_final: 0.7472 (mmt) REVERT: C 335 GLU cc_start: 0.8382 (tt0) cc_final: 0.8165 (tt0) REVERT: D 9 LYS cc_start: 0.8588 (mtpp) cc_final: 0.8339 (mtpp) REVERT: D 18 LYS cc_start: 0.8675 (mttt) cc_final: 0.8456 (mttm) REVERT: D 51 GLU cc_start: 0.7953 (tt0) cc_final: 0.7681 (tt0) REVERT: D 91 MET cc_start: 0.7454 (mtm) cc_final: 0.6903 (mtm) REVERT: D 95 GLU cc_start: 0.7331 (pt0) cc_final: 0.6895 (pt0) REVERT: D 147 MET cc_start: 0.7470 (tpp) cc_final: 0.7243 (tpp) REVERT: D 331 VAL cc_start: 0.8920 (p) cc_final: 0.8578 (m) outliers start: 18 outliers final: 12 residues processed: 235 average time/residue: 0.1031 time to fit residues: 33.7849 Evaluate side-chains 243 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 266 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 42 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.107355 restraints weight = 13873.920| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.88 r_work: 0.3267 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9766 Z= 0.168 Angle : 0.617 13.001 13279 Z= 0.282 Chirality : 0.043 0.150 1547 Planarity : 0.005 0.063 1676 Dihedral : 4.332 20.587 1328 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.64 % Allowed : 14.98 % Favored : 83.38 % 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: 1.24 (0.24), residues: 1227 helix: 1.70 (0.20), residues: 709 sheet: -0.93 (0.55), residues: 91 loop : -0.19 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 327 TYR 0.021 0.001 TYR A 185 PHE 0.045 0.002 PHE B 168 TRP 0.007 0.001 TRP A 166 HIS 0.004 0.001 HIS D 20 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 9758) covalent geometry : angle 0.57476 (13255) hydrogen bonds : bond 0.03675 ( 543) hydrogen bonds : angle 4.34405 ( 1563) metal coordination : bond 0.00449 ( 8) metal coordination : angle 5.29478 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 231 time to evaluate : 0.385 Fit side-chains REVERT: A 46 MET cc_start: 0.7938 (mmm) cc_final: 0.7486 (mmm) REVERT: A 152 MET cc_start: 0.7900 (ttm) cc_final: 0.7607 (ttm) REVERT: A 196 SER cc_start: 0.8574 (t) cc_final: 0.8283 (p) REVERT: B 65 ASP cc_start: 0.8112 (t0) cc_final: 0.7789 (t0) REVERT: B 80 SER cc_start: 0.9072 (m) cc_final: 0.8854 (p) REVERT: B 121 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7586 (mp) REVERT: B 125 LEU cc_start: 0.8369 (mt) cc_final: 0.8133 (mm) REVERT: B 182 ILE cc_start: 0.8131 (tp) cc_final: 0.7884 (tp) REVERT: B 227 SER cc_start: 0.8584 (OUTLIER) cc_final: 0.8335 (m) REVERT: B 233 MET cc_start: 0.8551 (mmt) cc_final: 0.8297 (mmt) REVERT: C 70 MET cc_start: 0.8096 (mmm) cc_final: 0.7256 (mmm) REVERT: C 133 LEU cc_start: 0.8113 (tp) cc_final: 0.7891 (tt) REVERT: C 161 ARG cc_start: 0.8319 (mmt90) cc_final: 0.8064 (mmm-85) REVERT: C 164 MET cc_start: 0.8373 (mtt) cc_final: 0.8114 (mtm) REVERT: C 225 ILE cc_start: 0.8290 (mm) cc_final: 0.8069 (mt) REVERT: C 248 MET cc_start: 0.8097 (mmp) cc_final: 0.7543 (mmt) REVERT: C 335 GLU cc_start: 0.8187 (tt0) cc_final: 0.7982 (tt0) REVERT: D 9 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8413 (mtpp) REVERT: D 51 GLU cc_start: 0.7915 (tt0) cc_final: 0.7682 (tt0) REVERT: D 91 MET cc_start: 0.7428 (mtm) cc_final: 0.6849 (mtm) REVERT: D 95 GLU cc_start: 0.7264 (pt0) cc_final: 0.6838 (pt0) REVERT: D 147 MET cc_start: 0.7367 (tpp) cc_final: 0.7112 (tpp) REVERT: D 331 VAL cc_start: 0.8863 (p) cc_final: 0.8581 (m) outliers start: 17 outliers final: 13 residues processed: 235 average time/residue: 0.1063 time to fit residues: 34.6845 Evaluate side-chains 246 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 231 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 266 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 15 optimal weight: 0.1980 chunk 54 optimal weight: 0.5980 chunk 119 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 84 optimal weight: 0.0030 chunk 80 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.119704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108441 restraints weight = 13649.627| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.88 r_work: 0.3259 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9766 Z= 0.125 Angle : 0.611 12.586 13279 Z= 0.277 Chirality : 0.042 0.146 1547 Planarity : 0.004 0.067 1676 Dihedral : 4.289 22.410 1328 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.64 % Allowed : 15.36 % Favored : 83.00 % 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: 1.31 (0.24), residues: 1227 helix: 1.78 (0.20), residues: 709 sheet: -0.89 (0.56), residues: 91 loop : -0.20 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 323 TYR 0.020 0.001 TYR A 185 PHE 0.041 0.002 PHE B 168 TRP 0.008 0.001 TRP A 166 HIS 0.003 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9758) covalent geometry : angle 0.56945 (13255) hydrogen bonds : bond 0.03442 ( 543) hydrogen bonds : angle 4.28794 ( 1563) metal coordination : bond 0.00350 ( 8) metal coordination : angle 5.26407 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 237 time to evaluate : 0.401 Fit side-chains REVERT: A 46 MET cc_start: 0.7901 (mmm) cc_final: 0.7459 (mmm) REVERT: A 196 SER cc_start: 0.8534 (t) cc_final: 0.8253 (p) REVERT: B 65 ASP cc_start: 0.8086 (t0) cc_final: 0.7764 (t0) REVERT: B 80 SER cc_start: 0.9085 (m) cc_final: 0.8850 (p) REVERT: B 125 LEU cc_start: 0.8299 (mt) cc_final: 0.8098 (mm) REVERT: B 182 ILE cc_start: 0.8109 (tp) cc_final: 0.7866 (tp) REVERT: B 227 SER cc_start: 0.8554 (OUTLIER) cc_final: 0.8302 (m) REVERT: B 233 MET cc_start: 0.8553 (mmt) cc_final: 0.8313 (mmt) REVERT: B 273 LEU cc_start: 0.8148 (mt) cc_final: 0.7914 (mm) REVERT: C 70 MET cc_start: 0.8073 (mmm) cc_final: 0.7262 (mmm) REVERT: C 133 LEU cc_start: 0.8107 (tp) cc_final: 0.7881 (tt) REVERT: C 161 ARG cc_start: 0.8309 (mmt90) cc_final: 0.8064 (mmm-85) REVERT: C 164 MET cc_start: 0.8334 (mtt) cc_final: 0.8082 (mtm) REVERT: C 225 ILE cc_start: 0.8256 (mm) cc_final: 0.8020 (mt) REVERT: C 248 MET cc_start: 0.8067 (mmp) cc_final: 0.7508 (mmt) REVERT: D 9 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8405 (mtpp) REVERT: D 51 GLU cc_start: 0.7915 (tt0) cc_final: 0.7687 (tt0) REVERT: D 91 MET cc_start: 0.7436 (mtm) cc_final: 0.6864 (mtm) REVERT: D 95 GLU cc_start: 0.7275 (pt0) cc_final: 0.6840 (pt0) REVERT: D 147 MET cc_start: 0.7364 (tpp) cc_final: 0.7128 (tpp) REVERT: D 216 LEU cc_start: 0.8092 (mp) cc_final: 0.7877 (mp) REVERT: D 331 VAL cc_start: 0.8892 (p) cc_final: 0.8581 (m) outliers start: 17 outliers final: 14 residues processed: 242 average time/residue: 0.1128 time to fit residues: 37.4735 Evaluate side-chains 248 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 233 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 266 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 0.0770 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 0.0970 overall best weight: 0.3914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.108953 restraints weight = 13760.105| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.88 r_work: 0.3265 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9766 Z= 0.119 Angle : 0.633 15.425 13279 Z= 0.282 Chirality : 0.041 0.148 1547 Planarity : 0.005 0.066 1676 Dihedral : 4.256 23.668 1328 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.64 % Allowed : 15.27 % Favored : 83.09 % 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: 1.35 (0.25), residues: 1227 helix: 1.80 (0.20), residues: 715 sheet: -0.91 (0.56), residues: 91 loop : -0.18 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 246 TYR 0.019 0.001 TYR A 185 PHE 0.038 0.002 PHE B 168 TRP 0.008 0.001 TRP A 166 HIS 0.003 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9758) covalent geometry : angle 0.59244 (13255) hydrogen bonds : bond 0.03385 ( 543) hydrogen bonds : angle 4.24333 ( 1563) metal coordination : bond 0.00346 ( 8) metal coordination : angle 5.25005 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2746.47 seconds wall clock time: 47 minutes 43.87 seconds (2863.87 seconds total)