Starting phenix.real_space_refine on Fri Jun 6 18:22:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wy8_32887/06_2025/7wy8_32887_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wy8_32887/06_2025/7wy8_32887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wy8_32887/06_2025/7wy8_32887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wy8_32887/06_2025/7wy8_32887.map" model { file = "/net/cci-nas-00/data/ceres_data/7wy8_32887/06_2025/7wy8_32887_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wy8_32887/06_2025/7wy8_32887_neut.cif" } resolution = 2.83 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= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5121 2.51 5 N 1393 2.21 5 O 1479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8049 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2123 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 3, 'TRANS': 258} Chain breaks: 1 Chain: "C" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1926 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "D" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 331} Time building chain proxies: 5.27, per 1000 atoms: 0.65 Number of scatterers: 8049 At special positions: 0 Unit cell: (80.3, 97.9, 133.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1479 8.00 N 1393 7.00 C 5121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R1008 " - pdb=" SG CYS R1080 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 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: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1906 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 40.6% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'R' and resid 925 through 929 removed outlier: 3.805A pdb=" N LEU R 928 " --> pdb=" O PHE R 925 " (cutoff:3.500A) Processing helix chain 'R' and resid 940 through 956 removed outlier: 3.933A pdb=" N LEU R 944 " --> pdb=" O VAL R 940 " (cutoff:3.500A) Processing helix chain 'R' and resid 958 through 969 removed outlier: 3.643A pdb=" N ILE R 962 " --> pdb=" O VAL R 958 " (cutoff:3.500A) Processing helix chain 'R' and resid 970 through 974 removed outlier: 3.770A pdb=" N LEU R 973 " --> pdb=" O PHE R 970 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN R 974 " --> pdb=" O ARG R 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 970 through 974' Processing helix chain 'R' and resid 975 through 999 removed outlier: 3.578A pdb=" N ILE R 999 " --> pdb=" O PHE R 995 " (cutoff:3.500A) Processing helix chain 'R' and resid 1008 through 1038 removed outlier: 4.042A pdb=" N HIS R1016 " --> pdb=" O ALA R1012 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET R1036 " --> pdb=" O GLN R1032 " (cutoff:3.500A) Processing helix chain 'R' and resid 1047 through 1056 Processing helix chain 'R' and resid 1056 through 1070 removed outlier: 3.574A pdb=" N ALA R1060 " --> pdb=" O TYR R1056 " (cutoff:3.500A) Processing helix chain 'R' and resid 1086 through 1088 No H-bonds generated for 'chain 'R' and resid 1086 through 1088' Processing helix chain 'R' and resid 1089 through 1113 Proline residue: R1095 - end of helix removed outlier: 3.736A pdb=" N LEU R1098 " --> pdb=" O GLY R1094 " (cutoff:3.500A) Processing helix chain 'R' and resid 1144 through 1152 Processing helix chain 'R' and resid 1155 through 1164 removed outlier: 3.745A pdb=" N TRP R1158 " --> pdb=" O GLY R1155 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA R1159 " --> pdb=" O LEU R1156 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR R1164 " --> pdb=" O GLY R1161 " (cutoff:3.500A) Processing helix chain 'R' and resid 1169 through 1181 removed outlier: 3.791A pdb=" N ALA R1173 " --> pdb=" O THR R1169 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER R1181 " --> pdb=" O THR R1177 " (cutoff:3.500A) Processing helix chain 'R' and resid 1182 through 1193 removed outlier: 3.625A pdb=" N PHE R1188 " --> pdb=" O GLY R1184 " (cutoff:3.500A) Processing helix chain 'R' and resid 1195 through 1207 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.779A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.508A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.824A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.735A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 No H-bonds generated for 'chain 'A' and resid 252 through 264' Processing helix chain 'A' and resid 265 through 278 removed outlier: 3.562A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.862A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.625A pdb=" N TYR A 318 " --> pdb=" O PHE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.585A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.603A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.579A pdb=" N THR D 91 " --> pdb=" O PRO D 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.867A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.266A pdb=" N GLY D 10 " --> pdb=" O THR D 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.053A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.082A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.964A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.969A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.945A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.759A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.973A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 376 hydrogen bonds defined for protein. 1041 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: 2.14 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2622 1.34 - 1.46: 1991 1.46 - 1.58: 3526 1.58 - 1.70: 0 1.70 - 1.83: 80 Bond restraints: 8219 Sorted by residual: bond pdb=" C LEU C 50 " pdb=" N LEU C 51 " ideal model delta sigma weight residual 1.332 1.277 0.055 1.35e-02 5.49e+03 1.68e+01 bond pdb=" N LYS R1113 " pdb=" CA LYS R1113 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.22e-02 6.72e+03 5.24e+00 bond pdb=" N MET R1114 " pdb=" CA MET R1114 " ideal model delta sigma weight residual 1.456 1.482 -0.025 1.28e-02 6.10e+03 3.95e+00 bond pdb=" CA PHE B 292 " pdb=" CB PHE B 292 " ideal model delta sigma weight residual 1.530 1.492 0.038 2.00e-02 2.50e+03 3.53e+00 bond pdb=" CB TRP D 36 " pdb=" CG TRP D 36 " ideal model delta sigma weight residual 1.498 1.450 0.048 3.10e-02 1.04e+03 2.43e+00 ... (remaining 8214 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 10691 1.78 - 3.56: 354 3.56 - 5.34: 64 5.34 - 7.11: 8 7.11 - 8.89: 6 Bond angle restraints: 11123 Sorted by residual: angle pdb=" N VAL R 958 " pdb=" CA VAL R 958 " pdb=" C VAL R 958 " ideal model delta sigma weight residual 112.12 107.19 4.93 8.40e-01 1.42e+00 3.45e+01 angle pdb=" N CYS B 204 " pdb=" CA CYS B 204 " pdb=" C CYS B 204 " ideal model delta sigma weight residual 108.58 100.71 7.87 1.82e+00 3.02e-01 1.87e+01 angle pdb=" N MET R1114 " pdb=" CA MET R1114 " pdb=" C MET R1114 " ideal model delta sigma weight residual 113.88 108.74 5.14 1.23e+00 6.61e-01 1.75e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 114.31 119.54 -5.23 1.29e+00 6.01e-01 1.64e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 121.70 128.88 -7.18 1.80e+00 3.09e-01 1.59e+01 ... (remaining 11118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.05: 4472 15.05 - 30.11: 296 30.11 - 45.16: 57 45.16 - 60.22: 30 60.22 - 75.27: 10 Dihedral angle restraints: 4865 sinusoidal: 1915 harmonic: 2950 Sorted by residual: dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual 93.00 50.64 42.36 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" CA PHE D 108 " pdb=" C PHE D 108 " pdb=" N ASP D 109 " pdb=" CA ASP D 109 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA THR B 65 " pdb=" C THR B 65 " pdb=" N ASP B 66 " pdb=" CA ASP B 66 " ideal model delta harmonic sigma weight residual 180.00 160.15 19.85 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 4862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1033 0.064 - 0.129: 195 0.129 - 0.193: 15 0.193 - 0.257: 2 0.257 - 0.322: 1 Chirality restraints: 1246 Sorted by residual: chirality pdb=" CA GLN B 75 " pdb=" N GLN B 75 " pdb=" C GLN B 75 " pdb=" CB GLN B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA ASP B 163 " pdb=" N ASP B 163 " pdb=" C ASP B 163 " pdb=" CB ASP B 163 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASN R1166 " pdb=" N ASN R1166 " pdb=" C ASN R1166 " pdb=" CB ASN R1166 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1243 not shown) Planarity restraints: 1414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 40 " 0.050 5.00e-02 4.00e+02 7.69e-02 9.46e+00 pdb=" N PRO D 41 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 41 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 41 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN R1004 " -0.037 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO R1005 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO R1005 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R1005 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO B 236 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.030 5.00e-02 4.00e+02 ... (remaining 1411 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1193 2.76 - 3.29: 7080 3.29 - 3.83: 12083 3.83 - 4.36: 14045 4.36 - 4.90: 25419 Nonbonded interactions: 59820 Sorted by model distance: nonbonded pdb=" O ASN R1166 " pdb=" OG1 THR R1169 " model vdw 2.220 3.040 nonbonded pdb=" OG1 THR R 966 " pdb=" OH TYR R1202 " model vdw 2.237 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.307 3.040 nonbonded pdb=" O PRO D 100 " pdb=" OG SER B 227 " model vdw 2.330 3.040 nonbonded pdb=" O VAL D 110 " pdb=" NH1 ARG D 118 " model vdw 2.331 3.120 ... (remaining 59815 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.500 Find NCS groups from input model: 0.070 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:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 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 : 0.007 0.055 8221 Z= 0.299 Angle : 0.816 8.893 11127 Z= 0.490 Chirality : 0.050 0.322 1246 Planarity : 0.006 0.077 1414 Dihedral : 12.025 75.273 2953 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: -0.39 (0.25), residues: 1001 helix: 0.49 (0.28), residues: 361 sheet: 1.01 (0.36), residues: 209 loop : -1.58 (0.25), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 82 HIS 0.009 0.002 HIS A 357 PHE 0.034 0.003 PHE A 376 TYR 0.019 0.002 TYR R1034 ARG 0.006 0.001 ARG D 98 Details of bonding type rmsd hydrogen bonds : bond 0.18244 ( 376) hydrogen bonds : angle 6.81733 ( 1041) SS BOND : bond 0.00566 ( 2) SS BOND : angle 3.45518 ( 4) covalent geometry : bond 0.00676 ( 8219) covalent geometry : angle 0.81358 (11123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.785 Fit side-chains REVERT: R 1088 PHE cc_start: 0.7386 (t80) cc_final: 0.7086 (t80) REVERT: R 1172 MET cc_start: 0.5424 (mmm) cc_final: 0.5170 (mmm) REVERT: A 314 GLU cc_start: 0.6745 (mp0) cc_final: 0.6476 (mp0) REVERT: B 156 GLN cc_start: 0.7993 (mt0) cc_final: 0.7687 (mt0) REVERT: B 304 ARG cc_start: 0.7324 (mtm180) cc_final: 0.7075 (ttm110) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 1.2543 time to fit residues: 250.6169 Evaluate side-chains 168 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R1183 GLN A 236 GLN A 292 ASN D 31 ASN B 75 GLN B 155 ASN B 239 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.151328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128795 restraints weight = 11083.096| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.98 r_work: 0.3572 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8221 Z= 0.157 Angle : 0.598 8.581 11127 Z= 0.328 Chirality : 0.043 0.163 1246 Planarity : 0.005 0.072 1414 Dihedral : 4.825 22.854 1106 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.19 % Allowed : 8.52 % Favored : 89.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.26), residues: 1001 helix: 1.59 (0.29), residues: 352 sheet: 0.96 (0.35), residues: 217 loop : -1.44 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE A 376 TYR 0.014 0.001 TYR D 95 ARG 0.006 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.06592 ( 376) hydrogen bonds : angle 4.70795 ( 1041) SS BOND : bond 0.00350 ( 2) SS BOND : angle 1.67072 ( 4) covalent geometry : bond 0.00339 ( 8219) covalent geometry : angle 0.59726 (11123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.841 Fit side-chains REVERT: R 997 ILE cc_start: 0.6891 (mm) cc_final: 0.6590 (tt) REVERT: R 1082 LEU cc_start: 0.8400 (mt) cc_final: 0.8071 (mm) REVERT: R 1092 PHE cc_start: 0.7131 (t80) cc_final: 0.6615 (t80) REVERT: C 42 GLU cc_start: 0.7811 (tp30) cc_final: 0.7502 (tp30) REVERT: A 60 MET cc_start: 0.6505 (mtp) cc_final: 0.6200 (ttm) REVERT: A 314 GLU cc_start: 0.7391 (mp0) cc_final: 0.7063 (mp0) REVERT: D 68 PHE cc_start: 0.7978 (m-10) cc_final: 0.7757 (m-10) REVERT: B 59 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.8021 (t80) outliers start: 19 outliers final: 12 residues processed: 179 average time/residue: 1.4719 time to fit residues: 278.2502 Evaluate side-chains 179 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.0980 chunk 66 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.149981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.127338 restraints weight = 11188.119| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.00 r_work: 0.3544 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8221 Z= 0.191 Angle : 0.615 7.704 11127 Z= 0.335 Chirality : 0.043 0.171 1246 Planarity : 0.004 0.059 1414 Dihedral : 4.775 23.742 1106 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.22 % Allowed : 9.55 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.40 (0.26), residues: 1001 helix: 1.76 (0.29), residues: 352 sheet: 0.93 (0.35), residues: 218 loop : -1.42 (0.26), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.006 0.001 HIS C 44 PHE 0.022 0.002 PHE A 376 TYR 0.017 0.002 TYR D 95 ARG 0.003 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.07089 ( 376) hydrogen bonds : angle 4.57323 ( 1041) SS BOND : bond 0.00352 ( 2) SS BOND : angle 1.56697 ( 4) covalent geometry : bond 0.00441 ( 8219) covalent geometry : angle 0.61422 (11123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.982 Fit side-chains REVERT: R 997 ILE cc_start: 0.7052 (mm) cc_final: 0.6810 (tt) REVERT: R 1069 VAL cc_start: 0.7617 (t) cc_final: 0.7403 (t) REVERT: R 1082 LEU cc_start: 0.8416 (mt) cc_final: 0.8108 (mm) REVERT: A 60 MET cc_start: 0.6668 (mtp) cc_final: 0.6258 (ttm) REVERT: A 314 GLU cc_start: 0.7369 (mp0) cc_final: 0.6987 (mp0) REVERT: D 68 PHE cc_start: 0.8012 (m-10) cc_final: 0.7792 (m-10) REVERT: B 59 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.8110 (t80) outliers start: 28 outliers final: 20 residues processed: 177 average time/residue: 1.3369 time to fit residues: 249.6570 Evaluate side-chains 188 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 67 optimal weight: 1.9990 chunk 96 optimal weight: 0.0470 chunk 76 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 0.0770 chunk 19 optimal weight: 3.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 236 GLN A 292 ASN D 31 ASN B 75 GLN B 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.152746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.130269 restraints weight = 11082.979| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.01 r_work: 0.3569 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8221 Z= 0.139 Angle : 0.543 7.096 11127 Z= 0.297 Chirality : 0.041 0.149 1246 Planarity : 0.004 0.052 1414 Dihedral : 4.496 21.331 1106 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.88 % Allowed : 11.05 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.62 (0.26), residues: 1001 helix: 2.03 (0.29), residues: 352 sheet: 1.22 (0.36), residues: 206 loop : -1.41 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.002 PHE B 241 TYR 0.014 0.001 TYR D 95 ARG 0.008 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.05783 ( 376) hydrogen bonds : angle 4.30840 ( 1041) SS BOND : bond 0.00260 ( 2) SS BOND : angle 1.04350 ( 4) covalent geometry : bond 0.00304 ( 8219) covalent geometry : angle 0.54298 (11123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 1.126 Fit side-chains REVERT: R 929 MET cc_start: 0.8063 (mmt) cc_final: 0.7722 (mmt) REVERT: R 997 ILE cc_start: 0.6961 (mm) cc_final: 0.6704 (tt) REVERT: R 1069 VAL cc_start: 0.7582 (t) cc_final: 0.7342 (t) REVERT: R 1082 LEU cc_start: 0.8356 (mt) cc_final: 0.8072 (mm) REVERT: R 1114 MET cc_start: 0.4839 (OUTLIER) cc_final: 0.4413 (ttm) REVERT: A 60 MET cc_start: 0.6667 (mtp) cc_final: 0.6372 (ttm) REVERT: A 314 GLU cc_start: 0.7343 (mp0) cc_final: 0.7030 (mp0) REVERT: D 68 PHE cc_start: 0.8021 (m-10) cc_final: 0.7804 (m-10) REVERT: B 143 THR cc_start: 0.8775 (OUTLIER) cc_final: 0.8462 (m) outliers start: 25 outliers final: 18 residues processed: 169 average time/residue: 1.4101 time to fit residues: 250.7177 Evaluate side-chains 183 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1093 ILE Chi-restraints excluded: chain R residue 1114 MET Chi-restraints excluded: chain R residue 1151 LEU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 39 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.151250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.128728 restraints weight = 11018.107| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.02 r_work: 0.3549 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8221 Z= 0.175 Angle : 0.586 9.606 11127 Z= 0.318 Chirality : 0.042 0.153 1246 Planarity : 0.004 0.051 1414 Dihedral : 4.583 22.689 1106 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.22 % Allowed : 12.31 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.66 (0.26), residues: 1001 helix: 2.07 (0.29), residues: 352 sheet: 1.21 (0.36), residues: 206 loop : -1.38 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS C 44 PHE 0.019 0.002 PHE B 151 TYR 0.015 0.002 TYR D 95 ARG 0.009 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.06602 ( 376) hydrogen bonds : angle 4.37075 ( 1041) SS BOND : bond 0.00312 ( 2) SS BOND : angle 1.18190 ( 4) covalent geometry : bond 0.00403 ( 8219) covalent geometry : angle 0.58557 (11123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.885 Fit side-chains REVERT: R 929 MET cc_start: 0.8053 (mmt) cc_final: 0.7818 (mmm) REVERT: R 997 ILE cc_start: 0.7114 (mm) cc_final: 0.6840 (tt) REVERT: R 1082 LEU cc_start: 0.8378 (mt) cc_final: 0.8115 (mm) REVERT: R 1114 MET cc_start: 0.4747 (mtt) cc_final: 0.4438 (ttm) REVERT: C 21 MET cc_start: 0.7540 (tpp) cc_final: 0.6965 (ttt) REVERT: A 60 MET cc_start: 0.6742 (mtp) cc_final: 0.6436 (ttm) REVERT: A 314 GLU cc_start: 0.7362 (mp0) cc_final: 0.7059 (mp0) REVERT: D 68 PHE cc_start: 0.8059 (m-10) cc_final: 0.7844 (m-10) REVERT: B 143 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8478 (m) REVERT: B 156 GLN cc_start: 0.8148 (mt0) cc_final: 0.7812 (mt0) outliers start: 28 outliers final: 25 residues processed: 179 average time/residue: 1.3048 time to fit residues: 246.1419 Evaluate side-chains 192 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1040 VAL Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1093 ILE Chi-restraints excluded: chain R residue 1151 LEU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 chunk 75 optimal weight: 0.1980 chunk 73 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R1032 GLN A 35 GLN A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.152572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.130130 restraints weight = 11119.545| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.02 r_work: 0.3575 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8221 Z= 0.134 Angle : 0.527 6.946 11127 Z= 0.289 Chirality : 0.041 0.157 1246 Planarity : 0.004 0.049 1414 Dihedral : 4.370 20.759 1106 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.11 % Allowed : 12.77 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.84 (0.26), residues: 1001 helix: 2.29 (0.29), residues: 351 sheet: 1.42 (0.36), residues: 199 loop : -1.35 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.015 0.002 PHE B 241 TYR 0.018 0.001 TYR B 289 ARG 0.006 0.000 ARG A 283 Details of bonding type rmsd hydrogen bonds : bond 0.05510 ( 376) hydrogen bonds : angle 4.20395 ( 1041) SS BOND : bond 0.00234 ( 2) SS BOND : angle 0.90323 ( 4) covalent geometry : bond 0.00294 ( 8219) covalent geometry : angle 0.52712 (11123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.796 Fit side-chains REVERT: R 997 ILE cc_start: 0.6979 (mm) cc_final: 0.6728 (tt) REVERT: R 1114 MET cc_start: 0.4711 (mtt) cc_final: 0.4464 (ttm) REVERT: C 21 MET cc_start: 0.7495 (tpp) cc_final: 0.6928 (ttt) REVERT: A 60 MET cc_start: 0.6719 (mtp) cc_final: 0.6482 (ttm) REVERT: A 252 ASP cc_start: 0.7696 (t70) cc_final: 0.7447 (t0) REVERT: A 314 GLU cc_start: 0.7344 (mp0) cc_final: 0.7054 (mp0) REVERT: D 68 PHE cc_start: 0.8056 (m-10) cc_final: 0.7847 (m-10) REVERT: B 143 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8468 (m) REVERT: B 156 GLN cc_start: 0.8143 (mt0) cc_final: 0.7845 (mt0) outliers start: 27 outliers final: 23 residues processed: 179 average time/residue: 1.2702 time to fit residues: 239.9961 Evaluate side-chains 189 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1006 ILE Chi-restraints excluded: chain R residue 1040 VAL Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1151 LEU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 50 ASN A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.150215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127901 restraints weight = 10959.256| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.96 r_work: 0.3555 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8221 Z= 0.175 Angle : 0.573 6.756 11127 Z= 0.314 Chirality : 0.042 0.160 1246 Planarity : 0.004 0.050 1414 Dihedral : 4.525 22.478 1106 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.03 % Allowed : 13.00 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.78 (0.26), residues: 1001 helix: 2.25 (0.28), residues: 351 sheet: 1.23 (0.36), residues: 206 loop : -1.36 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS C 44 PHE 0.019 0.002 PHE B 151 TYR 0.016 0.002 TYR B 289 ARG 0.003 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.06475 ( 376) hydrogen bonds : angle 4.31991 ( 1041) SS BOND : bond 0.00316 ( 2) SS BOND : angle 1.14273 ( 4) covalent geometry : bond 0.00404 ( 8219) covalent geometry : angle 0.57261 (11123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.835 Fit side-chains REVERT: R 997 ILE cc_start: 0.7127 (mm) cc_final: 0.6856 (tt) REVERT: C 21 MET cc_start: 0.7534 (tpp) cc_final: 0.6957 (ttt) REVERT: A 60 MET cc_start: 0.6763 (mtp) cc_final: 0.6522 (ttm) REVERT: A 252 ASP cc_start: 0.7626 (t70) cc_final: 0.7385 (t0) REVERT: A 314 GLU cc_start: 0.7343 (mp0) cc_final: 0.7055 (mp0) REVERT: D 68 PHE cc_start: 0.8068 (m-10) cc_final: 0.7862 (m-10) REVERT: B 156 GLN cc_start: 0.8166 (mt0) cc_final: 0.7837 (mt0) outliers start: 35 outliers final: 27 residues processed: 183 average time/residue: 1.3082 time to fit residues: 252.3976 Evaluate side-chains 193 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1040 VAL Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1093 ILE Chi-restraints excluded: chain R residue 1151 LEU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 0.0570 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 50 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 76 optimal weight: 0.0000 chunk 5 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 overall best weight: 0.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 50 ASN A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.153183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.130737 restraints weight = 11122.482| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.01 r_work: 0.3593 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8221 Z= 0.118 Angle : 0.511 6.847 11127 Z= 0.280 Chirality : 0.041 0.159 1246 Planarity : 0.004 0.050 1414 Dihedral : 4.224 19.594 1106 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.11 % Allowed : 14.27 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.96 (0.27), residues: 1001 helix: 2.41 (0.28), residues: 351 sheet: 1.46 (0.36), residues: 199 loop : -1.28 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE R1088 TYR 0.013 0.001 TYR D 95 ARG 0.002 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04917 ( 376) hydrogen bonds : angle 4.13468 ( 1041) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.83849 ( 4) covalent geometry : bond 0.00250 ( 8219) covalent geometry : angle 0.51074 (11123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.918 Fit side-chains REVERT: R 974 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7819 (mp10) REVERT: R 1006 ILE cc_start: 0.8456 (tp) cc_final: 0.8255 (tp) REVERT: C 21 MET cc_start: 0.7492 (tpp) cc_final: 0.6950 (ttt) REVERT: A 34 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7523 (tttt) REVERT: A 252 ASP cc_start: 0.7690 (t70) cc_final: 0.7461 (t0) REVERT: A 314 GLU cc_start: 0.7296 (mp0) cc_final: 0.7019 (mp0) REVERT: D 68 PHE cc_start: 0.8030 (m-10) cc_final: 0.7816 (m-10) REVERT: B 156 GLN cc_start: 0.8150 (mt0) cc_final: 0.7809 (mt0) REVERT: B 292 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7347 (m-80) outliers start: 27 outliers final: 20 residues processed: 179 average time/residue: 1.2691 time to fit residues: 239.9627 Evaluate side-chains 187 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1040 VAL Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1151 LEU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 81 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 213 GLN A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.150532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.128036 restraints weight = 11225.976| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.00 r_work: 0.3552 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8221 Z= 0.176 Angle : 0.578 6.899 11127 Z= 0.317 Chirality : 0.043 0.158 1246 Planarity : 0.004 0.050 1414 Dihedral : 4.460 21.944 1106 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.99 % Allowed : 14.61 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.85 (0.26), residues: 1001 helix: 2.29 (0.28), residues: 351 sheet: 1.28 (0.35), residues: 209 loop : -1.31 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS C 44 PHE 0.018 0.002 PHE B 151 TYR 0.016 0.002 TYR D 95 ARG 0.003 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.06346 ( 376) hydrogen bonds : angle 4.26298 ( 1041) SS BOND : bond 0.00294 ( 2) SS BOND : angle 1.10246 ( 4) covalent geometry : bond 0.00408 ( 8219) covalent geometry : angle 0.57818 (11123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.917 Fit side-chains REVERT: C 21 MET cc_start: 0.7529 (tpp) cc_final: 0.6978 (ttt) REVERT: A 252 ASP cc_start: 0.7646 (t70) cc_final: 0.7409 (t0) REVERT: A 314 GLU cc_start: 0.7339 (mp0) cc_final: 0.7061 (mp0) REVERT: D 34 MET cc_start: 0.8071 (mmt) cc_final: 0.7302 (mtt) REVERT: D 68 PHE cc_start: 0.8025 (m-10) cc_final: 0.7815 (m-10) REVERT: B 156 GLN cc_start: 0.8183 (mt0) cc_final: 0.7849 (mt0) outliers start: 26 outliers final: 22 residues processed: 179 average time/residue: 1.3048 time to fit residues: 246.5515 Evaluate side-chains 189 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1040 VAL Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1088 PHE Chi-restraints excluded: chain R residue 1151 LEU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 45 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 72 optimal weight: 0.0040 chunk 24 optimal weight: 1.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 50 ASN A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.152269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129929 restraints weight = 11099.033| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.98 r_work: 0.3579 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8221 Z= 0.133 Angle : 0.533 6.571 11127 Z= 0.293 Chirality : 0.041 0.159 1246 Planarity : 0.004 0.050 1414 Dihedral : 4.301 19.982 1106 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.65 % Allowed : 15.07 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.96 (0.27), residues: 1001 helix: 2.42 (0.28), residues: 351 sheet: 1.44 (0.36), residues: 199 loop : -1.29 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.015 0.002 PHE B 241 TYR 0.013 0.001 TYR D 95 ARG 0.002 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.05326 ( 376) hydrogen bonds : angle 4.12943 ( 1041) SS BOND : bond 0.00205 ( 2) SS BOND : angle 0.80826 ( 4) covalent geometry : bond 0.00293 ( 8219) covalent geometry : angle 0.53276 (11123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.843 Fit side-chains REVERT: C 21 MET cc_start: 0.7505 (tpp) cc_final: 0.6980 (ttt) REVERT: A 314 GLU cc_start: 0.7323 (mp0) cc_final: 0.7047 (mp0) REVERT: D 68 PHE cc_start: 0.8006 (m-10) cc_final: 0.7783 (m-10) REVERT: B 156 GLN cc_start: 0.8157 (mt0) cc_final: 0.7831 (mt0) REVERT: B 292 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7297 (m-80) outliers start: 23 outliers final: 22 residues processed: 175 average time/residue: 1.3012 time to fit residues: 240.2712 Evaluate side-chains 187 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 954 LEU Chi-restraints excluded: chain R residue 1040 VAL Chi-restraints excluded: chain R residue 1044 GLU Chi-restraints excluded: chain R residue 1088 PHE Chi-restraints excluded: chain R residue 1151 LEU Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 27 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.0470 chunk 58 optimal weight: 0.0980 chunk 91 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.151955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.129413 restraints weight = 11157.232| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.01 r_work: 0.3574 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8221 Z= 0.139 Angle : 0.540 6.569 11127 Z= 0.296 Chirality : 0.041 0.166 1246 Planarity : 0.004 0.050 1414 Dihedral : 4.298 20.321 1106 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.88 % Allowed : 15.19 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.99 (0.27), residues: 1001 helix: 2.43 (0.28), residues: 351 sheet: 1.49 (0.36), residues: 202 loop : -1.28 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.016 0.002 PHE B 241 TYR 0.013 0.001 TYR D 95 ARG 0.002 0.000 ARG A 232 Details of bonding type rmsd hydrogen bonds : bond 0.05529 ( 376) hydrogen bonds : angle 4.13751 ( 1041) SS BOND : bond 0.00240 ( 2) SS BOND : angle 0.95076 ( 4) covalent geometry : bond 0.00310 ( 8219) covalent geometry : angle 0.53985 (11123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7383.51 seconds wall clock time: 126 minutes 41.49 seconds (7601.49 seconds total)