Starting phenix.real_space_refine on Tue Feb 3 20:30:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ko2_62468/02_2026/9ko2_62468.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ko2_62468/02_2026/9ko2_62468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ko2_62468/02_2026/9ko2_62468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ko2_62468/02_2026/9ko2_62468.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ko2_62468/02_2026/9ko2_62468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ko2_62468/02_2026/9ko2_62468.map" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.046 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 51 5.16 5 C 4289 2.51 5 N 1108 2.21 5 O 1225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6673 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1681 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2249 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 5, 'TRANS': 298} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "C" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 450 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 62} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 6, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "R" Number of atoms: 2293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2293 Classifications: {'peptide': 300} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 6, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 6, 'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 81 Time building chain proxies: 1.61, per 1000 atoms: 0.24 Number of scatterers: 6673 At special positions: 0 Unit cell: (66.43, 93.44, 146, 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 51 16.00 O 1225 8.00 N 1108 7.00 C 4289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS C 34 " distance=2.03 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 129 " - pdb=" SG CYS R 210 " distance=2.02 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: 0.64 Conformation dependent library (CDL) restraints added in 270.6 milliseconds 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1676 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 9 sheets defined 42.5% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 4.434A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.701A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.662A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.635A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.796A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 67 removed outlier: 3.948A pdb=" N ARG C 67 " --> pdb=" O GLN C 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 87 Proline residue: R 62 - end of helix Processing helix chain 'R' and resid 91 through 120 removed outlier: 3.609A pdb=" N THR R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 125 through 159 removed outlier: 3.611A pdb=" N LYS R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 190 Processing helix chain 'R' and resid 190 through 196 Processing helix chain 'R' and resid 216 through 230 removed outlier: 4.168A pdb=" N PHE R 220 " --> pdb=" O HIS R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 253 removed outlier: 3.518A pdb=" N VAL R 245 " --> pdb=" O PHE R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 290 removed outlier: 3.830A pdb=" N ILE R 262 " --> pdb=" O ARG R 258 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 297 through 316 Processing helix chain 'R' and resid 317 through 326 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 342 removed outlier: 3.940A pdb=" N ARG R 334 " --> pdb=" O GLY R 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.328A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.339A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.581A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.779A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.560A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.743A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.947A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.948A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 197 through 200 removed outlier: 3.746A pdb=" N ARG R 209 " --> pdb=" O GLN R 200 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.83 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: 2130 1.34 - 1.46: 1578 1.46 - 1.58: 3028 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 6804 Sorted by residual: bond pdb=" N HIS R 165 " pdb=" CA HIS R 165 " ideal model delta sigma weight residual 1.457 1.498 -0.042 1.25e-02 6.40e+03 1.10e+01 bond pdb=" N ARG R 209 " pdb=" CA ARG R 209 " ideal model delta sigma weight residual 1.454 1.482 -0.027 1.27e-02 6.20e+03 4.57e+00 bond pdb=" N ARG R 54 " pdb=" CA ARG R 54 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.19e-02 7.06e+03 4.33e+00 bond pdb=" CG HIS R 165 " pdb=" CD2 HIS R 165 " ideal model delta sigma weight residual 1.354 1.335 0.019 1.10e-02 8.26e+03 2.95e+00 bond pdb=" CA THR C 2 " pdb=" C THR C 2 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.24e-02 6.50e+03 2.83e+00 ... (remaining 6799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 9129 2.02 - 4.05: 104 4.05 - 6.07: 17 6.07 - 8.10: 3 8.10 - 10.12: 2 Bond angle restraints: 9255 Sorted by residual: angle pdb=" C ASN C 3 " pdb=" N ASP C 4 " pdb=" CA ASP C 4 " ideal model delta sigma weight residual 123.05 114.58 8.47 1.40e+00 5.10e-01 3.66e+01 angle pdb=" C PHE R 333 " pdb=" CA PHE R 333 " pdb=" CB PHE R 333 " ideal model delta sigma weight residual 110.85 120.97 -10.12 1.70e+00 3.46e-01 3.54e+01 angle pdb=" CA PHE R 333 " pdb=" CB PHE R 333 " pdb=" CG PHE R 333 " ideal model delta sigma weight residual 113.80 107.87 5.93 1.00e+00 1.00e+00 3.51e+01 angle pdb=" N LEU B 300 " pdb=" CA LEU B 300 " pdb=" C LEU B 300 " ideal model delta sigma weight residual 114.75 108.82 5.93 1.26e+00 6.30e-01 2.21e+01 angle pdb=" C GLY C 1 " pdb=" N THR C 2 " pdb=" CA THR C 2 " ideal model delta sigma weight residual 122.19 116.01 6.18 1.41e+00 5.03e-01 1.92e+01 ... (remaining 9250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 3755 17.94 - 35.88: 195 35.88 - 53.82: 43 53.82 - 71.76: 9 71.76 - 89.70: 1 Dihedral angle restraints: 4003 sinusoidal: 1418 harmonic: 2585 Sorted by residual: dihedral pdb=" CA ASP A 9 " pdb=" C ASP A 9 " pdb=" N LYS A 10 " pdb=" CA LYS A 10 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA GLN B 220 " pdb=" C GLN B 220 " pdb=" N THR B 221 " pdb=" CA THR B 221 " ideal model delta harmonic sigma weight residual 180.00 162.38 17.62 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 4000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 777 0.037 - 0.075: 252 0.075 - 0.112: 63 0.112 - 0.150: 12 0.150 - 0.187: 4 Chirality restraints: 1108 Sorted by residual: chirality pdb=" CA ARG R 166 " pdb=" N ARG R 166 " pdb=" C ARG R 166 " pdb=" CB ARG R 166 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA ASN C 3 " pdb=" N ASN C 3 " pdb=" C ASN C 3 " pdb=" CB ASN C 3 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.23e-01 chirality pdb=" CA HIS R 167 " pdb=" N HIS R 167 " pdb=" C HIS R 167 " pdb=" CB HIS R 167 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.56e-01 ... (remaining 1105 not shown) Planarity restraints: 1156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 166 " -0.425 9.50e-02 1.11e+02 1.91e-01 2.23e+01 pdb=" NE ARG R 166 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG R 166 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG R 166 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 166 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 164 " -0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C ALA R 164 " 0.061 2.00e-02 2.50e+03 pdb=" O ALA R 164 " -0.022 2.00e-02 2.50e+03 pdb=" N HIS R 165 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 209 " 0.309 9.50e-02 1.11e+02 1.38e-01 1.17e+01 pdb=" NE ARG R 209 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG R 209 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG R 209 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG R 209 " 0.010 2.00e-02 2.50e+03 ... (remaining 1153 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 3677 3.00 - 3.48: 6959 3.48 - 3.95: 10939 3.95 - 4.43: 12807 4.43 - 4.90: 20654 Nonbonded interactions: 55036 Sorted by model distance: nonbonded pdb=" OD1 ASN C 3 " pdb=" NZ LYS R 57 " model vdw 2.530 3.120 nonbonded pdb=" NH1 ARG R 209 " pdb=" OG SER R 211 " model vdw 2.565 3.120 nonbonded pdb=" N THR B 87 " pdb=" OG1 THR B 87 " model vdw 2.593 2.496 nonbonded pdb=" N LEU B 300 " pdb=" N LYS B 301 " model vdw 2.606 2.560 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.610 3.040 ... (remaining 55031 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.910 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:9.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6807 Z= 0.160 Angle : 0.597 10.121 9261 Z= 0.367 Chirality : 0.041 0.187 1108 Planarity : 0.008 0.191 1156 Dihedral : 11.794 89.704 2318 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.34 % Allowed : 7.36 % Favored : 87.30 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.29), residues: 874 helix: 1.77 (0.27), residues: 365 sheet: 0.20 (0.39), residues: 164 loop : -1.67 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 166 TYR 0.006 0.001 TYR A 290 PHE 0.025 0.001 PHE R 333 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS A 244 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6804) covalent geometry : angle 0.59631 ( 9255) SS BOND : bond 0.00368 ( 3) SS BOND : angle 0.84582 ( 6) hydrogen bonds : bond 0.10352 ( 351) hydrogen bonds : angle 5.01831 ( 1026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.7066 (mtmt) REVERT: A 302 TYR cc_start: 0.6026 (t80) cc_final: 0.5235 (t80) REVERT: B 111 TYR cc_start: 0.6313 (OUTLIER) cc_final: 0.5818 (m-80) REVERT: B 234 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6541 (t80) REVERT: C 44 LEU cc_start: 0.1932 (OUTLIER) cc_final: 0.1621 (tt) REVERT: R 136 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5717 (t80) REVERT: R 166 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6237 (mtp85) REVERT: R 276 GLN cc_start: 0.6165 (OUTLIER) cc_final: 0.5169 (mp10) outliers start: 37 outliers final: 6 residues processed: 172 average time/residue: 0.4896 time to fit residues: 89.0009 Evaluate side-chains 99 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 294 ASN B 220 GLN R 160 GLN R 165 HIS R 259 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.209669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.165352 restraints weight = 8488.304| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.56 r_work: 0.3925 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6807 Z= 0.133 Angle : 0.584 8.226 9261 Z= 0.301 Chirality : 0.041 0.149 1108 Planarity : 0.004 0.038 1156 Dihedral : 7.720 85.927 971 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 6.20 % Allowed : 16.31 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.28), residues: 874 helix: 1.83 (0.27), residues: 368 sheet: 0.06 (0.37), residues: 173 loop : -1.82 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 209 TYR 0.023 0.001 TYR C 27 PHE 0.018 0.001 PHE A 189 TRP 0.014 0.002 TRP B 169 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 6804) covalent geometry : angle 0.58305 ( 9255) SS BOND : bond 0.00456 ( 3) SS BOND : angle 1.56429 ( 6) hydrogen bonds : bond 0.03811 ( 351) hydrogen bonds : angle 4.37231 ( 1026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 89 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 266 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.6996 (mt) REVERT: A 270 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6559 (mtmt) REVERT: A 276 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: A 302 TYR cc_start: 0.6575 (t80) cc_final: 0.5683 (t80) REVERT: B 111 TYR cc_start: 0.6508 (OUTLIER) cc_final: 0.5855 (m-80) REVERT: B 234 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6541 (m-80) REVERT: B 251 ARG cc_start: 0.6348 (mtm110) cc_final: 0.6121 (mtm-85) REVERT: B 254 ASP cc_start: 0.5898 (t0) cc_final: 0.5474 (t0) REVERT: B 262 MET cc_start: 0.6523 (mpt) cc_final: 0.6181 (mpt) REVERT: C 44 LEU cc_start: 0.2317 (OUTLIER) cc_final: 0.2082 (tt) REVERT: R 136 TYR cc_start: 0.6209 (OUTLIER) cc_final: 0.5594 (t80) REVERT: R 166 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7418 (mtm110) REVERT: R 276 GLN cc_start: 0.6391 (OUTLIER) cc_final: 0.4921 (mp10) REVERT: R 310 VAL cc_start: 0.7852 (t) cc_final: 0.7617 (t) outliers start: 43 outliers final: 15 residues processed: 119 average time/residue: 0.4537 time to fit residues: 57.3418 Evaluate side-chains 96 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain R residue 228 MET Chi-restraints excluded: chain R residue 259 ASN Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 53 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 0.0050 chunk 72 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.211890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.166509 restraints weight = 8541.599| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.64 r_work: 0.3931 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6807 Z= 0.126 Angle : 0.563 8.574 9261 Z= 0.291 Chirality : 0.041 0.185 1108 Planarity : 0.003 0.038 1156 Dihedral : 6.875 68.355 968 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.77 % Allowed : 16.88 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.28), residues: 874 helix: 1.83 (0.27), residues: 367 sheet: 0.11 (0.37), residues: 167 loop : -1.75 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 32 TYR 0.015 0.001 TYR C 27 PHE 0.014 0.001 PHE A 189 TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 6804) covalent geometry : angle 0.56279 ( 9255) SS BOND : bond 0.00352 ( 3) SS BOND : angle 1.01625 ( 6) hydrogen bonds : bond 0.03687 ( 351) hydrogen bonds : angle 4.31169 ( 1026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7003 (mt) REVERT: A 276 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: A 302 TYR cc_start: 0.6544 (t80) cc_final: 0.5690 (t80) REVERT: B 46 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7338 (tmm160) REVERT: B 111 TYR cc_start: 0.6527 (OUTLIER) cc_final: 0.5964 (m-80) REVERT: B 234 PHE cc_start: 0.7411 (OUTLIER) cc_final: 0.6509 (m-80) REVERT: B 254 ASP cc_start: 0.5987 (t0) cc_final: 0.5632 (t0) REVERT: B 262 MET cc_start: 0.6607 (mpt) cc_final: 0.6331 (mpt) REVERT: B 268 ASN cc_start: 0.8083 (t0) cc_final: 0.7862 (m110) REVERT: C 44 LEU cc_start: 0.2309 (OUTLIER) cc_final: 0.2070 (tt) REVERT: R 136 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.5647 (t80) REVERT: R 160 GLN cc_start: 0.6740 (mm-40) cc_final: 0.6504 (mm110) REVERT: R 166 ARG cc_start: 0.7649 (mpp80) cc_final: 0.7412 (mtm110) REVERT: R 276 GLN cc_start: 0.6427 (OUTLIER) cc_final: 0.4946 (mp10) REVERT: R 310 VAL cc_start: 0.7849 (t) cc_final: 0.7614 (t) outliers start: 40 outliers final: 20 residues processed: 121 average time/residue: 0.4722 time to fit residues: 60.6697 Evaluate side-chains 107 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 123 VAL Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 57 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.0570 chunk 3 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.207466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.163013 restraints weight = 8576.587| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 3.03 r_work: 0.3852 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6807 Z= 0.182 Angle : 0.616 8.176 9261 Z= 0.316 Chirality : 0.043 0.176 1108 Planarity : 0.004 0.035 1156 Dihedral : 6.694 65.768 960 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 6.35 % Allowed : 18.61 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.28), residues: 874 helix: 1.62 (0.27), residues: 368 sheet: -0.09 (0.36), residues: 174 loop : -1.67 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 214 TYR 0.010 0.001 TYR C 27 PHE 0.024 0.002 PHE B 151 TRP 0.012 0.002 TRP B 169 HIS 0.006 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 6804) covalent geometry : angle 0.61564 ( 9255) SS BOND : bond 0.00549 ( 3) SS BOND : angle 1.04099 ( 6) hydrogen bonds : bond 0.04031 ( 351) hydrogen bonds : angle 4.51945 ( 1026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 78 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 266 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7018 (mt) REVERT: A 270 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6653 (mtmt) REVERT: A 276 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: A 302 TYR cc_start: 0.6704 (t80) cc_final: 0.5766 (t80) REVERT: B 234 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.6772 (t80) REVERT: B 262 MET cc_start: 0.6635 (mpt) cc_final: 0.6361 (mpt) REVERT: C 44 LEU cc_start: 0.2150 (OUTLIER) cc_final: 0.1921 (tt) REVERT: R 136 TYR cc_start: 0.6258 (OUTLIER) cc_final: 0.5577 (t80) REVERT: R 160 GLN cc_start: 0.6835 (mm-40) cc_final: 0.6566 (mm110) REVERT: R 166 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7432 (mtm110) REVERT: R 276 GLN cc_start: 0.6510 (OUTLIER) cc_final: 0.5052 (mp10) outliers start: 44 outliers final: 22 residues processed: 113 average time/residue: 0.4333 time to fit residues: 52.0894 Evaluate side-chains 98 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.208821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.164822 restraints weight = 8638.014| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 3.02 r_work: 0.3865 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6807 Z= 0.137 Angle : 0.569 7.561 9261 Z= 0.293 Chirality : 0.041 0.186 1108 Planarity : 0.003 0.035 1156 Dihedral : 6.609 65.823 960 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 6.64 % Allowed : 19.77 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 874 helix: 1.68 (0.27), residues: 369 sheet: 0.10 (0.38), residues: 164 loop : -1.63 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 54 TYR 0.009 0.001 TYR C 27 PHE 0.016 0.001 PHE B 151 TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6804) covalent geometry : angle 0.56895 ( 9255) SS BOND : bond 0.00403 ( 3) SS BOND : angle 0.92360 ( 6) hydrogen bonds : bond 0.03753 ( 351) hydrogen bonds : angle 4.40793 ( 1026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 79 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6287 (tp30) REVERT: A 266 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7028 (mt) REVERT: A 276 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: A 302 TYR cc_start: 0.6708 (t80) cc_final: 0.5812 (t80) REVERT: A 349 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6331 (mptm) REVERT: B 234 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6509 (m-80) REVERT: B 262 MET cc_start: 0.6678 (mpt) cc_final: 0.6472 (mpt) REVERT: C 44 LEU cc_start: 0.2190 (OUTLIER) cc_final: 0.1984 (tt) REVERT: R 136 TYR cc_start: 0.6220 (OUTLIER) cc_final: 0.5592 (t80) REVERT: R 160 GLN cc_start: 0.6834 (mm-40) cc_final: 0.6540 (mm110) REVERT: R 166 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7446 (mtm110) REVERT: R 239 MET cc_start: 0.7179 (ttm) cc_final: 0.6844 (mtp) REVERT: R 276 GLN cc_start: 0.6443 (OUTLIER) cc_final: 0.4935 (mp10) outliers start: 46 outliers final: 21 residues processed: 117 average time/residue: 0.4704 time to fit residues: 58.4111 Evaluate side-chains 101 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 71 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 13 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 21 optimal weight: 0.0670 chunk 58 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN A 294 ASN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.207629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.163682 restraints weight = 8768.624| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 3.02 r_work: 0.3862 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6807 Z= 0.152 Angle : 0.577 7.304 9261 Z= 0.298 Chirality : 0.041 0.209 1108 Planarity : 0.003 0.035 1156 Dihedral : 6.662 65.307 960 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 6.64 % Allowed : 20.20 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.28), residues: 874 helix: 1.61 (0.26), residues: 369 sheet: -0.13 (0.39), residues: 162 loop : -1.63 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 54 TYR 0.012 0.001 TYR A 296 PHE 0.015 0.001 PHE B 151 TRP 0.014 0.002 TRP B 169 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6804) covalent geometry : angle 0.57660 ( 9255) SS BOND : bond 0.00400 ( 3) SS BOND : angle 0.91408 ( 6) hydrogen bonds : bond 0.03796 ( 351) hydrogen bonds : angle 4.43832 ( 1026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 79 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6292 (tp30) REVERT: A 266 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7036 (mt) REVERT: A 302 TYR cc_start: 0.6780 (t80) cc_final: 0.5877 (t80) REVERT: A 349 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6360 (mptm) REVERT: B 46 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7812 (ttp80) REVERT: B 101 MET cc_start: 0.7569 (ptm) cc_final: 0.7170 (ptp) REVERT: B 234 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.6709 (t80) REVERT: C 44 LEU cc_start: 0.2137 (OUTLIER) cc_final: 0.1918 (tt) REVERT: R 122 TRP cc_start: 0.6044 (t-100) cc_final: 0.5670 (t-100) REVERT: R 136 TYR cc_start: 0.6251 (OUTLIER) cc_final: 0.5475 (t80) REVERT: R 160 GLN cc_start: 0.6885 (mm-40) cc_final: 0.6578 (mm110) REVERT: R 166 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7388 (mtm110) REVERT: R 239 MET cc_start: 0.7218 (ttm) cc_final: 0.6934 (mtp) REVERT: R 276 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.4942 (mp10) REVERT: R 310 VAL cc_start: 0.7870 (t) cc_final: 0.7620 (t) outliers start: 46 outliers final: 22 residues processed: 119 average time/residue: 0.4298 time to fit residues: 54.0955 Evaluate side-chains 103 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 72 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 70 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 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 294 ASN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.206849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.162087 restraints weight = 8525.175| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.60 r_work: 0.3890 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6807 Z= 0.144 Angle : 0.586 7.207 9261 Z= 0.300 Chirality : 0.041 0.205 1108 Planarity : 0.003 0.035 1156 Dihedral : 6.659 65.233 960 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 6.20 % Allowed : 21.50 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.28), residues: 874 helix: 1.65 (0.26), residues: 369 sheet: -0.14 (0.38), residues: 162 loop : -1.64 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 32 TYR 0.009 0.001 TYR A 296 PHE 0.018 0.001 PHE A 189 TRP 0.014 0.002 TRP B 169 HIS 0.007 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6804) covalent geometry : angle 0.58597 ( 9255) SS BOND : bond 0.00378 ( 3) SS BOND : angle 0.83735 ( 6) hydrogen bonds : bond 0.03735 ( 351) hydrogen bonds : angle 4.40249 ( 1026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 71 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.6235 (tp30) REVERT: A 266 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7055 (mt) REVERT: A 276 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: A 302 TYR cc_start: 0.6784 (t80) cc_final: 0.5866 (t80) REVERT: B 46 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7726 (ttp80) REVERT: B 101 MET cc_start: 0.7477 (ptm) cc_final: 0.7107 (ptp) REVERT: B 234 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6612 (t80) REVERT: C 44 LEU cc_start: 0.2116 (OUTLIER) cc_final: 0.1886 (tt) REVERT: R 122 TRP cc_start: 0.6019 (t-100) cc_final: 0.5445 (t-100) REVERT: R 136 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.5456 (t80) REVERT: R 160 GLN cc_start: 0.6882 (mm-40) cc_final: 0.6548 (mm110) REVERT: R 166 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7351 (mtm110) REVERT: R 199 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.5925 (tt) REVERT: R 239 MET cc_start: 0.7244 (ttm) cc_final: 0.6998 (mtp) REVERT: R 276 GLN cc_start: 0.6403 (OUTLIER) cc_final: 0.4924 (mp10) REVERT: R 310 VAL cc_start: 0.7810 (t) cc_final: 0.7545 (t) outliers start: 43 outliers final: 22 residues processed: 112 average time/residue: 0.3712 time to fit residues: 44.2704 Evaluate side-chains 100 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 304 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 39 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 54 optimal weight: 0.0970 chunk 33 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.212211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.173065 restraints weight = 8600.423| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 2.77 r_work: 0.3953 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6807 Z= 0.113 Angle : 0.561 7.684 9261 Z= 0.289 Chirality : 0.041 0.216 1108 Planarity : 0.003 0.037 1156 Dihedral : 6.494 64.774 960 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.63 % Allowed : 21.36 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.28), residues: 874 helix: 1.84 (0.27), residues: 367 sheet: -0.08 (0.39), residues: 161 loop : -1.63 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 54 TYR 0.008 0.001 TYR A 296 PHE 0.012 0.001 PHE A 189 TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6804) covalent geometry : angle 0.56124 ( 9255) SS BOND : bond 0.00338 ( 3) SS BOND : angle 0.75981 ( 6) hydrogen bonds : bond 0.03456 ( 351) hydrogen bonds : angle 4.28108 ( 1026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: A 302 TYR cc_start: 0.6725 (t80) cc_final: 0.5894 (t80) REVERT: B 46 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7779 (ttp80) REVERT: B 101 MET cc_start: 0.7437 (ptm) cc_final: 0.7095 (ptp) REVERT: B 234 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6723 (t80) REVERT: C 44 LEU cc_start: 0.2213 (OUTLIER) cc_final: 0.1973 (tt) REVERT: R 136 TYR cc_start: 0.6209 (OUTLIER) cc_final: 0.5551 (t80) REVERT: R 160 GLN cc_start: 0.6913 (mm-40) cc_final: 0.6588 (mm110) REVERT: R 166 ARG cc_start: 0.7601 (mpp80) cc_final: 0.7315 (mtm110) REVERT: R 199 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5962 (tt) REVERT: R 239 MET cc_start: 0.7234 (ttm) cc_final: 0.6974 (mtp) REVERT: R 276 GLN cc_start: 0.6442 (OUTLIER) cc_final: 0.4970 (mp10) REVERT: R 310 VAL cc_start: 0.7853 (t) cc_final: 0.7608 (t) outliers start: 39 outliers final: 19 residues processed: 117 average time/residue: 0.3713 time to fit residues: 46.3901 Evaluate side-chains 101 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 85 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 64 optimal weight: 0.0970 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.210682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.169457 restraints weight = 8621.297| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.99 r_work: 0.3912 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6807 Z= 0.139 Angle : 0.616 8.741 9261 Z= 0.316 Chirality : 0.042 0.241 1108 Planarity : 0.003 0.036 1156 Dihedral : 6.569 64.489 960 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.47 % Allowed : 23.09 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.28), residues: 874 helix: 1.74 (0.27), residues: 367 sheet: -0.11 (0.38), residues: 169 loop : -1.58 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 32 TYR 0.009 0.001 TYR A 296 PHE 0.021 0.001 PHE A 189 TRP 0.017 0.002 TRP R 122 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6804) covalent geometry : angle 0.61615 ( 9255) SS BOND : bond 0.00444 ( 3) SS BOND : angle 0.63569 ( 6) hydrogen bonds : bond 0.03669 ( 351) hydrogen bonds : angle 4.37201 ( 1026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 MET cc_start: 0.7184 (tpp) cc_final: 0.6765 (tpt) REVERT: A 266 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7091 (mt) REVERT: A 276 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: A 302 TYR cc_start: 0.6755 (t80) cc_final: 0.5880 (t80) REVERT: B 46 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7841 (ttp80) REVERT: B 234 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.6662 (t80) REVERT: R 130 LYS cc_start: 0.4523 (OUTLIER) cc_final: 0.4133 (mmmt) REVERT: R 136 TYR cc_start: 0.6272 (OUTLIER) cc_final: 0.5565 (t80) REVERT: R 160 GLN cc_start: 0.6960 (mm-40) cc_final: 0.6627 (mm110) REVERT: R 166 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7377 (mtm110) REVERT: R 239 MET cc_start: 0.7250 (ttm) cc_final: 0.6984 (mtp) REVERT: R 276 GLN cc_start: 0.6468 (OUTLIER) cc_final: 0.4966 (mp10) REVERT: R 310 VAL cc_start: 0.7859 (t) cc_final: 0.7589 (t) outliers start: 31 outliers final: 18 residues processed: 105 average time/residue: 0.4479 time to fit residues: 49.9494 Evaluate side-chains 101 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain R residue 130 LYS Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 54 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.209836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.164950 restraints weight = 8599.210| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.61 r_work: 0.3919 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6807 Z= 0.144 Angle : 0.625 9.178 9261 Z= 0.318 Chirality : 0.042 0.233 1108 Planarity : 0.003 0.036 1156 Dihedral : 6.550 64.166 958 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.04 % Allowed : 23.23 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.28), residues: 874 helix: 1.68 (0.27), residues: 367 sheet: -0.01 (0.38), residues: 167 loop : -1.58 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 54 TYR 0.011 0.001 TYR A 296 PHE 0.014 0.001 PHE B 151 TRP 0.015 0.002 TRP B 169 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6804) covalent geometry : angle 0.62502 ( 9255) SS BOND : bond 0.00360 ( 3) SS BOND : angle 0.66583 ( 6) hydrogen bonds : bond 0.03723 ( 351) hydrogen bonds : angle 4.40447 ( 1026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1748 Ramachandran restraints generated. 874 Oldfield, 0 Emsley, 874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 276 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 302 TYR cc_start: 0.6834 (t80) cc_final: 0.5930 (t80) REVERT: B 46 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7784 (ttp80) REVERT: B 101 MET cc_start: 0.7441 (ptm) cc_final: 0.7134 (ptp) REVERT: B 234 PHE cc_start: 0.7438 (OUTLIER) cc_final: 0.6635 (t80) REVERT: R 54 ARG cc_start: 0.7636 (ttm110) cc_final: 0.7341 (ttm-80) REVERT: R 136 TYR cc_start: 0.6239 (OUTLIER) cc_final: 0.5448 (t80) REVERT: R 160 GLN cc_start: 0.6976 (mm-40) cc_final: 0.6620 (mm110) REVERT: R 166 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7393 (mtm110) REVERT: R 239 MET cc_start: 0.7253 (ttm) cc_final: 0.7004 (mtp) REVERT: R 276 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.4959 (mp10) REVERT: R 310 VAL cc_start: 0.7883 (t) cc_final: 0.7622 (t) outliers start: 28 outliers final: 20 residues processed: 96 average time/residue: 0.4439 time to fit residues: 45.1790 Evaluate side-chains 96 residues out of total 772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 70 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 111 TYR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 169 TRP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 153 ASP Chi-restraints excluded: chain R residue 166 ARG Chi-restraints excluded: chain R residue 276 GLN Chi-restraints excluded: chain R residue 277 LEU Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain R residue 332 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 65 optimal weight: 9.9990 chunk 37 optimal weight: 0.0000 chunk 11 optimal weight: 0.8980 chunk 61 optimal weight: 0.0570 chunk 60 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.211585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.170119 restraints weight = 8565.833| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.82 r_work: 0.3923 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6807 Z= 0.125 Angle : 0.611 9.711 9261 Z= 0.308 Chirality : 0.041 0.224 1108 Planarity : 0.003 0.046 1156 Dihedral : 6.495 64.720 958 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.47 % Allowed : 22.66 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.28), residues: 874 helix: 1.82 (0.27), residues: 364 sheet: 0.09 (0.38), residues: 164 loop : -1.63 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 54 TYR 0.010 0.001 TYR A 296 PHE 0.013 0.001 PHE A 189 TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6804) covalent geometry : angle 0.61067 ( 9255) SS BOND : bond 0.00251 ( 3) SS BOND : angle 0.66014 ( 6) hydrogen bonds : bond 0.03540 ( 351) hydrogen bonds : angle 4.33690 ( 1026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2305.31 seconds wall clock time: 40 minutes 7.53 seconds (2407.53 seconds total)