Starting phenix.real_space_refine on Sat Aug 23 02:36:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cr1_16801/08_2025/8cr1_16801.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cr1_16801/08_2025/8cr1_16801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cr1_16801/08_2025/8cr1_16801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cr1_16801/08_2025/8cr1_16801.map" model { file = "/net/cci-nas-00/data/ceres_data/8cr1_16801/08_2025/8cr1_16801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cr1_16801/08_2025/8cr1_16801.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.057 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 Zn 1 6.06 5 S 76 5.16 5 C 5978 2.51 5 N 1502 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9205 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2464 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 18, 'TRANS': 294} Chain breaks: 1 Chain: "C" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2138 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 1 Chain: "B" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2464 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 18, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2138 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 8, 'TRANS': 257} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2009 SG CYS A 289 35.437 43.592 12.321 1.00 37.49 S ATOM 2032 SG CYS A 292 33.793 45.853 15.139 1.00 32.41 S ATOM 6611 SG CYS B 289 35.863 47.142 12.343 1.00 37.99 S ATOM 6634 SG CYS B 292 37.505 44.880 15.160 1.00 34.33 S Time building chain proxies: 2.62, per 1000 atoms: 0.28 Number of scatterers: 9205 At special positions: 0 Unit cell: (72.09, 91.53, 136.08, 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) Zn 1 29.99 S 76 16.00 O 1648 8.00 N 1502 7.00 C 5978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 208 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 275 " - pdb=" SG CYS C1157 " distance=1.99 Simple disulfide: pdb=" SG CYS D 208 " - pdb=" SG CYS D 284 " distance=2.03 Simple disulfide: pdb=" SG CYS D 275 " - pdb=" SG CYS D1157 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 370.9 milliseconds Enol-peptide restraints added in 1.2 microseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 289 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 289 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 292 " pdb="ZN ZN A 401 " - pdb=" SG CYS B 292 " Number of angles added : 6 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2220 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 2 sheets defined 73.2% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 removed outlier: 3.714A pdb=" N ILE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 63 removed outlier: 3.622A pdb=" N CYS A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 83 removed outlier: 3.820A pdb=" N ASP A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 114 removed outlier: 4.013A pdb=" N LEU A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 122 Processing helix chain 'A' and resid 125 through 138 removed outlier: 4.219A pdb=" N LYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 159 removed outlier: 3.630A pdb=" N GLU A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 removed outlier: 3.644A pdb=" N LEU A 177 " --> pdb=" O LEU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 193 Processing helix chain 'A' and resid 193 through 205 removed outlier: 3.591A pdb=" N SER A 198 " --> pdb=" O LYS A 194 " (cutoff:3.500A) Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 215 through 238 removed outlier: 3.973A pdb=" N ALA A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Proline residue: A 227 - end of helix Processing helix chain 'A' and resid 239 through 242 removed outlier: 4.029A pdb=" N THR A 242 " --> pdb=" O PRO A 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'A' and resid 289 through 310 Processing helix chain 'A' and resid 327 through 340 Processing helix chain 'C' and resid 192 through 206 Processing helix chain 'C' and resid 214 through 231 Processing helix chain 'C' and resid 242 through 249 removed outlier: 3.951A pdb=" N ALA C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 291 Processing helix chain 'C' and resid 1006 through 1027 Processing helix chain 'C' and resid 1027 through 1032 Processing helix chain 'C' and resid 1032 through 1063 removed outlier: 4.349A pdb=" N VAL C1038 " --> pdb=" O PHE C1034 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU C1044 " --> pdb=" O GLN C1040 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN C1045 " --> pdb=" O LYS C1041 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C1053 " --> pdb=" O MET C1049 " (cutoff:3.500A) Processing helix chain 'C' and resid 1068 through 1124 Processing helix chain 'C' and resid 1132 through 1136 Processing helix chain 'C' and resid 1139 through 1144 Processing helix chain 'C' and resid 1151 through 1169 removed outlier: 3.769A pdb=" N THR C1156 " --> pdb=" O GLY C1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 34 removed outlier: 3.714A pdb=" N ILE B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 63 removed outlier: 3.622A pdb=" N CYS B 53 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 83 removed outlier: 3.820A pdb=" N ASP B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 removed outlier: 4.013A pdb=" N LEU B 109 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 122 Processing helix chain 'B' and resid 125 through 138 removed outlier: 4.219A pdb=" N LYS B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 159 removed outlier: 3.629A pdb=" N GLU B 144 " --> pdb=" O PRO B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 removed outlier: 3.644A pdb=" N LEU B 177 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 193 through 205 removed outlier: 3.591A pdb=" N SER B 198 " --> pdb=" O LYS B 194 " (cutoff:3.500A) Proline residue: B 199 - end of helix Processing helix chain 'B' and resid 215 through 238 removed outlier: 3.973A pdb=" N ALA B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 239 through 242 removed outlier: 4.028A pdb=" N THR B 242 " --> pdb=" O PRO B 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 239 through 242' Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 289 through 310 Processing helix chain 'B' and resid 327 through 340 Processing helix chain 'D' and resid 192 through 206 Processing helix chain 'D' and resid 214 through 231 Processing helix chain 'D' and resid 242 through 249 removed outlier: 3.952A pdb=" N ALA D 246 " --> pdb=" O VAL D 242 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 291 Processing helix chain 'D' and resid 1006 through 1027 Processing helix chain 'D' and resid 1027 through 1032 Processing helix chain 'D' and resid 1032 through 1063 removed outlier: 4.349A pdb=" N VAL D1038 " --> pdb=" O PHE D1034 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU D1044 " --> pdb=" O GLN D1040 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN D1045 " --> pdb=" O LYS D1041 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D1053 " --> pdb=" O MET D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1068 through 1124 Processing helix chain 'D' and resid 1132 through 1136 Processing helix chain 'D' and resid 1139 through 1144 Processing helix chain 'D' and resid 1151 through 1169 removed outlier: 3.769A pdb=" N THR D1156 " --> pdb=" O GLY D1152 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 removed outlier: 6.267A pdb=" N VAL A 68 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N MET A 103 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE A 70 " --> pdb=" O MET A 103 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 69 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ASP A 166 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE A 71 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN A 274 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE A 275 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 318 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A 277 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 92 through 93 removed outlier: 6.267A pdb=" N VAL B 68 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N MET B 103 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE B 70 " --> pdb=" O MET B 103 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU B 69 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ASP B 166 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ILE B 71 " --> pdb=" O ASP B 166 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN B 274 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 275 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU B 318 " --> pdb=" O ILE B 275 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL B 277 " --> pdb=" O LEU B 318 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2178 1.33 - 1.45: 1803 1.45 - 1.58: 5297 1.58 - 1.70: 0 1.70 - 1.82: 122 Bond restraints: 9400 Sorted by residual: bond pdb=" C PHE D1145 " pdb=" N PRO D1146 " ideal model delta sigma weight residual 1.333 1.352 -0.019 1.20e-02 6.94e+03 2.40e+00 bond pdb=" C PHE C1145 " pdb=" N PRO C1146 " ideal model delta sigma weight residual 1.333 1.351 -0.018 1.20e-02 6.94e+03 2.32e+00 bond pdb=" CA GLU B 251 " pdb=" CB GLU B 251 " ideal model delta sigma weight residual 1.534 1.511 0.023 1.65e-02 3.67e+03 2.00e+00 bond pdb=" CG GLU B 251 " pdb=" CD GLU B 251 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 1.91e+00 bond pdb=" CA GLU A 251 " pdb=" CB GLU A 251 " ideal model delta sigma weight residual 1.534 1.512 0.022 1.65e-02 3.67e+03 1.84e+00 ... (remaining 9395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 12508 2.37 - 4.75: 161 4.75 - 7.12: 32 7.12 - 9.50: 7 9.50 - 11.87: 4 Bond angle restraints: 12712 Sorted by residual: angle pdb=" CB MET B 127 " pdb=" CG MET B 127 " pdb=" SD MET B 127 " ideal model delta sigma weight residual 112.70 124.57 -11.87 3.00e+00 1.11e-01 1.57e+01 angle pdb=" CB MET A 127 " pdb=" CG MET A 127 " pdb=" SD MET A 127 " ideal model delta sigma weight residual 112.70 124.54 -11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" C ALA A 135 " pdb=" N MET A 136 " pdb=" CA MET A 136 " ideal model delta sigma weight residual 122.38 115.86 6.52 1.81e+00 3.05e-01 1.30e+01 angle pdb=" C ALA B 135 " pdb=" N MET B 136 " pdb=" CA MET B 136 " ideal model delta sigma weight residual 122.38 115.87 6.51 1.81e+00 3.05e-01 1.29e+01 angle pdb=" CB LYS A 290 " pdb=" CG LYS A 290 " pdb=" CD LYS A 290 " ideal model delta sigma weight residual 111.30 118.90 -7.60 2.30e+00 1.89e-01 1.09e+01 ... (remaining 12707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 5154 17.86 - 35.71: 462 35.71 - 53.57: 84 53.57 - 71.42: 14 71.42 - 89.28: 6 Dihedral angle restraints: 5720 sinusoidal: 2316 harmonic: 3404 Sorted by residual: dihedral pdb=" CB CYS C 208 " pdb=" SG CYS C 208 " pdb=" SG CYS C 284 " pdb=" CB CYS C 284 " ideal model delta sinusoidal sigma weight residual 93.00 39.72 53.28 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CB CYS D 208 " pdb=" SG CYS D 208 " pdb=" SG CYS D 284 " pdb=" CB CYS D 284 " ideal model delta sinusoidal sigma weight residual 93.00 39.74 53.26 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" SG CYS C 275 " pdb=" CB CYS C1157 " pdb=" SG CYS C1157 " pdb=" CA CYS C1157 " ideal model delta sinusoidal sigma weight residual -73.00 -9.64 -63.36 1 2.00e+01 2.50e-03 1.32e+01 ... (remaining 5717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 936 0.036 - 0.071: 361 0.071 - 0.107: 119 0.107 - 0.143: 44 0.143 - 0.178: 8 Chirality restraints: 1468 Sorted by residual: chirality pdb=" CA GLU D 286 " pdb=" N GLU D 286 " pdb=" C GLU D 286 " pdb=" CB GLU D 286 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.94e-01 chirality pdb=" CA GLU C 286 " pdb=" N GLU C 286 " pdb=" C GLU C 286 " pdb=" CB GLU C 286 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CA GLU C 269 " pdb=" N GLU C 269 " pdb=" C GLU C 269 " pdb=" CB GLU C 269 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1465 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 106 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO B 107 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO B 107 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 107 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 106 " 0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO A 107 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 107 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 107 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 217 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.45e+00 pdb=" C PHE D 217 " -0.037 2.00e-02 2.50e+03 pdb=" O PHE D 217 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU D 218 " 0.012 2.00e-02 2.50e+03 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1817 2.77 - 3.31: 9587 3.31 - 3.84: 15649 3.84 - 4.37: 17043 4.37 - 4.90: 29045 Nonbonded interactions: 73141 Sorted by model distance: nonbonded pdb=" OG SER A 80 " pdb=" OE2 GLU A 104 " model vdw 2.243 3.040 nonbonded pdb=" OG SER B 80 " pdb=" OE2 GLU B 104 " model vdw 2.244 3.040 nonbonded pdb=" O ASP A 308 " pdb=" NH2 ARG C1074 " model vdw 2.262 3.120 nonbonded pdb=" NE1 TRP A 39 " pdb=" OE1 GLN A 235 " model vdw 2.296 3.120 nonbonded pdb=" NE1 TRP B 39 " pdb=" OE1 GLN B 235 " model vdw 2.296 3.120 ... (remaining 73136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 344) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.140 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9408 Z= 0.157 Angle : 0.737 11.871 12726 Z= 0.367 Chirality : 0.045 0.178 1468 Planarity : 0.005 0.058 1582 Dihedral : 14.007 89.275 3488 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.10 % Allowed : 0.00 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.25), residues: 1142 helix: 1.01 (0.18), residues: 794 sheet: -2.23 (0.45), residues: 92 loop : -1.75 (0.41), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 204 TYR 0.012 0.001 TYR D 277 PHE 0.036 0.002 PHE D1019 TRP 0.022 0.002 TRP D1158 HIS 0.004 0.001 HIS B 323 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9400) covalent geometry : angle 0.72338 (12712) SS BOND : bond 0.03004 ( 4) SS BOND : angle 2.50616 ( 8) hydrogen bonds : bond 0.10744 ( 622) hydrogen bonds : angle 5.04411 ( 1824) metal coordination : bond 0.00183 ( 4) metal coordination : angle 5.98601 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 193 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 MET cc_start: 0.3999 (pmm) cc_final: 0.1398 (mmt) outliers start: 1 outliers final: 1 residues processed: 194 average time/residue: 0.1063 time to fit residues: 28.2545 Evaluate side-chains 135 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1008 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 40.0000 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.0170 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 GLN C1022 ASN D1022 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.246238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.189350 restraints weight = 10500.206| |-----------------------------------------------------------------------------| r_work (start): 0.4253 rms_B_bonded: 1.88 r_work: 0.3813 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9408 Z= 0.168 Angle : 0.662 7.334 12726 Z= 0.335 Chirality : 0.045 0.153 1468 Planarity : 0.005 0.057 1582 Dihedral : 4.147 27.012 1230 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.98 % Allowed : 12.21 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.25), residues: 1142 helix: 1.27 (0.18), residues: 796 sheet: -2.29 (0.45), residues: 92 loop : -1.93 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 204 TYR 0.010 0.001 TYR A 302 PHE 0.022 0.002 PHE C 214 TRP 0.033 0.002 TRP C1158 HIS 0.003 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 9400) covalent geometry : angle 0.65338 (12712) SS BOND : bond 0.00149 ( 4) SS BOND : angle 1.32715 ( 8) hydrogen bonds : bond 0.04298 ( 622) hydrogen bonds : angle 4.47366 ( 1824) metal coordination : bond 0.01455 ( 4) metal coordination : angle 4.81282 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7611 (mp0) cc_final: 0.7144 (mp0) REVERT: A 326 ARG cc_start: 0.7364 (ttp80) cc_final: 0.7008 (ptm160) REVERT: C 1066 MET cc_start: 0.8424 (mmt) cc_final: 0.8178 (mmm) REVERT: B 293 GLU cc_start: 0.7672 (mp0) cc_final: 0.7112 (mp0) REVERT: B 326 ARG cc_start: 0.7229 (ttp80) cc_final: 0.6845 (ptm160) REVERT: D 267 MET cc_start: 0.7948 (ptm) cc_final: 0.7614 (ptt) outliers start: 10 outliers final: 7 residues processed: 166 average time/residue: 0.1118 time to fit residues: 25.1419 Evaluate side-chains 149 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 108 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1008 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.246465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.4265 r_free = 0.4265 target = 0.185156 restraints weight = 10502.598| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 1.63 r_work: 0.3840 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9408 Z= 0.144 Angle : 0.622 6.920 12726 Z= 0.315 Chirality : 0.043 0.153 1468 Planarity : 0.005 0.060 1582 Dihedral : 3.939 13.870 1228 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.56 % Allowed : 17.29 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.25), residues: 1142 helix: 1.46 (0.18), residues: 796 sheet: -2.39 (0.43), residues: 92 loop : -1.87 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 259 TYR 0.010 0.001 TYR B 342 PHE 0.016 0.001 PHE D 214 TRP 0.038 0.002 TRP D1158 HIS 0.002 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9400) covalent geometry : angle 0.61531 (12712) SS BOND : bond 0.00596 ( 4) SS BOND : angle 1.10477 ( 8) hydrogen bonds : bond 0.03908 ( 622) hydrogen bonds : angle 4.25396 ( 1824) metal coordination : bond 0.01132 ( 4) metal coordination : angle 4.21377 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7418 (mp0) cc_final: 0.6924 (mp0) REVERT: A 326 ARG cc_start: 0.7285 (ttp80) cc_final: 0.6965 (ptm160) REVERT: C 258 ASN cc_start: 0.8060 (m110) cc_final: 0.7835 (m110) REVERT: C 1066 MET cc_start: 0.8301 (mmt) cc_final: 0.8083 (mmm) REVERT: B 326 ARG cc_start: 0.7300 (ttp80) cc_final: 0.6977 (ptm160) REVERT: D 267 MET cc_start: 0.8000 (ptm) cc_final: 0.7677 (ptt) REVERT: D 1116 MET cc_start: 0.9076 (mmm) cc_final: 0.8685 (mtp) outliers start: 16 outliers final: 9 residues processed: 163 average time/residue: 0.1064 time to fit residues: 23.7267 Evaluate side-chains 151 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1008 HIS Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS C1022 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.243363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.175315 restraints weight = 10454.421| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.05 r_work: 0.3648 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9408 Z= 0.234 Angle : 0.687 9.798 12726 Z= 0.346 Chirality : 0.046 0.153 1468 Planarity : 0.005 0.060 1582 Dihedral : 4.111 14.135 1228 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.73 % Allowed : 19.04 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.25), residues: 1142 helix: 1.39 (0.18), residues: 796 sheet: -3.09 (0.39), residues: 98 loop : -1.86 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 192 TYR 0.012 0.001 TYR A 302 PHE 0.020 0.002 PHE A 41 TRP 0.040 0.002 TRP D1158 HIS 0.023 0.002 HIS D1008 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 9400) covalent geometry : angle 0.66988 (12712) SS BOND : bond 0.00266 ( 4) SS BOND : angle 0.96281 ( 8) hydrogen bonds : bond 0.04296 ( 622) hydrogen bonds : angle 4.30350 ( 1824) metal coordination : bond 0.01502 ( 4) metal coordination : angle 7.06907 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7380 (mp0) cc_final: 0.6921 (mp0) REVERT: A 326 ARG cc_start: 0.7454 (ttp80) cc_final: 0.7115 (ptm160) REVERT: C 258 ASN cc_start: 0.8057 (m110) cc_final: 0.7827 (m110) REVERT: C 1022 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8229 (m110) REVERT: B 293 GLU cc_start: 0.7425 (mp0) cc_final: 0.6939 (mp0) REVERT: B 326 ARG cc_start: 0.7502 (ttp80) cc_final: 0.7111 (ptm160) REVERT: D 267 MET cc_start: 0.8098 (ptm) cc_final: 0.7814 (ptt) REVERT: D 1049 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7049 (tmm) outliers start: 28 outliers final: 14 residues processed: 162 average time/residue: 0.1100 time to fit residues: 24.2497 Evaluate side-chains 153 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1022 ASN Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Chi-restraints excluded: chain D residue 1109 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 68 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 86 optimal weight: 0.0370 chunk 104 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 17 optimal weight: 0.0470 chunk 108 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1022 ASN B 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.245281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3979 r_free = 0.3979 target = 0.162417 restraints weight = 10355.636| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.25 r_work: 0.3661 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9408 Z= 0.137 Angle : 0.632 7.988 12726 Z= 0.317 Chirality : 0.043 0.157 1468 Planarity : 0.005 0.065 1582 Dihedral : 3.999 13.561 1228 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.52 % Allowed : 18.85 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.26), residues: 1142 helix: 1.55 (0.18), residues: 796 sheet: -3.09 (0.40), residues: 98 loop : -1.81 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1050 TYR 0.020 0.001 TYR C 230 PHE 0.015 0.001 PHE C 214 TRP 0.042 0.002 TRP D1158 HIS 0.002 0.001 HIS D1008 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9400) covalent geometry : angle 0.61746 (12712) SS BOND : bond 0.00205 ( 4) SS BOND : angle 3.41368 ( 8) hydrogen bonds : bond 0.03879 ( 622) hydrogen bonds : angle 4.18125 ( 1824) metal coordination : bond 0.01034 ( 4) metal coordination : angle 4.76577 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: A 326 ARG cc_start: 0.7313 (ttp80) cc_final: 0.6963 (ptm160) REVERT: B 293 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6509 (mp0) REVERT: B 326 ARG cc_start: 0.7343 (ttp80) cc_final: 0.6986 (ptm160) REVERT: D 267 MET cc_start: 0.8097 (ptm) cc_final: 0.7835 (ptt) REVERT: D 283 PHE cc_start: 0.8374 (t80) cc_final: 0.8091 (t80) REVERT: D 286 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6412 (pm20) REVERT: D 1022 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8288 (m110) REVERT: D 1049 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7050 (tmm) REVERT: D 1116 MET cc_start: 0.9113 (mmm) cc_final: 0.8740 (mtp) outliers start: 36 outliers final: 18 residues processed: 180 average time/residue: 0.0922 time to fit residues: 22.7607 Evaluate side-chains 163 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1022 ASN Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1008 HIS Chi-restraints excluded: chain D residue 1022 ASN Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Chi-restraints excluded: chain D residue 1109 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 73 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1022 ASN D1008 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.242600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.157910 restraints weight = 10422.768| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.98 r_work: 0.3464 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9408 Z= 0.206 Angle : 0.701 10.144 12726 Z= 0.357 Chirality : 0.045 0.162 1468 Planarity : 0.005 0.058 1582 Dihedral : 4.130 14.226 1228 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.12 % Allowed : 19.73 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.25), residues: 1142 helix: 1.50 (0.18), residues: 792 sheet: -2.93 (0.41), residues: 92 loop : -1.96 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1050 TYR 0.036 0.001 TYR C 230 PHE 0.016 0.001 PHE B 252 TRP 0.056 0.003 TRP D1158 HIS 0.004 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 9400) covalent geometry : angle 0.66904 (12712) SS BOND : bond 0.00369 ( 4) SS BOND : angle 6.28720 ( 8) hydrogen bonds : bond 0.04171 ( 622) hydrogen bonds : angle 4.23109 ( 1824) metal coordination : bond 0.01319 ( 4) metal coordination : angle 6.42061 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.5220 (ppp) cc_final: 0.4965 (ppp) REVERT: A 293 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6826 (mp0) REVERT: A 326 ARG cc_start: 0.7407 (ttp80) cc_final: 0.7017 (ptm160) REVERT: C 218 LEU cc_start: 0.8709 (tp) cc_final: 0.8493 (mt) REVERT: C 1116 MET cc_start: 0.9190 (mmm) cc_final: 0.8692 (mtp) REVERT: B 204 MET cc_start: 0.5360 (ppp) cc_final: 0.5132 (ppp) REVERT: B 293 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6831 (mp0) REVERT: B 326 ARG cc_start: 0.7377 (ttp80) cc_final: 0.6984 (ptm160) REVERT: D 267 MET cc_start: 0.8124 (ptm) cc_final: 0.7822 (ptt) REVERT: D 1049 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6971 (tmm) outliers start: 32 outliers final: 21 residues processed: 171 average time/residue: 0.0819 time to fit residues: 19.4041 Evaluate side-chains 161 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 230 TYR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1022 ASN Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 1008 HIS Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Chi-restraints excluded: chain D residue 1109 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 82 optimal weight: 0.0770 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.243795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.165308 restraints weight = 10351.192| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 3.08 r_work: 0.3477 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9408 Z= 0.156 Angle : 0.671 8.360 12726 Z= 0.341 Chirality : 0.044 0.166 1468 Planarity : 0.005 0.056 1582 Dihedral : 4.097 14.373 1228 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.83 % Allowed : 20.51 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.25), residues: 1142 helix: 1.57 (0.18), residues: 792 sheet: -2.93 (0.43), residues: 92 loop : -1.97 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1050 TYR 0.039 0.001 TYR C 230 PHE 0.014 0.001 PHE B 252 TRP 0.065 0.003 TRP D1158 HIS 0.005 0.001 HIS D1008 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9400) covalent geometry : angle 0.65377 (12712) SS BOND : bond 0.00509 ( 4) SS BOND : angle 4.13459 ( 8) hydrogen bonds : bond 0.03971 ( 622) hydrogen bonds : angle 4.18549 ( 1824) metal coordination : bond 0.01069 ( 4) metal coordination : angle 5.28393 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6779 (mp0) REVERT: A 326 ARG cc_start: 0.7410 (ttp80) cc_final: 0.7022 (ptm160) REVERT: C 218 LEU cc_start: 0.8715 (tp) cc_final: 0.8497 (mt) REVERT: C 225 MET cc_start: 0.6813 (mtp) cc_final: 0.5787 (mmp) REVERT: C 1116 MET cc_start: 0.9196 (mmm) cc_final: 0.8756 (mtp) REVERT: B 293 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: B 326 ARG cc_start: 0.7398 (ttp80) cc_final: 0.6997 (ptm160) REVERT: D 267 MET cc_start: 0.8105 (ptm) cc_final: 0.7811 (ptt) REVERT: D 1022 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8297 (m110) REVERT: D 1049 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6951 (ppp) REVERT: D 1116 MET cc_start: 0.9150 (mmm) cc_final: 0.8800 (mtp) outliers start: 29 outliers final: 21 residues processed: 160 average time/residue: 0.0845 time to fit residues: 18.9101 Evaluate side-chains 164 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 230 TYR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1109 TYR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1008 HIS Chi-restraints excluded: chain D residue 1022 ASN Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Chi-restraints excluded: chain D residue 1109 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 56 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 HIS D1008 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.243742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.164119 restraints weight = 10335.871| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 3.04 r_work: 0.3515 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9408 Z= 0.169 Angle : 0.682 9.429 12726 Z= 0.348 Chirality : 0.045 0.171 1468 Planarity : 0.005 0.056 1582 Dihedral : 4.081 15.311 1228 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.32 % Allowed : 20.90 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.25), residues: 1142 helix: 1.57 (0.18), residues: 792 sheet: -2.97 (0.42), residues: 92 loop : -1.99 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 185 TYR 0.038 0.001 TYR C 230 PHE 0.013 0.001 PHE B 252 TRP 0.079 0.004 TRP D1158 HIS 0.003 0.001 HIS A 314 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9400) covalent geometry : angle 0.66532 (12712) SS BOND : bond 0.01034 ( 4) SS BOND : angle 3.91888 ( 8) hydrogen bonds : bond 0.03986 ( 622) hydrogen bonds : angle 4.18346 ( 1824) metal coordination : bond 0.01143 ( 4) metal coordination : angle 5.30625 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.5180 (ppp) cc_final: 0.4924 (ppp) REVERT: A 293 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6685 (mp0) REVERT: A 326 ARG cc_start: 0.7467 (ttp80) cc_final: 0.7059 (ptm160) REVERT: C 218 LEU cc_start: 0.8693 (tp) cc_final: 0.8480 (mt) REVERT: C 225 MET cc_start: 0.6924 (mtp) cc_final: 0.5857 (mmp) REVERT: C 1048 GLN cc_start: 0.8109 (pp30) cc_final: 0.7819 (tp40) REVERT: C 1116 MET cc_start: 0.9200 (mmm) cc_final: 0.8848 (mtp) REVERT: B 204 MET cc_start: 0.5144 (ppp) cc_final: 0.4932 (ppp) REVERT: B 293 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: B 326 ARG cc_start: 0.7441 (ttp80) cc_final: 0.7027 (ptm160) REVERT: D 261 MET cc_start: 0.7363 (ppp) cc_final: 0.7079 (pmm) REVERT: D 267 MET cc_start: 0.8130 (ptm) cc_final: 0.7832 (ptt) REVERT: D 1116 MET cc_start: 0.9163 (mmm) cc_final: 0.8771 (mtp) outliers start: 34 outliers final: 26 residues processed: 173 average time/residue: 0.0809 time to fit residues: 19.6590 Evaluate side-chains 172 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 230 TYR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1109 TYR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1008 HIS Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 55 optimal weight: 0.0470 chunk 83 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8680 ------------------------------------------------------------------------------- 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 = 0.4725 r_free = 0.4725 target = 0.244105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.162940 restraints weight = 10491.993| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.52 r_work: 0.3508 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9408 Z= 0.167 Angle : 0.697 9.978 12726 Z= 0.354 Chirality : 0.045 0.174 1468 Planarity : 0.005 0.056 1582 Dihedral : 4.088 16.065 1228 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.93 % Allowed : 21.68 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.26), residues: 1142 helix: 1.58 (0.18), residues: 796 sheet: -2.96 (0.42), residues: 92 loop : -1.98 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D1050 TYR 0.038 0.001 TYR C 230 PHE 0.038 0.001 PHE D 283 TRP 0.096 0.004 TRP D1158 HIS 0.006 0.001 HIS D1008 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9400) covalent geometry : angle 0.68405 (12712) SS BOND : bond 0.00435 ( 4) SS BOND : angle 3.11312 ( 8) hydrogen bonds : bond 0.03965 ( 622) hydrogen bonds : angle 4.20519 ( 1824) metal coordination : bond 0.01113 ( 4) metal coordination : angle 5.14536 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 MET cc_start: 0.5188 (ppp) cc_final: 0.4958 (ppp) REVERT: A 293 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: A 326 ARG cc_start: 0.7494 (ttp80) cc_final: 0.7075 (ptm160) REVERT: C 218 LEU cc_start: 0.8661 (tp) cc_final: 0.8459 (mt) REVERT: C 225 MET cc_start: 0.6926 (mtp) cc_final: 0.5875 (mmp) REVERT: C 1048 GLN cc_start: 0.8099 (pp30) cc_final: 0.7861 (tp40) REVERT: C 1116 MET cc_start: 0.9192 (mmm) cc_final: 0.8809 (mtp) REVERT: B 204 MET cc_start: 0.5159 (ppp) cc_final: 0.4934 (ppp) REVERT: B 293 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: B 326 ARG cc_start: 0.7461 (ttp80) cc_final: 0.7160 (ptm160) REVERT: D 267 MET cc_start: 0.8128 (ptm) cc_final: 0.7828 (ptt) REVERT: D 1049 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6930 (tmm) REVERT: D 1116 MET cc_start: 0.9162 (mmm) cc_final: 0.8755 (mtp) outliers start: 30 outliers final: 26 residues processed: 169 average time/residue: 0.0881 time to fit residues: 21.0431 Evaluate side-chains 175 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 230 TYR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1109 TYR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Chi-restraints excluded: chain D residue 1109 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 1 optimal weight: 0.0870 chunk 84 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 40 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1022 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.245061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.162950 restraints weight = 10357.225| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.02 r_work: 0.3553 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9408 Z= 0.146 Angle : 0.698 10.715 12726 Z= 0.359 Chirality : 0.045 0.176 1468 Planarity : 0.005 0.056 1582 Dihedral : 4.052 16.350 1228 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.73 % Allowed : 21.88 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.26), residues: 1142 helix: 1.60 (0.18), residues: 798 sheet: -2.91 (0.43), residues: 92 loop : -1.94 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1050 TYR 0.038 0.001 TYR C 230 PHE 0.036 0.001 PHE D 283 TRP 0.112 0.004 TRP D1158 HIS 0.002 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9400) covalent geometry : angle 0.68659 (12712) SS BOND : bond 0.00386 ( 4) SS BOND : angle 3.38416 ( 8) hydrogen bonds : bond 0.03896 ( 622) hydrogen bonds : angle 4.17510 ( 1824) metal coordination : bond 0.00955 ( 4) metal coordination : angle 4.26752 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 MET cc_start: 0.4816 (OUTLIER) cc_final: 0.4576 (tpt) REVERT: A 204 MET cc_start: 0.5204 (ppp) cc_final: 0.4972 (ppp) REVERT: A 293 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6571 (mp0) REVERT: A 326 ARG cc_start: 0.7435 (ttp80) cc_final: 0.7149 (ptm160) REVERT: C 218 LEU cc_start: 0.8636 (tp) cc_final: 0.8424 (mt) REVERT: C 225 MET cc_start: 0.6910 (mtp) cc_final: 0.5915 (mmp) REVERT: C 1048 GLN cc_start: 0.8077 (pp30) cc_final: 0.7863 (tp40) REVERT: C 1116 MET cc_start: 0.9159 (mmm) cc_final: 0.8812 (mtp) REVERT: B 204 MET cc_start: 0.5194 (ppp) cc_final: 0.4977 (ppp) REVERT: B 293 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: B 326 ARG cc_start: 0.7379 (ttp80) cc_final: 0.7094 (ptm160) REVERT: D 267 MET cc_start: 0.8121 (ptm) cc_final: 0.7822 (ptt) outliers start: 28 outliers final: 23 residues processed: 166 average time/residue: 0.0797 time to fit residues: 18.4569 Evaluate side-chains 175 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 127 MET Chi-restraints excluded: chain A residue 165 PHE Chi-restraints excluded: chain A residue 172 HIS Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain C residue 230 TYR Chi-restraints excluded: chain C residue 269 GLU Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 1049 MET Chi-restraints excluded: chain C residue 1062 THR Chi-restraints excluded: chain C residue 1109 TYR Chi-restraints excluded: chain C residue 1157 CYS Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 279 GLN Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain D residue 230 TYR Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 286 GLU Chi-restraints excluded: chain D residue 1049 MET Chi-restraints excluded: chain D residue 1062 THR Chi-restraints excluded: chain D residue 1068 GLU Chi-restraints excluded: chain D residue 1109 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 0.0970 chunk 13 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 20.0000 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1008 HIS D1008 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.245364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.163467 restraints weight = 10261.395| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.82 r_work: 0.3538 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9408 Z= 0.155 Angle : 0.721 11.104 12726 Z= 0.374 Chirality : 0.046 0.184 1468 Planarity : 0.005 0.056 1582 Dihedral : 4.065 19.932 1228 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.03 % Allowed : 22.17 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.26), residues: 1142 helix: 1.58 (0.18), residues: 800 sheet: -2.87 (0.43), residues: 92 loop : -1.96 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1050 TYR 0.037 0.001 TYR C 230 PHE 0.036 0.001 PHE D 283 TRP 0.110 0.006 TRP D1158 HIS 0.003 0.001 HIS D 285 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9400) covalent geometry : angle 0.71104 (12712) SS BOND : bond 0.00464 ( 4) SS BOND : angle 3.15991 ( 8) hydrogen bonds : bond 0.03990 ( 622) hydrogen bonds : angle 4.15578 ( 1824) metal coordination : bond 0.01008 ( 4) metal coordination : angle 4.22703 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3010.22 seconds wall clock time: 52 minutes 6.59 seconds (3126.59 seconds total)