Starting phenix.real_space_refine on Tue May 13 00:25:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z21_39742/05_2025/8z21_39742_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z21_39742/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z21_39742/05_2025/8z21_39742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z21_39742/05_2025/8z21_39742.map" model { file = "/net/cci-nas-00/data/ceres_data/8z21_39742/05_2025/8z21_39742_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z21_39742/05_2025/8z21_39742_neut.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.64, per 1000 atoms: 0.80 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.98 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: 2.59 Time building geometry restraints manager: 2.97 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: 17.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 28.010 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.650 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.094 0.017 TRP D 83 HIS 0.010 0.002 HIS B 213 PHE 0.168 0.011 PHE C 169 TYR 0.188 0.021 TYR D 260 ARG 0.006 0.001 ARG D 234 Details of bonding type rmsd hydrogen bonds : bond 0.17682 ( 543) hydrogen bonds : angle 7.27494 ( 1563) metal coordination : bond 0.17631 ( 8) metal coordination : angle 6.82078 ( 24) covalent geometry : bond 0.01556 ( 9758) covalent geometry : angle 1.87464 (13255) *********************** 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 : 0.925 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: 0.2678 time to fit residues: 93.8962 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 : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 D 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.119426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.106970 restraints weight = 13644.219| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.10 r_work: 0.3245 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1780 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= 0.169 Angle : 0.688 11.714 13279 Z= 0.333 Chirality : 0.045 0.154 1547 Planarity : 0.004 0.043 1676 Dihedral : 5.410 31.445 1328 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.45 % Allowed : 6.86 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.24), residues: 1227 helix: 0.68 (0.19), residues: 706 sheet: -0.60 (0.57), residues: 77 loop : -0.26 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 254 HIS 0.004 0.001 HIS D 20 PHE 0.025 0.002 PHE B 239 TYR 0.027 0.002 TYR A 185 ARG 0.005 0.001 ARG D 129 Details of bonding type rmsd hydrogen bonds : bond 0.04637 ( 543) hydrogen bonds : angle 5.04750 ( 1563) metal coordination : bond 0.00831 ( 8) metal coordination : angle 5.94645 ( 24) covalent geometry : bond 0.00393 ( 9758) covalent geometry : angle 0.64078 (13255) *********************** 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 298 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 283 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 46 MET cc_start: 0.7907 (mmm) cc_final: 0.7648 (mmm) REVERT: A 132 MET cc_start: 0.7549 (mmp) cc_final: 0.7185 (mmt) REVERT: A 152 MET cc_start: 0.8014 (ttt) cc_final: 0.7778 (ttt) REVERT: A 196 SER cc_start: 0.8541 (t) cc_final: 0.8308 (p) REVERT: A 218 ARG cc_start: 0.8064 (ttt90) cc_final: 0.7847 (ttt-90) REVERT: B 65 ASP cc_start: 0.8154 (t0) cc_final: 0.7781 (t0) REVERT: B 113 LEU cc_start: 0.8204 (mt) cc_final: 0.8001 (mp) REVERT: B 121 LEU cc_start: 0.8073 (tt) cc_final: 0.7557 (mp) REVERT: B 124 SER cc_start: 0.8563 (m) cc_final: 0.8161 (p) REVERT: B 125 LEU cc_start: 0.8453 (mm) cc_final: 0.8234 (mm) REVERT: B 159 PHE cc_start: 0.8107 (m-10) cc_final: 0.7900 (m-10) REVERT: B 182 ILE cc_start: 0.8036 (tp) cc_final: 0.7826 (tp) REVERT: B 184 ARG cc_start: 0.8447 (tmt170) cc_final: 0.7946 (ttp80) REVERT: B 294 ARG cc_start: 0.7859 (ttm-80) cc_final: 0.7606 (ttm-80) REVERT: C 145 GLU cc_start: 0.7822 (tp30) cc_final: 0.7543 (tp30) REVERT: C 162 MET cc_start: 0.7956 (mmm) cc_final: 0.7282 (mmm) REVERT: C 188 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7909 (mmtp) REVERT: C 208 MET cc_start: 0.8294 (mmm) cc_final: 0.8076 (mmt) REVERT: C 248 MET cc_start: 0.8118 (mmp) cc_final: 0.7501 (mmt) REVERT: C 331 LYS cc_start: 0.8195 (tptp) cc_final: 0.7949 (tptp) REVERT: D 9 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8360 (mtpp) REVERT: D 91 MET cc_start: 0.7305 (mtm) cc_final: 0.6796 (mtm) REVERT: D 95 GLU cc_start: 0.7233 (pt0) cc_final: 0.6691 (pt0) REVERT: D 189 ASP cc_start: 0.7583 (t0) cc_final: 0.7358 (t0) REVERT: D 238 MET cc_start: 0.8563 (mtp) cc_final: 0.8306 (mtm) REVERT: D 329 LEU cc_start: 0.8589 (mm) cc_final: 0.8270 (mp) REVERT: D 330 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8084 (mtpp) outliers start: 15 outliers final: 10 residues processed: 288 average time/residue: 0.2901 time to fit residues: 108.0337 Evaluate side-chains 278 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 268 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 133 VAL 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 74 optimal weight: 0.9980 chunk 95 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 84 optimal weight: 0.0980 chunk 94 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.120098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.107821 restraints weight = 13812.447| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.09 r_work: 0.3240 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9766 Z= 0.125 Angle : 0.599 9.209 13279 Z= 0.284 Chirality : 0.043 0.153 1547 Planarity : 0.004 0.046 1676 Dihedral : 4.773 25.823 1328 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.13 % Allowed : 8.21 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.24), residues: 1227 helix: 1.24 (0.20), residues: 706 sheet: -0.93 (0.55), residues: 83 loop : -0.20 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 26 HIS 0.004 0.001 HIS D 20 PHE 0.023 0.002 PHE B 239 TYR 0.021 0.001 TYR A 185 ARG 0.010 0.001 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 543) hydrogen bonds : angle 4.59615 ( 1563) metal coordination : bond 0.00397 ( 8) metal coordination : angle 5.33139 ( 24) covalent geometry : bond 0.00289 ( 9758) covalent geometry : angle 0.55497 (13255) *********************** 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 291 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 269 time to evaluate : 1.049 Fit side-chains REVERT: A 46 MET cc_start: 0.7804 (mmm) cc_final: 0.7464 (mmm) REVERT: A 75 PHE cc_start: 0.8316 (m-80) cc_final: 0.8075 (m-80) REVERT: A 132 MET cc_start: 0.7627 (mmp) cc_final: 0.7269 (mmt) REVERT: A 152 MET cc_start: 0.7853 (ttt) cc_final: 0.7509 (ttt) REVERT: A 157 ILE cc_start: 0.8187 (mm) cc_final: 0.7946 (mt) REVERT: A 196 SER cc_start: 0.8539 (t) cc_final: 0.8266 (p) REVERT: A 222 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.8086 (tpt170) REVERT: B 65 ASP cc_start: 0.8193 (t0) cc_final: 0.7886 (t0) REVERT: B 80 SER cc_start: 0.9049 (m) cc_final: 0.8825 (p) REVERT: B 121 LEU cc_start: 0.8017 (tt) cc_final: 0.7491 (mp) REVERT: B 124 SER cc_start: 0.8537 (m) cc_final: 0.8164 (p) REVERT: B 125 LEU cc_start: 0.8433 (mm) cc_final: 0.8225 (mm) REVERT: B 182 ILE cc_start: 0.8044 (tp) cc_final: 0.7825 (tp) REVERT: B 221 VAL cc_start: 0.8242 (t) cc_final: 0.7904 (m) REVERT: B 233 MET cc_start: 0.8494 (mmp) cc_final: 0.8108 (mmt) REVERT: C 21 ASN cc_start: 0.7810 (t0) cc_final: 0.7593 (t0) REVERT: C 161 ARG cc_start: 0.8340 (mmt90) cc_final: 0.8063 (mmm-85) REVERT: C 164 MET cc_start: 0.8548 (mtt) cc_final: 0.8312 (mtp) REVERT: C 168 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7830 (mm-30) REVERT: C 248 MET cc_start: 0.8121 (mmp) cc_final: 0.7488 (mmt) REVERT: C 288 ASN cc_start: 0.8655 (m-40) cc_final: 0.8439 (m-40) REVERT: D 9 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8352 (mtpp) REVERT: D 91 MET cc_start: 0.7306 (mtm) cc_final: 0.6746 (mtm) REVERT: D 95 GLU cc_start: 0.7193 (pt0) cc_final: 0.6675 (pt0) REVERT: D 216 LEU cc_start: 0.8421 (mt) cc_final: 0.8220 (mp) REVERT: D 329 LEU cc_start: 0.8559 (mm) cc_final: 0.8281 (mp) REVERT: D 331 VAL cc_start: 0.8852 (p) cc_final: 0.8581 (m) outliers start: 22 outliers final: 11 residues processed: 275 average time/residue: 0.2247 time to fit residues: 84.7610 Evaluate side-chains 269 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 257 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 144 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 D residue 44 THR Chi-restraints excluded: chain D residue 120 ILE 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 53 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.120680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.108455 restraints weight = 13695.062| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.08 r_work: 0.3232 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9766 Z= 0.153 Angle : 0.612 11.205 13279 Z= 0.283 Chirality : 0.043 0.195 1547 Planarity : 0.004 0.049 1676 Dihedral : 4.612 22.588 1328 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.32 % Allowed : 11.40 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1227 helix: 1.45 (0.20), residues: 707 sheet: -1.10 (0.54), residues: 83 loop : -0.19 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 166 HIS 0.004 0.001 HIS D 242 PHE 0.024 0.002 PHE A 17 TYR 0.021 0.001 TYR A 185 ARG 0.009 0.000 ARG C 327 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 543) hydrogen bonds : angle 4.45705 ( 1563) metal coordination : bond 0.00428 ( 8) metal coordination : angle 5.34852 ( 24) covalent geometry : bond 0.00365 ( 9758) covalent geometry : angle 0.56837 (13255) *********************** 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 282 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 258 time to evaluate : 1.057 Fit side-chains REVERT: A 46 MET cc_start: 0.7873 (mmm) cc_final: 0.7512 (mmm) REVERT: A 132 MET cc_start: 0.7627 (mmp) cc_final: 0.7313 (mmp) REVERT: A 152 MET cc_start: 0.7912 (ttt) cc_final: 0.7577 (ttt) REVERT: A 157 ILE cc_start: 0.8259 (mm) cc_final: 0.8013 (mt) REVERT: A 196 SER cc_start: 0.8552 (t) cc_final: 0.8267 (p) REVERT: A 222 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8116 (tpt170) REVERT: B 65 ASP cc_start: 0.8273 (t0) cc_final: 0.7937 (t0) REVERT: B 80 SER cc_start: 0.9095 (m) cc_final: 0.8855 (p) REVERT: B 121 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7517 (mp) REVERT: B 124 SER cc_start: 0.8542 (m) cc_final: 0.8162 (p) REVERT: B 182 ILE cc_start: 0.8093 (tp) cc_final: 0.7873 (tp) REVERT: C 133 LEU cc_start: 0.7982 (tp) cc_final: 0.7779 (tt) REVERT: C 161 ARG cc_start: 0.8376 (mmt90) cc_final: 0.8104 (mmm-85) REVERT: C 208 MET cc_start: 0.8300 (mmm) cc_final: 0.8081 (mmt) REVERT: C 225 ILE cc_start: 0.8206 (mm) cc_final: 0.7964 (mt) REVERT: C 248 MET cc_start: 0.8118 (mmp) cc_final: 0.7470 (mmt) REVERT: D 9 LYS cc_start: 0.8628 (mtpp) cc_final: 0.8367 (mtpp) REVERT: D 91 MET cc_start: 0.7412 (mtm) cc_final: 0.6852 (mtm) REVERT: D 95 GLU cc_start: 0.7280 (pt0) cc_final: 0.6777 (pt0) REVERT: D 147 MET cc_start: 0.7330 (tpp) cc_final: 0.7050 (tpp) REVERT: D 186 ILE cc_start: 0.8282 (pt) cc_final: 0.8060 (mt) REVERT: D 329 LEU cc_start: 0.8572 (mm) cc_final: 0.8314 (mp) REVERT: D 331 VAL cc_start: 0.8914 (p) cc_final: 0.8622 (m) outliers start: 24 outliers final: 14 residues processed: 269 average time/residue: 0.2437 time to fit residues: 90.9333 Evaluate side-chains 273 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 257 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ARG 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 140 LEU 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 253 SER Chi-restraints excluded: chain B residue 264 SER 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 151 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 236 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 90 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3518 r_free = 0.3518 target = 0.118752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106677 restraints weight = 13626.501| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.01 r_work: 0.3233 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9766 Z= 0.164 Angle : 0.614 11.874 13279 Z= 0.284 Chirality : 0.043 0.153 1547 Planarity : 0.004 0.049 1676 Dihedral : 4.536 21.533 1328 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.32 % Allowed : 12.37 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.24), residues: 1227 helix: 1.51 (0.20), residues: 706 sheet: -1.16 (0.53), residues: 86 loop : -0.21 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 166 HIS 0.004 0.001 HIS D 20 PHE 0.032 0.002 PHE B 168 TYR 0.026 0.002 TYR B 64 ARG 0.004 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 543) hydrogen bonds : angle 4.43620 ( 1563) metal coordination : bond 0.00472 ( 8) metal coordination : angle 5.30374 ( 24) covalent geometry : bond 0.00393 ( 9758) covalent geometry : angle 0.57159 (13255) *********************** 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 266 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7891 (mmm) cc_final: 0.7482 (mmm) REVERT: A 132 MET cc_start: 0.7596 (mmp) cc_final: 0.7304 (mmp) REVERT: A 152 MET cc_start: 0.7887 (ttt) cc_final: 0.7562 (ttt) REVERT: A 157 ILE cc_start: 0.8270 (mm) cc_final: 0.8018 (mt) REVERT: A 196 SER cc_start: 0.8555 (t) cc_final: 0.8268 (p) REVERT: A 222 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8067 (mpt180) REVERT: B 65 ASP cc_start: 0.8220 (t0) cc_final: 0.7887 (t0) REVERT: B 80 SER cc_start: 0.9082 (m) cc_final: 0.8777 (p) REVERT: B 121 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7442 (mp) REVERT: B 124 SER cc_start: 0.8526 (m) cc_final: 0.8135 (p) REVERT: B 182 ILE cc_start: 0.8098 (tp) cc_final: 0.7868 (tp) REVERT: B 233 MET cc_start: 0.8467 (mmp) cc_final: 0.8236 (mmt) REVERT: C 133 LEU cc_start: 0.8025 (tp) cc_final: 0.7810 (tt) REVERT: C 161 ARG cc_start: 0.8358 (mmt90) cc_final: 0.7920 (mmm-85) REVERT: C 164 MET cc_start: 0.8479 (mtt) cc_final: 0.8194 (mtm) REVERT: C 208 MET cc_start: 0.8294 (mmm) cc_final: 0.8061 (mmt) REVERT: C 225 ILE cc_start: 0.8241 (mm) cc_final: 0.7993 (mt) REVERT: C 248 MET cc_start: 0.8116 (mmp) cc_final: 0.7486 (mmt) REVERT: D 9 LYS cc_start: 0.8594 (mtpp) cc_final: 0.8340 (mtpp) REVERT: D 91 MET cc_start: 0.7407 (mtm) cc_final: 0.6876 (mtm) REVERT: D 95 GLU cc_start: 0.7300 (pt0) cc_final: 0.6817 (pt0) REVERT: D 147 MET cc_start: 0.7315 (tpp) cc_final: 0.7062 (tpp) REVERT: D 238 MET cc_start: 0.8563 (mtp) cc_final: 0.8354 (mtt) REVERT: D 329 LEU cc_start: 0.8566 (mm) cc_final: 0.8317 (mp) REVERT: D 331 VAL cc_start: 0.8938 (p) cc_final: 0.8612 (m) outliers start: 24 outliers final: 15 residues processed: 250 average time/residue: 0.2273 time to fit residues: 77.1402 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 : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 222 ARG 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 D residue 17 LEU 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 151 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 266 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 31 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 0.0470 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107537 restraints weight = 13669.003| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.01 r_work: 0.3240 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9766 Z= 0.117 Angle : 0.582 11.354 13279 Z= 0.268 Chirality : 0.041 0.148 1547 Planarity : 0.004 0.054 1676 Dihedral : 4.354 20.554 1328 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.22 % Allowed : 13.04 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.24), residues: 1227 helix: 1.64 (0.20), residues: 710 sheet: -1.19 (0.53), residues: 87 loop : -0.15 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 166 HIS 0.004 0.001 HIS A 54 PHE 0.034 0.002 PHE B 168 TYR 0.026 0.001 TYR B 64 ARG 0.008 0.000 ARG C 327 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 543) hydrogen bonds : angle 4.31970 ( 1563) metal coordination : bond 0.00391 ( 8) metal coordination : angle 5.21834 ( 24) covalent geometry : bond 0.00274 ( 9758) covalent geometry : angle 0.53864 (13255) *********************** 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 262 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.934 Fit side-chains REVERT: A 46 MET cc_start: 0.7882 (mmm) cc_final: 0.7243 (mmm) REVERT: A 132 MET cc_start: 0.7607 (mmp) cc_final: 0.7364 (mmp) REVERT: A 152 MET cc_start: 0.7846 (ttt) cc_final: 0.7516 (ttt) REVERT: A 157 ILE cc_start: 0.8268 (mm) cc_final: 0.8027 (mt) REVERT: A 196 SER cc_start: 0.8540 (t) cc_final: 0.8254 (p) REVERT: A 222 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8104 (tpt170) REVERT: B 65 ASP cc_start: 0.8208 (t0) cc_final: 0.7875 (t0) REVERT: B 80 SER cc_start: 0.9075 (m) cc_final: 0.8783 (p) REVERT: B 121 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7731 (mp) REVERT: B 182 ILE cc_start: 0.8065 (tp) cc_final: 0.7823 (tp) REVERT: B 233 MET cc_start: 0.8453 (mmp) cc_final: 0.8226 (mmt) REVERT: C 70 MET cc_start: 0.8118 (mmm) cc_final: 0.7332 (mmm) REVERT: C 133 LEU cc_start: 0.8031 (tp) cc_final: 0.7813 (tt) REVERT: C 161 ARG cc_start: 0.8335 (mmt90) cc_final: 0.8103 (mmm-85) REVERT: C 164 MET cc_start: 0.8482 (mtt) cc_final: 0.8204 (mtm) REVERT: C 208 MET cc_start: 0.8287 (mmm) cc_final: 0.8054 (mmt) REVERT: C 225 ILE cc_start: 0.8200 (mm) cc_final: 0.7948 (mt) REVERT: C 248 MET cc_start: 0.8080 (mmp) cc_final: 0.7469 (mmt) REVERT: D 9 LYS cc_start: 0.8584 (mtpp) cc_final: 0.8336 (mtpp) REVERT: D 91 MET cc_start: 0.7455 (mtm) cc_final: 0.6900 (mtm) REVERT: D 95 GLU cc_start: 0.7309 (pt0) cc_final: 0.6813 (pt0) REVERT: D 147 MET cc_start: 0.7414 (tpp) cc_final: 0.7177 (tpp) REVERT: D 329 LEU cc_start: 0.8500 (mm) cc_final: 0.8280 (mp) REVERT: D 331 VAL cc_start: 0.8887 (p) cc_final: 0.8603 (m) outliers start: 23 outliers final: 16 residues processed: 247 average time/residue: 0.2203 time to fit residues: 74.2793 Evaluate side-chains 247 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 229 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 222 ARG 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 144 LEU 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 285 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 236 LEU Chi-restraints excluded: chain D residue 266 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 38 optimal weight: 0.9980 chunk 52 optimal weight: 0.0570 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 86 optimal weight: 0.0020 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 overall best weight: 0.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 HIS ** D 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.121460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109197 restraints weight = 13754.000| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.09 r_work: 0.3240 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3015 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= 0.119 Angle : 0.594 11.569 13279 Z= 0.271 Chirality : 0.041 0.148 1547 Planarity : 0.004 0.057 1676 Dihedral : 4.267 20.682 1328 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.22 % Allowed : 14.01 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.24), residues: 1227 helix: 1.69 (0.20), residues: 710 sheet: -0.91 (0.54), residues: 91 loop : -0.14 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 176 HIS 0.003 0.001 HIS B 82 PHE 0.041 0.002 PHE B 168 TYR 0.019 0.001 TYR B 64 ARG 0.007 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 543) hydrogen bonds : angle 4.28764 ( 1563) metal coordination : bond 0.00375 ( 8) metal coordination : angle 5.25409 ( 24) covalent geometry : bond 0.00280 ( 9758) covalent geometry : angle 0.55136 (13255) *********************** 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 258 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 0.964 Fit side-chains REVERT: A 46 MET cc_start: 0.7972 (mmm) cc_final: 0.7472 (mmm) REVERT: A 132 MET cc_start: 0.7626 (mmp) cc_final: 0.7406 (mmp) REVERT: A 152 MET cc_start: 0.7881 (ttt) cc_final: 0.7663 (ttm) REVERT: A 157 ILE cc_start: 0.8264 (mm) cc_final: 0.8030 (mt) REVERT: A 196 SER cc_start: 0.8561 (t) cc_final: 0.8258 (p) REVERT: A 198 ILE cc_start: 0.8558 (mm) cc_final: 0.8307 (mt) REVERT: A 222 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8134 (tpt170) REVERT: B 65 ASP cc_start: 0.8238 (t0) cc_final: 0.7935 (t0) REVERT: B 80 SER cc_start: 0.9086 (m) cc_final: 0.8825 (p) REVERT: B 121 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 125 LEU cc_start: 0.8305 (mt) cc_final: 0.8063 (mm) REVERT: B 155 LEU cc_start: 0.8435 (tt) cc_final: 0.8220 (tt) REVERT: B 182 ILE cc_start: 0.8064 (tp) cc_final: 0.7829 (tp) REVERT: B 233 MET cc_start: 0.8457 (mmp) cc_final: 0.8239 (mmt) REVERT: B 273 LEU cc_start: 0.8138 (mt) cc_final: 0.7857 (mm) REVERT: C 70 MET cc_start: 0.8104 (mmm) cc_final: 0.7333 (mmm) REVERT: C 133 LEU cc_start: 0.8052 (tp) cc_final: 0.7820 (tt) REVERT: C 161 ARG cc_start: 0.8320 (mmt90) cc_final: 0.8097 (mmm-85) REVERT: C 164 MET cc_start: 0.8466 (mtt) cc_final: 0.8191 (mtm) REVERT: C 208 MET cc_start: 0.8311 (mmm) cc_final: 0.8072 (mmt) REVERT: C 225 ILE cc_start: 0.8232 (mm) cc_final: 0.7980 (mt) REVERT: C 248 MET cc_start: 0.8040 (mmp) cc_final: 0.7625 (mmt) REVERT: D 9 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8347 (mtpp) REVERT: D 73 LEU cc_start: 0.8330 (mp) cc_final: 0.8127 (mp) REVERT: D 91 MET cc_start: 0.7499 (mtm) cc_final: 0.6941 (mtm) REVERT: D 95 GLU cc_start: 0.7334 (pt0) cc_final: 0.6879 (pt0) REVERT: D 147 MET cc_start: 0.7437 (tpp) cc_final: 0.7219 (tpp) REVERT: D 329 LEU cc_start: 0.8495 (mm) cc_final: 0.8273 (mp) REVERT: D 331 VAL cc_start: 0.8931 (p) cc_final: 0.8614 (m) outliers start: 23 outliers final: 16 residues processed: 245 average time/residue: 0.2285 time to fit residues: 76.0015 Evaluate side-chains 252 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 234 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 222 ARG 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 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 285 ILE Chi-restraints excluded: chain D residue 17 LEU 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 236 LEU 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 43 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 chunk 7 optimal weight: 0.0060 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.121355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.109076 restraints weight = 13906.720| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.10 r_work: 0.3236 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9766 Z= 0.127 Angle : 0.594 11.915 13279 Z= 0.271 Chirality : 0.042 0.149 1547 Planarity : 0.004 0.060 1676 Dihedral : 4.217 20.709 1328 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.93 % Allowed : 14.30 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.24), residues: 1227 helix: 1.73 (0.20), residues: 710 sheet: -0.90 (0.55), residues: 91 loop : -0.13 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 166 HIS 0.003 0.001 HIS B 82 PHE 0.039 0.002 PHE B 168 TYR 0.028 0.001 TYR B 64 ARG 0.007 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 543) hydrogen bonds : angle 4.25222 ( 1563) metal coordination : bond 0.00377 ( 8) metal coordination : angle 5.25984 ( 24) covalent geometry : bond 0.00300 ( 9758) covalent geometry : angle 0.55033 (13255) *********************** 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 253 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 1.056 Fit side-chains REVERT: A 46 MET cc_start: 0.8001 (mmm) cc_final: 0.7476 (mmm) REVERT: A 152 MET cc_start: 0.7873 (ttt) cc_final: 0.7554 (ttt) REVERT: A 157 ILE cc_start: 0.8262 (mm) cc_final: 0.8034 (mt) REVERT: A 196 SER cc_start: 0.8585 (t) cc_final: 0.8285 (p) REVERT: A 222 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.8116 (tpt170) REVERT: A 254 TYR cc_start: 0.8379 (m-80) cc_final: 0.8076 (m-80) REVERT: B 65 ASP cc_start: 0.8223 (t0) cc_final: 0.7915 (t0) REVERT: B 80 SER cc_start: 0.9096 (m) cc_final: 0.8837 (p) REVERT: B 121 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7565 (mp) REVERT: B 125 LEU cc_start: 0.8290 (mt) cc_final: 0.8061 (mm) REVERT: B 182 ILE cc_start: 0.8052 (tp) cc_final: 0.7813 (tp) REVERT: B 233 MET cc_start: 0.8456 (mmp) cc_final: 0.8235 (mmt) REVERT: B 273 LEU cc_start: 0.8148 (mt) cc_final: 0.7865 (mm) REVERT: C 70 MET cc_start: 0.8095 (mmm) cc_final: 0.7257 (mmm) REVERT: C 133 LEU cc_start: 0.8062 (tp) cc_final: 0.7822 (tt) REVERT: C 161 ARG cc_start: 0.8316 (mmt90) cc_final: 0.8095 (mmm-85) REVERT: C 164 MET cc_start: 0.8461 (mtt) cc_final: 0.8186 (mtm) REVERT: C 225 ILE cc_start: 0.8259 (mm) cc_final: 0.8010 (mt) REVERT: C 248 MET cc_start: 0.8053 (mmp) cc_final: 0.7615 (mmt) REVERT: D 9 LYS cc_start: 0.8607 (mtpp) cc_final: 0.8360 (mtpp) REVERT: D 18 LYS cc_start: 0.8669 (mttp) cc_final: 0.8429 (mttm) REVERT: D 91 MET cc_start: 0.7535 (mtm) cc_final: 0.6953 (mtm) REVERT: D 95 GLU cc_start: 0.7345 (pt0) cc_final: 0.6902 (pt0) REVERT: D 147 MET cc_start: 0.7453 (tpp) cc_final: 0.7234 (tpp) REVERT: D 331 VAL cc_start: 0.8906 (p) cc_final: 0.8586 (m) outliers start: 20 outliers final: 18 residues processed: 240 average time/residue: 0.2373 time to fit residues: 77.2644 Evaluate side-chains 251 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 231 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 222 ARG 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 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 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 236 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 112 optimal weight: 1.9990 chunk 95 optimal weight: 0.0170 chunk 10 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 54 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 3 optimal weight: 0.1980 chunk 53 optimal weight: 0.6980 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.120453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108859 restraints weight = 13855.218| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.01 r_work: 0.3244 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9766 Z= 0.103 Angle : 0.591 11.347 13279 Z= 0.267 Chirality : 0.041 0.143 1547 Planarity : 0.004 0.065 1676 Dihedral : 4.128 21.269 1328 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.03 % Allowed : 14.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1227 helix: 1.81 (0.20), residues: 711 sheet: -0.70 (0.56), residues: 90 loop : -0.07 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 166 HIS 0.003 0.001 HIS B 82 PHE 0.039 0.002 PHE B 168 TYR 0.024 0.001 TYR B 64 ARG 0.007 0.000 ARG C 246 Details of bonding type rmsd hydrogen bonds : bond 0.03199 ( 543) hydrogen bonds : angle 4.20800 ( 1563) metal coordination : bond 0.00314 ( 8) metal coordination : angle 5.27757 ( 24) covalent geometry : bond 0.00237 ( 9758) covalent geometry : angle 0.54770 (13255) *********************** 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 252 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.981 Fit side-chains REVERT: A 46 MET cc_start: 0.8037 (mmm) cc_final: 0.7504 (mmm) REVERT: A 152 MET cc_start: 0.7859 (ttt) cc_final: 0.7636 (ttm) REVERT: A 196 SER cc_start: 0.8549 (t) cc_final: 0.8257 (p) REVERT: A 222 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.8037 (mpt180) REVERT: B 65 ASP cc_start: 0.8151 (t0) cc_final: 0.7850 (t0) REVERT: B 80 SER cc_start: 0.9085 (m) cc_final: 0.8816 (p) REVERT: B 121 LEU cc_start: 0.7953 (tt) cc_final: 0.7667 (mp) REVERT: B 182 ILE cc_start: 0.8010 (tp) cc_final: 0.7769 (tp) REVERT: B 233 MET cc_start: 0.8450 (mmp) cc_final: 0.8171 (mmt) REVERT: B 273 LEU cc_start: 0.8090 (mt) cc_final: 0.7830 (mm) REVERT: C 70 MET cc_start: 0.8058 (mmm) cc_final: 0.7331 (mmm) REVERT: C 133 LEU cc_start: 0.8050 (tp) cc_final: 0.7805 (tt) REVERT: C 161 ARG cc_start: 0.8270 (mmt90) cc_final: 0.8008 (mmm-85) REVERT: C 164 MET cc_start: 0.8396 (mtt) cc_final: 0.8127 (mtm) REVERT: C 225 ILE cc_start: 0.8170 (mm) cc_final: 0.7928 (mt) REVERT: C 248 MET cc_start: 0.8051 (mmp) cc_final: 0.7569 (mmt) REVERT: C 327 ARG cc_start: 0.7380 (tpt-90) cc_final: 0.5607 (tpt-90) REVERT: D 9 LYS cc_start: 0.8596 (mtpp) cc_final: 0.8357 (mtpp) REVERT: D 18 LYS cc_start: 0.8639 (mttp) cc_final: 0.8400 (mttm) REVERT: D 91 MET cc_start: 0.7490 (mtm) cc_final: 0.6907 (mtm) REVERT: D 95 GLU cc_start: 0.7312 (pt0) cc_final: 0.6892 (pt0) REVERT: D 331 VAL cc_start: 0.8870 (p) cc_final: 0.8584 (m) outliers start: 21 outliers final: 15 residues processed: 240 average time/residue: 0.2323 time to fit residues: 75.3053 Evaluate side-chains 250 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 285 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 236 LEU 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: 0.9980 chunk 31 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 230 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.119212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.107971 restraints weight = 13943.440| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.89 r_work: 0.3269 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9766 Z= 0.155 Angle : 0.632 12.677 13279 Z= 0.285 Chirality : 0.043 0.175 1547 Planarity : 0.004 0.066 1676 Dihedral : 4.207 19.363 1328 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.55 % Allowed : 15.65 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.24), residues: 1227 helix: 1.77 (0.20), residues: 710 sheet: -0.80 (0.56), residues: 90 loop : -0.11 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 166 HIS 0.004 0.001 HIS B 82 PHE 0.046 0.002 PHE B 168 TYR 0.023 0.001 TYR B 64 ARG 0.008 0.001 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 543) hydrogen bonds : angle 4.29197 ( 1563) metal coordination : bond 0.00393 ( 8) metal coordination : angle 5.28926 ( 24) covalent geometry : bond 0.00375 ( 9758) covalent geometry : angle 0.59077 (13255) ********************** 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 249 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 1.122 Fit side-chains REVERT: A 46 MET cc_start: 0.7900 (mmm) cc_final: 0.7413 (mmm) REVERT: A 152 MET cc_start: 0.7741 (ttt) cc_final: 0.7456 (ttt) REVERT: A 196 SER cc_start: 0.8550 (t) cc_final: 0.8264 (p) REVERT: A 222 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8071 (mpt180) REVERT: B 65 ASP cc_start: 0.8118 (t0) cc_final: 0.7813 (t0) REVERT: B 80 SER cc_start: 0.9086 (m) cc_final: 0.8819 (p) REVERT: B 121 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7712 (mp) REVERT: B 182 ILE cc_start: 0.8095 (tp) cc_final: 0.7865 (tp) REVERT: B 227 SER cc_start: 0.8583 (t) cc_final: 0.8337 (m) REVERT: B 273 LEU cc_start: 0.8147 (mt) cc_final: 0.7901 (mm) REVERT: C 70 MET cc_start: 0.8068 (mmm) cc_final: 0.7241 (mmm) REVERT: C 133 LEU cc_start: 0.8105 (tp) cc_final: 0.7866 (tt) REVERT: C 164 MET cc_start: 0.8328 (mtt) cc_final: 0.8074 (mtm) REVERT: C 225 ILE cc_start: 0.8278 (mm) cc_final: 0.8036 (mt) REVERT: C 248 MET cc_start: 0.8031 (mmp) cc_final: 0.7597 (mmt) REVERT: D 9 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8438 (mtpp) REVERT: D 91 MET cc_start: 0.7494 (mtm) cc_final: 0.6916 (mtm) REVERT: D 95 GLU cc_start: 0.7288 (pt0) cc_final: 0.6888 (pt0) REVERT: D 331 VAL cc_start: 0.8884 (p) cc_final: 0.8580 (m) outliers start: 16 outliers final: 14 residues processed: 240 average time/residue: 0.2277 time to fit residues: 75.1769 Evaluate side-chains 242 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 226 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 222 ARG 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 143 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 285 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 236 LEU 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 1 optimal weight: 0.2980 chunk 93 optimal weight: 0.3980 chunk 16 optimal weight: 0.0570 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 48 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 overall best weight: 0.2856 ------------------------------------------------------------------------------- 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 = 0.3538 r_free = 0.3538 target = 0.120439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108871 restraints weight = 13858.452| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.00 r_work: 0.3261 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9766 Z= 0.107 Angle : 0.610 11.914 13279 Z= 0.273 Chirality : 0.041 0.153 1547 Planarity : 0.004 0.066 1676 Dihedral : 4.120 18.380 1328 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.45 % Allowed : 16.14 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1227 helix: 1.90 (0.20), residues: 704 sheet: -0.75 (0.57), residues: 91 loop : -0.11 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 166 HIS 0.003 0.001 HIS D 230 PHE 0.040 0.002 PHE B 168 TYR 0.024 0.001 TYR B 64 ARG 0.008 0.000 ARG C 325 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 543) hydrogen bonds : angle 4.22498 ( 1563) metal coordination : bond 0.00319 ( 8) metal coordination : angle 5.28933 ( 24) covalent geometry : bond 0.00246 ( 9758) covalent geometry : angle 0.56800 (13255) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5440.06 seconds wall clock time: 95 minutes 21.42 seconds (5721.42 seconds total)