Starting phenix.real_space_refine on Wed Sep 17 10:21:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wy8_32887/09_2025/7wy8_32887_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wy8_32887/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7wy8_32887/09_2025/7wy8_32887_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wy8_32887/09_2025/7wy8_32887_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wy8_32887/09_2025/7wy8_32887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wy8_32887/09_2025/7wy8_32887.map" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.11, per 1000 atoms: 0.26 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: 0.43 Conformation dependent library (CDL) restraints added in 396.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.18 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: 0.83 Time building geometry restraints manager: 0.66 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.900 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.390 ------------------------------------------------------------------------------- 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 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: -0.39 (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 ARG 0.006 0.001 ARG D 98 TYR 0.019 0.002 TYR R1034 PHE 0.034 0.003 PHE A 376 TRP 0.020 0.003 TRP B 82 HIS 0.009 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00676 ( 8219) covalent geometry : angle 0.81358 (11123) SS BOND : bond 0.00566 ( 2) SS BOND : angle 3.45518 ( 4) hydrogen bonds : bond 0.18244 ( 376) hydrogen bonds : angle 6.81733 ( 1041) *********************** 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 : 0.323 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: 0.6165 time to fit residues: 122.8169 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 : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0470 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.150878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.128323 restraints weight = 11072.937| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.98 r_work: 0.3566 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8221 Z= 0.167 Angle : 0.609 8.214 11127 Z= 0.334 Chirality : 0.043 0.166 1246 Planarity : 0.005 0.073 1414 Dihedral : 4.854 23.340 1106 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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 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: 0.29 (0.26), residues: 1001 helix: 1.57 (0.29), residues: 352 sheet: 0.95 (0.35), residues: 217 loop : -1.43 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 283 TYR 0.015 0.002 TYR D 95 PHE 0.019 0.002 PHE A 376 TRP 0.021 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8219) covalent geometry : angle 0.60850 (11123) SS BOND : bond 0.00392 ( 2) SS BOND : angle 1.82622 ( 4) hydrogen bonds : bond 0.06725 ( 376) hydrogen bonds : angle 4.73150 ( 1041) *********************** 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 194 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.318 Fit side-chains REVERT: R 997 ILE cc_start: 0.6895 (mm) cc_final: 0.6599 (tt) REVERT: R 1082 LEU cc_start: 0.8410 (mt) cc_final: 0.8088 (mm) REVERT: R 1092 PHE cc_start: 0.7124 (t80) cc_final: 0.6637 (t80) REVERT: C 42 GLU cc_start: 0.7805 (tp30) cc_final: 0.7497 (tp30) REVERT: A 60 MET cc_start: 0.6534 (mtp) cc_final: 0.6219 (ttm) REVERT: A 314 GLU cc_start: 0.7399 (mp0) cc_final: 0.7047 (mp0) REVERT: D 68 PHE cc_start: 0.7967 (m-10) cc_final: 0.7747 (m-10) REVERT: B 59 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.8093 (t80) REVERT: B 156 GLN cc_start: 0.8172 (mt0) cc_final: 0.7851 (mt0) outliers start: 19 outliers final: 11 residues processed: 181 average time/residue: 0.6457 time to fit residues: 122.7150 Evaluate side-chains 180 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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 22 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 35 optimal weight: 0.3980 chunk 47 optimal weight: 0.0870 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 292 ASN D 31 ASN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.152798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.130327 restraints weight = 11041.843| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.98 r_work: 0.3584 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.1647 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= 0.132 Angle : 0.543 7.457 11127 Z= 0.296 Chirality : 0.041 0.172 1246 Planarity : 0.004 0.058 1414 Dihedral : 4.495 21.115 1106 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.65 % Allowed : 10.24 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.57 (0.26), residues: 1001 helix: 1.94 (0.29), residues: 352 sheet: 1.28 (0.36), residues: 202 loop : -1.43 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 232 TYR 0.014 0.001 TYR B 289 PHE 0.015 0.002 PHE B 241 TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8219) covalent geometry : angle 0.54256 (11123) SS BOND : bond 0.00318 ( 2) SS BOND : angle 1.19507 ( 4) hydrogen bonds : bond 0.05641 ( 376) hydrogen bonds : angle 4.34683 ( 1041) *********************** 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 181 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.254 Fit side-chains REVERT: R 997 ILE cc_start: 0.6868 (mm) cc_final: 0.6659 (tt) REVERT: R 1069 VAL cc_start: 0.7439 (t) cc_final: 0.7214 (t) REVERT: R 1082 LEU cc_start: 0.8455 (mt) cc_final: 0.8142 (mm) REVERT: A 60 MET cc_start: 0.6592 (mtp) cc_final: 0.6254 (ttm) REVERT: A 314 GLU cc_start: 0.7342 (mp0) cc_final: 0.7003 (mp0) REVERT: D 68 PHE cc_start: 0.7997 (m-10) cc_final: 0.7789 (m-10) REVERT: B 105 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7802 (m-80) REVERT: B 143 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8469 (m) outliers start: 23 outliers final: 12 residues processed: 166 average time/residue: 0.6564 time to fit residues: 114.7322 Evaluate side-chains 170 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 251 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain D residue 17 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 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 312 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.0870 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 30 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.152225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.129707 restraints weight = 11304.410| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.02 r_work: 0.3571 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8221 Z= 0.140 Angle : 0.536 7.048 11127 Z= 0.294 Chirality : 0.041 0.151 1246 Planarity : 0.004 0.050 1414 Dihedral : 4.413 21.177 1106 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.99 % Allowed : 11.16 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.72 (0.26), residues: 1001 helix: 2.11 (0.29), residues: 352 sheet: 1.28 (0.36), residues: 206 loop : -1.34 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 373 TYR 0.014 0.001 TYR D 95 PHE 0.016 0.002 PHE A 376 TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8219) covalent geometry : angle 0.53567 (11123) SS BOND : bond 0.00244 ( 2) SS BOND : angle 1.09512 ( 4) hydrogen bonds : bond 0.05791 ( 376) hydrogen bonds : angle 4.25671 ( 1041) *********************** 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 188 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.312 Fit side-chains REVERT: R 997 ILE cc_start: 0.6972 (mm) cc_final: 0.6738 (tt) REVERT: R 1069 VAL cc_start: 0.7562 (t) cc_final: 0.7312 (t) REVERT: R 1082 LEU cc_start: 0.8375 (mt) cc_final: 0.8097 (mm) REVERT: R 1114 MET cc_start: 0.4730 (OUTLIER) cc_final: 0.4240 (ttm) REVERT: A 60 MET cc_start: 0.6628 (mtp) cc_final: 0.6293 (ttm) REVERT: A 314 GLU cc_start: 0.7360 (mp0) cc_final: 0.7036 (mp0) REVERT: A 319 THR cc_start: 0.8364 (t) cc_final: 0.8100 (m) REVERT: D 68 PHE cc_start: 0.8027 (m-10) cc_final: 0.7814 (m-10) REVERT: B 143 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8483 (m) REVERT: B 156 GLN cc_start: 0.8134 (mt0) cc_final: 0.7866 (mt0) outliers start: 26 outliers final: 19 residues processed: 172 average time/residue: 0.6649 time to fit residues: 120.3478 Evaluate side-chains 183 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 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 275 SER 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 D residue 59 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.151126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.128578 restraints weight = 11113.511| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.99 r_work: 0.3557 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8221 Z= 0.168 Angle : 0.568 9.671 11127 Z= 0.310 Chirality : 0.042 0.153 1246 Planarity : 0.004 0.050 1414 Dihedral : 4.502 22.251 1106 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.80 % Allowed : 11.62 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.74 (0.26), residues: 1001 helix: 2.14 (0.29), residues: 352 sheet: 1.22 (0.36), residues: 206 loop : -1.32 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.015 0.002 TYR D 95 PHE 0.018 0.002 PHE B 151 TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 8219) covalent geometry : angle 0.56722 (11123) SS BOND : bond 0.00284 ( 2) SS BOND : angle 1.13193 ( 4) hydrogen bonds : bond 0.06389 ( 376) hydrogen bonds : angle 4.27711 ( 1041) *********************** 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 194 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.302 Fit side-chains REVERT: R 997 ILE cc_start: 0.7081 (mm) cc_final: 0.6823 (tt) REVERT: R 1082 LEU cc_start: 0.8386 (mt) cc_final: 0.8099 (mm) REVERT: R 1114 MET cc_start: 0.4662 (mtt) cc_final: 0.4329 (ttm) REVERT: A 60 MET cc_start: 0.6712 (mtp) cc_final: 0.6430 (ttm) REVERT: A 314 GLU cc_start: 0.7397 (mp0) cc_final: 0.7096 (mp0) REVERT: A 319 THR cc_start: 0.8327 (t) cc_final: 0.8090 (m) REVERT: D 68 PHE cc_start: 0.8027 (m-10) cc_final: 0.7814 (m-10) REVERT: B 143 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8482 (m) REVERT: B 156 GLN cc_start: 0.8151 (mt0) cc_final: 0.7808 (mt0) outliers start: 33 outliers final: 24 residues processed: 174 average time/residue: 0.6531 time to fit residues: 119.4604 Evaluate side-chains 184 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 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 275 SER Chi-restraints excluded: chain A residue 283 ARG 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 59 SER Chi-restraints excluded: chain D residue 78 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 51 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 0.1980 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.150943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.128493 restraints weight = 11076.763| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.99 r_work: 0.3555 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8221 Z= 0.171 Angle : 0.566 6.800 11127 Z= 0.310 Chirality : 0.042 0.153 1246 Planarity : 0.004 0.050 1414 Dihedral : 4.513 22.208 1106 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.03 % Allowed : 12.08 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.77 (0.26), residues: 1001 helix: 2.20 (0.28), residues: 351 sheet: 1.18 (0.36), residues: 206 loop : -1.30 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.015 0.002 TYR D 95 PHE 0.019 0.002 PHE B 151 TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 8219) covalent geometry : angle 0.56552 (11123) SS BOND : bond 0.00280 ( 2) SS BOND : angle 1.11727 ( 4) hydrogen bonds : bond 0.06389 ( 376) hydrogen bonds : angle 4.28098 ( 1041) *********************** 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 198 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.318 Fit side-chains REVERT: R 997 ILE cc_start: 0.7106 (mm) cc_final: 0.6834 (tt) REVERT: R 1114 MET cc_start: 0.4750 (OUTLIER) cc_final: 0.4357 (ttm) REVERT: C 21 MET cc_start: 0.7517 (tpp) cc_final: 0.6932 (ttt) REVERT: A 60 MET cc_start: 0.6702 (mtp) cc_final: 0.6464 (ttm) REVERT: A 314 GLU cc_start: 0.7389 (mp0) cc_final: 0.7085 (mp0) REVERT: A 319 THR cc_start: 0.8316 (t) cc_final: 0.8068 (m) REVERT: D 68 PHE cc_start: 0.8021 (m-10) cc_final: 0.7798 (m-10) REVERT: B 143 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8489 (m) REVERT: B 156 GLN cc_start: 0.8151 (mt0) cc_final: 0.7846 (mt0) outliers start: 35 outliers final: 25 residues processed: 178 average time/residue: 0.6508 time to fit residues: 122.0542 Evaluate side-chains 188 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 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 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 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 61 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 98 optimal weight: 4.9990 chunk 83 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.151383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.128861 restraints weight = 11153.004| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.01 r_work: 0.3557 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8221 Z= 0.165 Angle : 0.557 6.784 11127 Z= 0.307 Chirality : 0.042 0.165 1246 Planarity : 0.004 0.050 1414 Dihedral : 4.496 22.044 1106 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.03 % Allowed : 12.54 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.77 (0.26), residues: 1001 helix: 2.19 (0.28), residues: 352 sheet: 1.19 (0.36), residues: 206 loop : -1.30 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 232 TYR 0.017 0.002 TYR B 289 PHE 0.018 0.002 PHE B 151 TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8219) covalent geometry : angle 0.55706 (11123) SS BOND : bond 0.00270 ( 2) SS BOND : angle 1.05098 ( 4) hydrogen bonds : bond 0.06260 ( 376) hydrogen bonds : angle 4.27073 ( 1041) *********************** 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 196 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 0.291 Fit side-chains REVERT: R 929 MET cc_start: 0.8051 (mmt) cc_final: 0.7722 (mmt) REVERT: R 997 ILE cc_start: 0.7108 (mm) cc_final: 0.6838 (tt) REVERT: R 1114 MET cc_start: 0.4718 (OUTLIER) cc_final: 0.4469 (ttm) REVERT: C 21 MET cc_start: 0.7535 (tpp) cc_final: 0.6953 (ttt) REVERT: A 60 MET cc_start: 0.6721 (mtp) cc_final: 0.6493 (ttm) REVERT: A 252 ASP cc_start: 0.7641 (t70) cc_final: 0.7427 (t0) REVERT: A 314 GLU cc_start: 0.7369 (mp0) cc_final: 0.7084 (mp0) REVERT: A 319 THR cc_start: 0.8296 (t) cc_final: 0.8059 (m) REVERT: D 68 PHE cc_start: 0.8003 (m-10) cc_final: 0.7775 (m-10) REVERT: B 143 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8490 (m) REVERT: B 156 GLN cc_start: 0.8168 (mt0) cc_final: 0.7818 (mt0) outliers start: 35 outliers final: 27 residues processed: 175 average time/residue: 0.6766 time to fit residues: 124.6575 Evaluate side-chains 189 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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 1044 GLU Chi-restraints excluded: chain R residue 1093 ILE Chi-restraints excluded: chain R residue 1114 MET 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 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 61 MET 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 65 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 0.0010 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 47 optimal weight: 0.0050 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 overall best weight: 0.2600 ------------------------------------------------------------------------------- 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 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 = 0.4010 r_free = 0.4010 target = 0.154688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.132330 restraints weight = 11201.344| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.01 r_work: 0.3619 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8221 Z= 0.102 Angle : 0.477 6.335 11127 Z= 0.263 Chirality : 0.040 0.140 1246 Planarity : 0.003 0.049 1414 Dihedral : 4.082 18.119 1106 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.76 % Allowed : 14.38 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.27), residues: 1001 helix: 2.48 (0.29), residues: 352 sheet: 1.35 (0.36), residues: 202 loop : -1.20 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 373 TYR 0.013 0.001 TYR B 289 PHE 0.013 0.001 PHE B 241 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 8219) covalent geometry : angle 0.47711 (11123) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.78226 ( 4) hydrogen bonds : bond 0.04272 ( 376) hydrogen bonds : angle 3.96963 ( 1041) *********************** 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 186 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.319 Fit side-chains REVERT: R 929 MET cc_start: 0.8028 (mmt) cc_final: 0.7743 (mmt) REVERT: R 1006 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8214 (tp) REVERT: C 21 MET cc_start: 0.7504 (tpp) cc_final: 0.6964 (ttt) REVERT: A 314 GLU cc_start: 0.7359 (mp0) cc_final: 0.7028 (mp0) REVERT: A 319 THR cc_start: 0.8247 (t) cc_final: 0.7998 (m) REVERT: D 68 PHE cc_start: 0.7954 (m-10) cc_final: 0.7707 (m-10) REVERT: B 105 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: B 143 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8499 (m) REVERT: B 156 GLN cc_start: 0.8131 (mt0) cc_final: 0.7802 (mt0) outliers start: 24 outliers final: 15 residues processed: 171 average time/residue: 0.6102 time to fit residues: 110.3572 Evaluate side-chains 176 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 1044 GLU Chi-restraints excluded: chain R residue 1093 ILE Chi-restraints excluded: chain R residue 1163 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain A residue 251 SER 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 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 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 1 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 0.0050 chunk 80 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.151567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.129125 restraints weight = 11074.133| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.98 r_work: 0.3566 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8221 Z= 0.163 Angle : 0.560 6.614 11127 Z= 0.307 Chirality : 0.042 0.167 1246 Planarity : 0.004 0.052 1414 Dihedral : 4.372 21.065 1106 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.53 % Allowed : 15.07 % 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 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: 0.99 (0.27), residues: 1001 helix: 2.42 (0.28), residues: 351 sheet: 1.08 (0.35), residues: 217 loop : -1.13 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 283 TYR 0.016 0.002 TYR B 289 PHE 0.019 0.002 PHE A 222 TRP 0.021 0.002 TRP B 99 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8219) covalent geometry : angle 0.55987 (11123) SS BOND : bond 0.00265 ( 2) SS BOND : angle 1.01978 ( 4) hydrogen bonds : bond 0.05976 ( 376) hydrogen bonds : angle 4.16779 ( 1041) *********************** 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 191 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.316 Fit side-chains REVERT: R 929 MET cc_start: 0.8076 (mmt) cc_final: 0.7729 (mmt) REVERT: C 21 MET cc_start: 0.7524 (tpp) cc_final: 0.6963 (ttt) REVERT: A 252 ASP cc_start: 0.7702 (t70) cc_final: 0.7484 (t0) REVERT: A 314 GLU cc_start: 0.7344 (mp0) cc_final: 0.7052 (mp0) REVERT: A 319 THR cc_start: 0.8294 (t) cc_final: 0.8023 (m) REVERT: D 68 PHE cc_start: 0.7958 (m-10) cc_final: 0.7721 (m-10) REVERT: B 156 GLN cc_start: 0.8161 (mt0) cc_final: 0.7816 (mt0) outliers start: 22 outliers final: 17 residues processed: 178 average time/residue: 0.6597 time to fit residues: 123.4350 Evaluate side-chains 185 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 1163 MET Chi-restraints excluded: chain C residue 50 LEU 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 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 146 LEU Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 0.0970 chunk 39 optimal weight: 0.5980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 213 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 = 0.152045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.129610 restraints weight = 11141.686| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.00 r_work: 0.3575 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8221 Z= 0.142 Angle : 0.541 6.512 11127 Z= 0.297 Chirality : 0.042 0.160 1246 Planarity : 0.004 0.056 1414 Dihedral : 4.296 20.125 1106 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.19 % Allowed : 15.65 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.27), residues: 1001 helix: 2.44 (0.28), residues: 351 sheet: 1.23 (0.36), residues: 210 loop : -1.15 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 283 TYR 0.014 0.001 TYR B 289 PHE 0.016 0.002 PHE B 151 TRP 0.019 0.002 TRP B 99 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8219) covalent geometry : angle 0.54041 (11123) SS BOND : bond 0.00220 ( 2) SS BOND : angle 0.90891 ( 4) hydrogen bonds : bond 0.05489 ( 376) hydrogen bonds : angle 4.12438 ( 1041) ********************** 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 184 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.337 Fit side-chains REVERT: R 929 MET cc_start: 0.8085 (mmt) cc_final: 0.7742 (mmt) REVERT: R 1006 ILE cc_start: 0.8495 (tp) cc_final: 0.8294 (tp) REVERT: C 21 MET cc_start: 0.7535 (tpp) cc_final: 0.6995 (ttt) REVERT: A 314 GLU cc_start: 0.7322 (mp0) cc_final: 0.7035 (mp0) REVERT: B 156 GLN cc_start: 0.8156 (mt0) cc_final: 0.7805 (mt0) outliers start: 19 outliers final: 18 residues processed: 174 average time/residue: 0.6808 time to fit residues: 124.7085 Evaluate side-chains 183 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 1163 MET Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain A residue 251 SER 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 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 234 PHE Chi-restraints excluded: chain B residue 292 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 70 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 30 optimal weight: 0.0050 chunk 42 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 = 0.3975 r_free = 0.3975 target = 0.151904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.129446 restraints weight = 11010.395| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.00 r_work: 0.3568 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8221 Z= 0.145 Angle : 0.546 6.503 11127 Z= 0.299 Chirality : 0.042 0.160 1246 Planarity : 0.004 0.055 1414 Dihedral : 4.312 20.489 1106 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.42 % Allowed : 15.77 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.27), residues: 1001 helix: 2.45 (0.28), residues: 351 sheet: 1.21 (0.36), residues: 209 loop : -1.14 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 283 TYR 0.015 0.001 TYR B 289 PHE 0.016 0.002 PHE B 151 TRP 0.019 0.002 TRP B 99 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8219) covalent geometry : angle 0.54583 (11123) SS BOND : bond 0.00246 ( 2) SS BOND : angle 0.93062 ( 4) hydrogen bonds : bond 0.05620 ( 376) hydrogen bonds : angle 4.15383 ( 1041) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3536.33 seconds wall clock time: 60 minutes 48.32 seconds (3648.32 seconds total)