Starting phenix.real_space_refine on Thu Jul 2 07:31:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gy7_34371/07_2026/8gy7_34371_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gy7_34371/07_2026/8gy7_34371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gy7_34371/07_2026/8gy7_34371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gy7_34371/07_2026/8gy7_34371.map" model { file = "/net/cci-nas-00/data/ceres_data/8gy7_34371/07_2026/8gy7_34371_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gy7_34371/07_2026/8gy7_34371_neut.cif" } resolution = 3.3 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= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 56 5.16 5 C 4890 2.51 5 N 1322 2.21 5 O 1392 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7661 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1920 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2604 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 411 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 158 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 1, 'TRANS': 16} Chain: "P" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 413 Classifications: {'peptide': 51} Incomplete info: {'backbone_only': 3} Link IDs: {'PTRANS': 1, 'TRANS': 49} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2154 Classifications: {'peptide': 274} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 261} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 1.63, per 1000 atoms: 0.21 Number of scatterers: 7661 At special positions: 0 Unit cell: (76.96, 120.64, 120.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 56 16.00 O 1392 8.00 N 1322 7.00 C 4890 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 21 " - pdb=" SG CYS R 253 " distance=2.05 Simple disulfide: pdb=" SG CYS R 245 " - pdb=" SG CYS R 251 " distance=2.16 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: 0.55 Conformation dependent library (CDL) restraints added in 426.7 milliseconds 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1822 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 46.3% alpha, 16.8% 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 6 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.576A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.544A pdb=" N THR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 41 removed outlier: 4.114A pdb=" N ASN B 41 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'P' and resid 36 through 63 Processing helix chain 'R' and resid 27 through 49 removed outlier: 3.832A pdb=" N PHE R 31 " --> pdb=" O PRO R 27 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL R 49 " --> pdb=" O VAL R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 88 Processing helix chain 'R' and resid 96 through 134 removed outlier: 3.533A pdb=" N THR R 101 " --> pdb=" O SER R 97 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ALA R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 142 Processing helix chain 'R' and resid 143 through 168 Processing helix chain 'R' and resid 171 through 208 removed outlier: 3.875A pdb=" N PHE R 182 " --> pdb=" O PHE R 178 " (cutoff:3.500A) Proline residue: R 183 - end of helix removed outlier: 3.647A pdb=" N HIS R 195 " --> pdb=" O CYS R 191 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS R 206 " --> pdb=" O SER R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 231 Processing helix chain 'R' and resid 232 through 245 Processing helix chain 'R' and resid 248 through 256 Processing helix chain 'R' and resid 257 through 272 removed outlier: 3.658A pdb=" N ASN R 268 " --> pdb=" O LEU R 264 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ALA R 269 " --> pdb=" O ILE R 265 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL R 270 " --> pdb=" O MET R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 277 Processing helix chain 'R' and resid 280 through 291 Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 186 removed outlier: 7.070A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.712A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N CYS B 322 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.695A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 110 removed outlier: 4.410A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N CYS B 126 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N GLU B 143 " --> pdb=" O CYS B 126 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN B 130 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 158 removed outlier: 3.507A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N THR B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 192 through 197 removed outlier: 4.137A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.958A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.743A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 13 through 15 415 hydrogen bonds defined for protein. 1203 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: 1.26 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1311 1.32 - 1.45: 2079 1.45 - 1.57: 4347 1.57 - 1.69: 1 1.69 - 1.81: 83 Bond restraints: 7821 Sorted by residual: bond pdb=" C LEU R 210 " pdb=" N PRO R 211 " ideal model delta sigma weight residual 1.335 1.412 -0.076 1.30e-02 5.92e+03 3.46e+01 bond pdb=" CA ARG A 208 " pdb=" C ARG A 208 " ideal model delta sigma weight residual 1.521 1.468 0.053 1.29e-02 6.01e+03 1.68e+01 bond pdb=" CA SER R 19 " pdb=" CB SER R 19 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.64e-02 3.72e+03 1.14e+01 bond pdb=" C LYS A 27 " pdb=" N GLN A 28 " ideal model delta sigma weight residual 1.335 1.297 0.038 1.36e-02 5.41e+03 7.92e+00 bond pdb=" CB PRO A 288 " pdb=" CG PRO A 288 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.65e+00 ... (remaining 7816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 10258 1.95 - 3.90: 268 3.90 - 5.85: 45 5.85 - 7.80: 10 7.80 - 9.75: 4 Bond angle restraints: 10585 Sorted by residual: angle pdb=" CA PRO A 288 " pdb=" N PRO A 288 " pdb=" CD PRO A 288 " ideal model delta sigma weight residual 112.00 102.25 9.75 1.40e+00 5.10e-01 4.85e+01 angle pdb=" C CYS R 251 " pdb=" CA CYS R 251 " pdb=" CB CYS R 251 " ideal model delta sigma weight residual 110.92 101.46 9.46 1.59e+00 3.96e-01 3.54e+01 angle pdb=" N SER R 108 " pdb=" CA SER R 108 " pdb=" C SER R 108 " ideal model delta sigma weight residual 111.14 104.89 6.25 1.08e+00 8.57e-01 3.35e+01 angle pdb=" C LYS A 27 " pdb=" N GLN A 28 " pdb=" CA GLN A 28 " ideal model delta sigma weight residual 120.29 114.02 6.27 1.42e+00 4.96e-01 1.95e+01 angle pdb=" N ASN R 54 " pdb=" CA ASN R 54 " pdb=" C ASN R 54 " ideal model delta sigma weight residual 111.36 106.73 4.63 1.09e+00 8.42e-01 1.81e+01 ... (remaining 10580 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 3954 15.02 - 30.04: 476 30.04 - 45.06: 176 45.06 - 60.08: 42 60.08 - 75.10: 10 Dihedral angle restraints: 4658 sinusoidal: 1844 harmonic: 2814 Sorted by residual: dihedral pdb=" CA LYS A 210 " pdb=" C LYS A 210 " pdb=" N TRP A 211 " pdb=" CA TRP A 211 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" C CYS R 251 " pdb=" N CYS R 251 " pdb=" CA CYS R 251 " pdb=" CB CYS R 251 " ideal model delta harmonic sigma weight residual -122.60 -109.95 -12.65 0 2.50e+00 1.60e-01 2.56e+01 dihedral pdb=" CA ASP B 252 " pdb=" C ASP B 252 " pdb=" N ALA B 253 " pdb=" CA ALA B 253 " ideal model delta harmonic sigma weight residual 180.00 157.82 22.18 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 4655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1013 0.059 - 0.117: 154 0.117 - 0.176: 28 0.176 - 0.235: 5 0.235 - 0.294: 1 Chirality restraints: 1201 Sorted by residual: chirality pdb=" CA CYS R 251 " pdb=" N CYS R 251 " pdb=" C CYS R 251 " pdb=" CB CYS R 251 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA SER R 19 " pdb=" N SER R 19 " pdb=" C SER R 19 " pdb=" CB SER R 19 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ILE R 154 " pdb=" N ILE R 154 " pdb=" C ILE R 154 " pdb=" CB ILE R 154 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 1198 not shown) Planarity restraints: 1339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 287 " -0.080 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 288 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 53 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C LYS R 53 " -0.049 2.00e-02 2.50e+03 pdb=" O LYS R 53 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN R 54 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 288 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C LYS R 288 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS R 288 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS R 289 " 0.012 2.00e-02 2.50e+03 ... (remaining 1336 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 98 2.58 - 3.16: 6953 3.16 - 3.74: 12443 3.74 - 4.32: 16961 4.32 - 4.90: 28174 Nonbonded interactions: 64629 Sorted by model distance: nonbonded pdb=" OD2 ASP R 107 " pdb="CA CA R 501 " model vdw 2.006 3.250 nonbonded pdb=" O ASP B 263 " pdb=" OD1 ASP B 263 " model vdw 2.209 3.040 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.223 3.040 nonbonded pdb=" OG SER B 284 " pdb=" OD2 ASP G 48 " model vdw 2.236 3.040 nonbonded pdb=" O GLU M 5 " pdb="CA CA R 501 " model vdw 2.262 3.250 ... (remaining 64624 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: 0.010 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.190 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 : 0.005 0.138 7823 Z= 0.256 Angle : 0.845 28.452 10589 Z= 0.481 Chirality : 0.047 0.294 1201 Planarity : 0.006 0.114 1339 Dihedral : 15.855 75.099 2830 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.96 % Allowed : 25.42 % Favored : 73.62 % Cbeta Deviations : 0.22 % 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 (0.27), residues: 954 helix: 1.45 (0.25), residues: 419 sheet: -0.08 (0.42), residues: 157 loop : -1.15 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 284 TYR 0.013 0.001 TYR A 230 PHE 0.026 0.002 PHE R 157 TRP 0.028 0.002 TRP A 248 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.25 ( 7821) covalent geometry : angle 0.76108 / 0.45 (10585) SS BOND : bond 0.08931 / 4.26 ( 2) SS BOND : angle 18.84994 / 7.66 ( 4) hydrogen bonds : bond 0.15566 / 10.30 ( 415) hydrogen bonds : angle 6.60514 / 4.50 ( 1203) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 261 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8337 (mtpm) cc_final: 0.7870 (mtpm) REVERT: A 239 ASP cc_start: 0.7896 (m-30) cc_final: 0.7570 (t0) REVERT: A 337 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7431 (mt-10) REVERT: B 57 ARG cc_start: 0.7262 (mtt90) cc_final: 0.6743 (mtt90) REVERT: B 64 TYR cc_start: 0.8217 (m-80) cc_final: 0.7914 (m-80) REVERT: B 66 MET cc_start: 0.7912 (ptm) cc_final: 0.7629 (ptm) REVERT: B 116 TYR cc_start: 0.8295 (m-80) cc_final: 0.7675 (m-80) REVERT: B 178 THR cc_start: 0.8576 (p) cc_final: 0.8213 (t) REVERT: B 256 ARG cc_start: 0.7990 (mtt-85) cc_final: 0.7477 (mtt90) REVERT: B 268 THR cc_start: 0.8735 (m) cc_final: 0.8490 (p) REVERT: B 316 HIS cc_start: 0.7748 (m-70) cc_final: 0.7475 (m-70) REVERT: B 339 SER cc_start: 0.8479 (m) cc_final: 0.8278 (t) REVERT: B 345 ASN cc_start: 0.7686 (t0) cc_final: 0.7169 (p0) REVERT: M 4 MET cc_start: 0.7738 (mmt) cc_final: 0.7446 (tpt) REVERT: R 40 LEU cc_start: 0.7737 (mt) cc_final: 0.7536 (mt) REVERT: R 77 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6475 (tppp) REVERT: R 143 THR cc_start: 0.8480 (t) cc_final: 0.8104 (p) outliers start: 8 outliers final: 4 residues processed: 265 average time/residue: 0.1147 time to fit residues: 38.3912 Evaluate side-chains 262 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 257 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 77 LYS Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 166 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 28 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN A 324 HIS ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 HIS B 225 GLN R 54 ASN R 214 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111069 restraints weight = 11774.427| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.21 r_work: 0.3258 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7823 Z= 0.178 Angle : 0.654 8.330 10589 Z= 0.343 Chirality : 0.044 0.177 1201 Planarity : 0.005 0.060 1339 Dihedral : 5.496 58.615 1062 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.48 % Allowed : 20.38 % Favored : 76.14 % 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: 0.52 (0.27), residues: 954 helix: 1.54 (0.24), residues: 426 sheet: -0.45 (0.39), residues: 173 loop : -0.63 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 341 TYR 0.019 0.002 TYR A 230 PHE 0.018 0.002 PHE A 189 TRP 0.016 0.002 TRP B 216 HIS 0.012 0.002 HIS B 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 ( 7821) covalent geometry : angle 0.65365 / 0.34 (10585) SS BOND : bond 0.00807 / 0.39 ( 2) SS BOND : angle 1.61286 / 0.79 ( 4) hydrogen bonds : bond 0.04772 / 3.17 ( 415) hydrogen bonds : angle 5.15340 / 3.55 ( 1203) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 261 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.7693 (t) cc_final: 0.7445 (p) REVERT: A 230 TYR cc_start: 0.8679 (m-10) cc_final: 0.8389 (m-10) REVERT: A 239 ASP cc_start: 0.8266 (m-30) cc_final: 0.7952 (t0) REVERT: A 260 LYS cc_start: 0.8602 (mtmp) cc_final: 0.8219 (ptpp) REVERT: A 267 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8093 (ttpt) REVERT: A 310 ASP cc_start: 0.7560 (m-30) cc_final: 0.7151 (m-30) REVERT: A 337 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 347 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7697 (ttm-80) REVERT: B 27 ARG cc_start: 0.8158 (mtm180) cc_final: 0.7942 (mtm180) REVERT: B 37 GLN cc_start: 0.8398 (pm20) cc_final: 0.7937 (pm20) REVERT: B 47 ARG cc_start: 0.7760 (ptt-90) cc_final: 0.7329 (ptt-90) REVERT: B 57 ARG cc_start: 0.7815 (mtt90) cc_final: 0.7431 (mtt90) REVERT: B 64 TYR cc_start: 0.8316 (m-80) cc_final: 0.7881 (m-80) REVERT: B 80 GLN cc_start: 0.7332 (mt0) cc_final: 0.6615 (mt0) REVERT: B 115 ASN cc_start: 0.8414 (m110) cc_final: 0.7952 (m-40) REVERT: B 142 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7511 (tpp80) REVERT: B 235 ASN cc_start: 0.8203 (m-40) cc_final: 0.7939 (m110) REVERT: B 255 CYS cc_start: 0.8137 (t) cc_final: 0.7711 (p) REVERT: B 279 THR cc_start: 0.8460 (m) cc_final: 0.8257 (p) REVERT: B 309 ARG cc_start: 0.8254 (mtm-85) cc_final: 0.7730 (mtm-85) REVERT: B 316 HIS cc_start: 0.7789 (m-70) cc_final: 0.7587 (m-70) REVERT: B 339 SER cc_start: 0.8404 (m) cc_final: 0.8029 (t) REVERT: B 345 ASN cc_start: 0.7660 (t0) cc_final: 0.6943 (p0) REVERT: M 4 MET cc_start: 0.7491 (mmt) cc_final: 0.7152 (mmt) REVERT: R 271 ILE cc_start: 0.8585 (tt) cc_final: 0.8383 (tt) outliers start: 29 outliers final: 17 residues processed: 275 average time/residue: 0.1002 time to fit residues: 34.9704 Evaluate side-chains 273 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 254 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 204 THR Chi-restraints excluded: chain R residue 214 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 57 optimal weight: 7.9990 chunk 26 optimal weight: 0.0020 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 61 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 overall best weight: 0.5146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 GLN A 195 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN B 225 GLN B 242 ASN B 244 ASN R 214 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.127283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.111747 restraints weight = 11677.822| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.12 r_work: 0.3278 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7823 Z= 0.150 Angle : 0.599 8.049 10589 Z= 0.317 Chirality : 0.042 0.158 1201 Planarity : 0.004 0.057 1339 Dihedral : 5.154 58.594 1055 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.08 % Allowed : 21.34 % Favored : 74.58 % 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: 0.66 (0.28), residues: 954 helix: 1.68 (0.24), residues: 426 sheet: -0.54 (0.39), residues: 176 loop : -0.50 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 232 TYR 0.012 0.001 TYR A 230 PHE 0.017 0.002 PHE A 189 TRP 0.013 0.002 TRP B 174 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 7821) covalent geometry : angle 0.59762 / 0.32 (10585) SS BOND : bond 0.00666 / 0.35 ( 2) SS BOND : angle 1.90011 / 1.03 ( 4) hydrogen bonds : bond 0.04411 / 2.94 ( 415) hydrogen bonds : angle 4.99225 / 3.47 ( 1203) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.7674 (t) cc_final: 0.7426 (p) REVERT: A 230 TYR cc_start: 0.8655 (m-10) cc_final: 0.8357 (m-10) REVERT: A 239 ASP cc_start: 0.8300 (m-30) cc_final: 0.8009 (t0) REVERT: A 260 LYS cc_start: 0.8668 (mtmp) cc_final: 0.8169 (ptpp) REVERT: A 267 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8120 (ttpt) REVERT: A 274 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8600 (mptt) REVERT: A 340 ARG cc_start: 0.8493 (tpp-160) cc_final: 0.8129 (tpt170) REVERT: A 347 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7545 (ttm-80) REVERT: A 351 GLN cc_start: 0.8495 (mt0) cc_final: 0.8191 (mt0) REVERT: B 47 ARG cc_start: 0.7765 (ptt-90) cc_final: 0.7396 (ptt-90) REVERT: B 57 ARG cc_start: 0.7719 (mtt90) cc_final: 0.7355 (mtt90) REVERT: B 64 TYR cc_start: 0.8319 (m-80) cc_final: 0.8025 (m-80) REVERT: B 104 TRP cc_start: 0.8538 (m100) cc_final: 0.8202 (m100) REVERT: B 115 ASN cc_start: 0.8456 (m110) cc_final: 0.7999 (m-40) REVERT: B 116 TYR cc_start: 0.8454 (m-80) cc_final: 0.7799 (m-80) REVERT: B 117 VAL cc_start: 0.8838 (p) cc_final: 0.8577 (t) REVERT: B 142 ARG cc_start: 0.8082 (tpp80) cc_final: 0.7477 (tpp80) REVERT: B 159 ASP cc_start: 0.8023 (m-30) cc_final: 0.7482 (m-30) REVERT: B 176 ILE cc_start: 0.8560 (mm) cc_final: 0.7564 (mm) REVERT: B 255 CYS cc_start: 0.8144 (t) cc_final: 0.7691 (p) REVERT: B 259 ASP cc_start: 0.7994 (t0) cc_final: 0.7763 (t0) REVERT: B 279 THR cc_start: 0.8424 (m) cc_final: 0.8204 (p) REVERT: B 309 ARG cc_start: 0.8235 (mtm-85) cc_final: 0.7665 (mtm-85) REVERT: B 316 HIS cc_start: 0.7762 (m-70) cc_final: 0.7471 (m-70) REVERT: B 328 ASP cc_start: 0.8081 (p0) cc_final: 0.7859 (p0) REVERT: B 338 ASP cc_start: 0.7994 (p0) cc_final: 0.7421 (p0) REVERT: B 339 SER cc_start: 0.8437 (m) cc_final: 0.7967 (t) REVERT: R 53 LYS cc_start: 0.8614 (tppt) cc_final: 0.8160 (ttpt) REVERT: R 195 HIS cc_start: 0.8425 (OUTLIER) cc_final: 0.7416 (t70) outliers start: 34 outliers final: 17 residues processed: 268 average time/residue: 0.0932 time to fit residues: 31.9870 Evaluate side-chains 266 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 195 HIS Chi-restraints excluded: chain R residue 214 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 77 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 64 optimal weight: 0.0470 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN G 24 ASN R 214 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.110764 restraints weight = 11888.221| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.23 r_work: 0.3259 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7823 Z= 0.161 Angle : 0.593 7.753 10589 Z= 0.310 Chirality : 0.042 0.169 1201 Planarity : 0.004 0.052 1339 Dihedral : 4.752 22.161 1053 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.56 % Allowed : 22.18 % Favored : 73.26 % 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: 0.67 (0.27), residues: 954 helix: 1.67 (0.24), residues: 426 sheet: -0.55 (0.39), residues: 176 loop : -0.46 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 341 TYR 0.011 0.001 TYR A 230 PHE 0.019 0.002 PHE A 189 TRP 0.015 0.002 TRP B 174 HIS 0.007 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 7821) covalent geometry : angle 0.59175 / 0.31 (10585) SS BOND : bond 0.00552 / 0.29 ( 2) SS BOND : angle 2.28923 / 1.15 ( 4) hydrogen bonds : bond 0.04236 / 2.83 ( 415) hydrogen bonds : angle 4.89736 / 3.42 ( 1203) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 252 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.7654 (t) cc_final: 0.7398 (p) REVERT: A 19 ILE cc_start: 0.8355 (tp) cc_final: 0.7858 (tp) REVERT: A 239 ASP cc_start: 0.8317 (m-30) cc_final: 0.7989 (t0) REVERT: A 267 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8113 (ttpt) REVERT: A 274 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8615 (mptt) REVERT: A 310 ASP cc_start: 0.7493 (m-30) cc_final: 0.7137 (m-30) REVERT: A 321 ASP cc_start: 0.8042 (t0) cc_final: 0.7780 (t0) REVERT: A 340 ARG cc_start: 0.8470 (tpp-160) cc_final: 0.8078 (tpt170) REVERT: A 347 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7634 (ttm-80) REVERT: B 37 GLN cc_start: 0.8583 (pm20) cc_final: 0.8360 (pm20) REVERT: B 47 ARG cc_start: 0.7794 (ptt-90) cc_final: 0.7408 (ptt-90) REVERT: B 57 ARG cc_start: 0.7765 (mtt90) cc_final: 0.7461 (mtt90) REVERT: B 64 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.8064 (m-80) REVERT: B 104 TRP cc_start: 0.8569 (m100) cc_final: 0.8329 (m100) REVERT: B 115 ASN cc_start: 0.8484 (m110) cc_final: 0.8000 (m-40) REVERT: B 117 VAL cc_start: 0.8814 (p) cc_final: 0.8553 (t) REVERT: B 142 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7448 (tpp80) REVERT: B 176 ILE cc_start: 0.8569 (mm) cc_final: 0.7616 (mm) REVERT: B 235 ASN cc_start: 0.8121 (m-40) cc_final: 0.7865 (m110) REVERT: B 244 ASN cc_start: 0.8337 (m-40) cc_final: 0.8023 (t0) REVERT: B 255 CYS cc_start: 0.8199 (t) cc_final: 0.7751 (p) REVERT: B 256 ARG cc_start: 0.8368 (mtt-85) cc_final: 0.7919 (mtt90) REVERT: B 263 ASP cc_start: 0.8104 (t0) cc_final: 0.7644 (t0) REVERT: B 265 GLU cc_start: 0.8037 (pt0) cc_final: 0.7777 (pt0) REVERT: B 279 THR cc_start: 0.8453 (m) cc_final: 0.8223 (p) REVERT: B 309 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.7759 (mtm-85) REVERT: B 328 ASP cc_start: 0.8101 (p0) cc_final: 0.7887 (p0) REVERT: B 339 SER cc_start: 0.8418 (m) cc_final: 0.7997 (t) REVERT: R 53 LYS cc_start: 0.8612 (tppt) cc_final: 0.8131 (ttpt) REVERT: R 195 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.7397 (t70) outliers start: 38 outliers final: 24 residues processed: 269 average time/residue: 0.1024 time to fit residues: 35.0867 Evaluate side-chains 280 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain R residue 47 LEU Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 143 THR Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 195 HIS Chi-restraints excluded: chain R residue 214 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 0.0670 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 70 optimal weight: 0.0670 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN B 225 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.126875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111770 restraints weight = 12037.352| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.18 r_work: 0.3274 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7823 Z= 0.147 Angle : 0.581 7.911 10589 Z= 0.305 Chirality : 0.042 0.168 1201 Planarity : 0.004 0.048 1339 Dihedral : 4.680 22.424 1053 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.20 % Allowed : 22.78 % 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: 0.73 (0.28), residues: 954 helix: 1.76 (0.24), residues: 426 sheet: -0.53 (0.39), residues: 176 loop : -0.47 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 155 TYR 0.010 0.001 TYR R 76 PHE 0.017 0.001 PHE B 246 TRP 0.014 0.002 TRP B 174 HIS 0.008 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 ( 7821) covalent geometry : angle 0.58006 / 0.30 (10585) SS BOND : bond 0.00449 / 0.23 ( 2) SS BOND : angle 1.76891 / 0.93 ( 4) hydrogen bonds : bond 0.04139 / 2.76 ( 415) hydrogen bonds : angle 4.79465 / 3.34 ( 1203) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 249 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.7596 (t) cc_final: 0.7359 (p) REVERT: A 19 ILE cc_start: 0.8342 (tp) cc_final: 0.7846 (tp) REVERT: A 230 TYR cc_start: 0.8752 (m-10) cc_final: 0.8541 (m-80) REVERT: A 234 GLN cc_start: 0.8725 (tp40) cc_final: 0.8520 (tp-100) REVERT: A 239 ASP cc_start: 0.8219 (m-30) cc_final: 0.7901 (t0) REVERT: A 267 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8111 (ttpt) REVERT: A 274 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8698 (mptt) REVERT: A 313 LEU cc_start: 0.8633 (mm) cc_final: 0.8240 (mt) REVERT: A 321 ASP cc_start: 0.8085 (t0) cc_final: 0.7841 (t0) REVERT: A 340 ARG cc_start: 0.8512 (tpp-160) cc_final: 0.8117 (tpt170) REVERT: A 347 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7675 (ttm-80) REVERT: B 27 ARG cc_start: 0.7868 (mtt180) cc_final: 0.7635 (mtt180) REVERT: B 47 ARG cc_start: 0.7815 (ptt-90) cc_final: 0.7595 (ptt-90) REVERT: B 64 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7966 (m-80) REVERT: B 104 TRP cc_start: 0.8571 (m100) cc_final: 0.8229 (m100) REVERT: B 115 ASN cc_start: 0.8513 (m110) cc_final: 0.7969 (m110) REVERT: B 116 TYR cc_start: 0.8464 (m-80) cc_final: 0.7746 (m-80) REVERT: B 117 VAL cc_start: 0.8784 (p) cc_final: 0.8528 (t) REVERT: B 142 ARG cc_start: 0.8109 (tpp80) cc_final: 0.7410 (tpp80) REVERT: B 175 ASP cc_start: 0.7359 (m-30) cc_final: 0.7133 (m-30) REVERT: B 176 ILE cc_start: 0.8592 (mm) cc_final: 0.7634 (mm) REVERT: B 239 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: B 244 ASN cc_start: 0.8218 (m-40) cc_final: 0.7887 (t0) REVERT: B 255 CYS cc_start: 0.8125 (t) cc_final: 0.7777 (p) REVERT: B 263 ASP cc_start: 0.7970 (t0) cc_final: 0.7719 (t0) REVERT: B 279 THR cc_start: 0.8419 (m) cc_final: 0.8188 (p) REVERT: B 309 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7689 (mtm-85) REVERT: B 328 ASP cc_start: 0.8075 (p0) cc_final: 0.7854 (p0) REVERT: B 338 ASP cc_start: 0.7948 (p0) cc_final: 0.7600 (p0) REVERT: B 339 SER cc_start: 0.8297 (m) cc_final: 0.7843 (t) REVERT: R 53 LYS cc_start: 0.8579 (tppt) cc_final: 0.8095 (ttpt) REVERT: R 195 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7312 (t70) REVERT: R 266 MET cc_start: 0.8093 (mmm) cc_final: 0.7699 (mmm) outliers start: 35 outliers final: 21 residues processed: 266 average time/residue: 0.0948 time to fit residues: 32.2252 Evaluate side-chains 276 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 249 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 195 HIS Chi-restraints excluded: chain R residue 227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 4 optimal weight: 0.0370 chunk 61 optimal weight: 0.0770 chunk 34 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 235 ASN B 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.128017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.112685 restraints weight = 11909.015| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.20 r_work: 0.3290 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7823 Z= 0.124 Angle : 0.566 7.886 10589 Z= 0.298 Chirality : 0.042 0.204 1201 Planarity : 0.004 0.045 1339 Dihedral : 4.558 20.915 1053 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.32 % Allowed : 23.38 % Favored : 72.30 % 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: 0.79 (0.28), residues: 954 helix: 1.88 (0.24), residues: 421 sheet: -0.56 (0.39), residues: 176 loop : -0.48 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 87 TYR 0.010 0.001 TYR R 76 PHE 0.020 0.001 PHE B 246 TRP 0.016 0.002 TRP B 174 HIS 0.004 0.001 HIS R 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 7821) covalent geometry : angle 0.56567 / 0.30 (10585) SS BOND : bond 0.00622 / 0.32 ( 2) SS BOND : angle 1.50890 / 0.79 ( 4) hydrogen bonds : bond 0.03955 / 2.64 ( 415) hydrogen bonds : angle 4.70720 / 3.28 ( 1203) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.245 Fit side-chains REVERT: A 13 VAL cc_start: 0.7549 (t) cc_final: 0.7271 (p) REVERT: A 19 ILE cc_start: 0.8349 (tp) cc_final: 0.7857 (tp) REVERT: A 239 ASP cc_start: 0.8150 (m-30) cc_final: 0.7847 (t0) REVERT: A 241 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8497 (ttmm) REVERT: A 260 LYS cc_start: 0.8766 (mtmp) cc_final: 0.7992 (mtmm) REVERT: A 267 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8037 (ttpt) REVERT: A 274 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8689 (mptt) REVERT: A 313 LEU cc_start: 0.8617 (mm) cc_final: 0.8212 (mt) REVERT: A 340 ARG cc_start: 0.8500 (tpp-160) cc_final: 0.8111 (tpt170) REVERT: A 347 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7497 (ttm-80) REVERT: A 351 GLN cc_start: 0.8605 (mt0) cc_final: 0.8331 (mt0) REVERT: B 64 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: B 90 TYR cc_start: 0.7419 (m-10) cc_final: 0.7186 (m-80) REVERT: B 104 TRP cc_start: 0.8547 (m100) cc_final: 0.8221 (m100) REVERT: B 115 ASN cc_start: 0.8557 (m110) cc_final: 0.8078 (m110) REVERT: B 116 TYR cc_start: 0.8439 (m-80) cc_final: 0.7755 (m-80) REVERT: B 117 VAL cc_start: 0.8753 (p) cc_final: 0.8532 (t) REVERT: B 142 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7309 (tpp80) REVERT: B 176 ILE cc_start: 0.8544 (mm) cc_final: 0.7651 (mm) REVERT: B 222 MET cc_start: 0.7444 (mmm) cc_final: 0.7182 (mmm) REVERT: B 233 ASP cc_start: 0.7407 (m-30) cc_final: 0.7194 (t0) REVERT: B 239 PHE cc_start: 0.8474 (OUTLIER) cc_final: 0.7769 (m-80) REVERT: B 244 ASN cc_start: 0.8205 (m-40) cc_final: 0.7899 (t0) REVERT: B 255 CYS cc_start: 0.8144 (t) cc_final: 0.7747 (p) REVERT: B 256 ARG cc_start: 0.8298 (mtt-85) cc_final: 0.7941 (mtt90) REVERT: B 268 THR cc_start: 0.8818 (t) cc_final: 0.8543 (t) REVERT: B 309 ARG cc_start: 0.8270 (mtm-85) cc_final: 0.7984 (mtm-85) REVERT: B 328 ASP cc_start: 0.8070 (p0) cc_final: 0.7840 (p0) REVERT: B 338 ASP cc_start: 0.7906 (p0) cc_final: 0.7553 (p0) REVERT: B 339 SER cc_start: 0.8265 (m) cc_final: 0.7788 (t) REVERT: R 30 ILE cc_start: 0.7454 (OUTLIER) cc_final: 0.7213 (tp) REVERT: R 53 LYS cc_start: 0.8616 (tppt) cc_final: 0.8135 (ttpt) REVERT: R 195 HIS cc_start: 0.8305 (OUTLIER) cc_final: 0.7232 (t70) REVERT: R 242 MET cc_start: 0.8365 (tmm) cc_final: 0.8087 (ttp) REVERT: R 245 CYS cc_start: 0.7731 (p) cc_final: 0.7504 (p) REVERT: R 266 MET cc_start: 0.8020 (mmm) cc_final: 0.7649 (mmm) outliers start: 36 outliers final: 22 residues processed: 262 average time/residue: 0.1023 time to fit residues: 33.8862 Evaluate side-chains 270 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 318 ASN Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 195 HIS Chi-restraints excluded: chain R residue 227 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 3 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 84 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 34 optimal weight: 0.0570 chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.111534 restraints weight = 11749.455| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.16 r_work: 0.3284 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7823 Z= 0.143 Angle : 0.575 7.766 10589 Z= 0.304 Chirality : 0.042 0.179 1201 Planarity : 0.004 0.044 1339 Dihedral : 4.553 22.508 1053 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.56 % Allowed : 23.50 % Favored : 71.94 % 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: 0.77 (0.27), residues: 954 helix: 1.85 (0.24), residues: 426 sheet: -0.57 (0.38), residues: 176 loop : -0.50 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 232 TYR 0.019 0.001 TYR A 230 PHE 0.019 0.001 PHE B 246 TRP 0.017 0.002 TRP B 174 HIS 0.008 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7821) covalent geometry : angle 0.57424 / 0.30 (10585) SS BOND : bond 0.00447 / 0.23 ( 2) SS BOND : angle 1.38569 / 0.74 ( 4) hydrogen bonds : bond 0.03960 / 2.64 ( 415) hydrogen bonds : angle 4.68788 / 3.27 ( 1203) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 0.179 Fit side-chains REVERT: A 13 VAL cc_start: 0.7605 (t) cc_final: 0.7347 (p) REVERT: A 19 ILE cc_start: 0.8365 (tp) cc_final: 0.7884 (tp) REVERT: A 239 ASP cc_start: 0.8150 (m-30) cc_final: 0.7842 (t0) REVERT: A 241 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8503 (ttmm) REVERT: A 260 LYS cc_start: 0.8741 (mtmp) cc_final: 0.7925 (mtmm) REVERT: A 267 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8051 (ttpt) REVERT: A 274 LYS cc_start: 0.8983 (mttt) cc_final: 0.8691 (mptt) REVERT: A 313 LEU cc_start: 0.8600 (mm) cc_final: 0.8193 (mt) REVERT: A 321 ASP cc_start: 0.7697 (t0) cc_final: 0.7412 (p0) REVERT: A 340 ARG cc_start: 0.8510 (tpp-160) cc_final: 0.8115 (tpt170) REVERT: A 347 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7656 (ttm-80) REVERT: B 37 GLN cc_start: 0.8494 (pm20) cc_final: 0.8164 (pm20) REVERT: B 64 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7937 (m-80) REVERT: B 90 TYR cc_start: 0.7452 (m-10) cc_final: 0.7201 (m-80) REVERT: B 104 TRP cc_start: 0.8552 (m100) cc_final: 0.8238 (m100) REVERT: B 115 ASN cc_start: 0.8564 (m110) cc_final: 0.8084 (m110) REVERT: B 116 TYR cc_start: 0.8439 (m-80) cc_final: 0.7775 (m-80) REVERT: B 117 VAL cc_start: 0.8769 (p) cc_final: 0.8522 (t) REVERT: B 142 ARG cc_start: 0.7959 (tpp80) cc_final: 0.7315 (tpp80) REVERT: B 164 THR cc_start: 0.8449 (p) cc_final: 0.8213 (p) REVERT: B 175 ASP cc_start: 0.7197 (m-30) cc_final: 0.6752 (m-30) REVERT: B 222 MET cc_start: 0.7442 (mmm) cc_final: 0.7159 (mmm) REVERT: B 224 ARG cc_start: 0.7914 (tpp80) cc_final: 0.7298 (ttm110) REVERT: B 233 ASP cc_start: 0.7298 (m-30) cc_final: 0.7055 (t0) REVERT: B 239 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: B 244 ASN cc_start: 0.8133 (m-40) cc_final: 0.7839 (t0) REVERT: B 263 ASP cc_start: 0.7816 (t0) cc_final: 0.7384 (t70) REVERT: B 309 ARG cc_start: 0.8311 (mtm-85) cc_final: 0.8028 (mtm-85) REVERT: B 328 ASP cc_start: 0.8057 (p0) cc_final: 0.7856 (p0) REVERT: B 338 ASP cc_start: 0.7844 (p0) cc_final: 0.7486 (p0) REVERT: B 339 SER cc_start: 0.8259 (m) cc_final: 0.7776 (t) REVERT: B 345 ASN cc_start: 0.7810 (t0) cc_final: 0.7224 (p0) REVERT: R 30 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7202 (tp) REVERT: R 87 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7773 (ttp-170) REVERT: R 195 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7211 (t70) REVERT: R 242 MET cc_start: 0.8346 (tmm) cc_final: 0.8063 (ttp) REVERT: R 245 CYS cc_start: 0.7738 (p) cc_final: 0.7501 (p) REVERT: R 266 MET cc_start: 0.8035 (mmm) cc_final: 0.7700 (mmm) outliers start: 38 outliers final: 25 residues processed: 274 average time/residue: 0.0912 time to fit residues: 32.0895 Evaluate side-chains 281 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 195 HIS Chi-restraints excluded: chain R residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 0.0670 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 351 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.127110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111938 restraints weight = 11914.732| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.19 r_work: 0.3291 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7823 Z= 0.133 Angle : 0.575 8.639 10589 Z= 0.302 Chirality : 0.041 0.189 1201 Planarity : 0.004 0.044 1339 Dihedral : 4.550 21.543 1053 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.56 % Allowed : 24.70 % Favored : 70.74 % 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: 0.82 (0.27), residues: 954 helix: 1.94 (0.24), residues: 421 sheet: -0.50 (0.39), residues: 173 loop : -0.54 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 232 TYR 0.014 0.001 TYR A 230 PHE 0.020 0.001 PHE B 246 TRP 0.018 0.002 TRP B 174 HIS 0.007 0.001 HIS A 329 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 7821) covalent geometry : angle 0.57475 / 0.30 (10585) SS BOND : bond 0.00394 / 0.20 ( 2) SS BOND : angle 1.21274 / 0.64 ( 4) hydrogen bonds : bond 0.03930 / 2.63 ( 415) hydrogen bonds : angle 4.70101 / 3.27 ( 1203) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: A 13 VAL cc_start: 0.7524 (t) cc_final: 0.7254 (p) REVERT: A 19 ILE cc_start: 0.8366 (tp) cc_final: 0.7884 (tp) REVERT: A 232 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8111 (mtp85) REVERT: A 239 ASP cc_start: 0.8130 (m-30) cc_final: 0.7823 (t0) REVERT: A 241 LYS cc_start: 0.8705 (ttmm) cc_final: 0.8495 (ttmm) REVERT: A 260 LYS cc_start: 0.8678 (mtmp) cc_final: 0.7828 (mtmm) REVERT: A 267 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8020 (ttpt) REVERT: A 274 LYS cc_start: 0.8971 (mttt) cc_final: 0.8677 (mptt) REVERT: A 313 LEU cc_start: 0.8573 (mm) cc_final: 0.8155 (mt) REVERT: A 340 ARG cc_start: 0.8511 (tpp-160) cc_final: 0.8108 (tpt170) REVERT: A 347 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7625 (ttm-80) REVERT: B 64 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: B 104 TRP cc_start: 0.8567 (m100) cc_final: 0.8232 (m100) REVERT: B 115 ASN cc_start: 0.8576 (m110) cc_final: 0.8103 (m110) REVERT: B 116 TYR cc_start: 0.8441 (m-80) cc_final: 0.7779 (m-80) REVERT: B 117 VAL cc_start: 0.8766 (p) cc_final: 0.8528 (t) REVERT: B 142 ARG cc_start: 0.7965 (tpp80) cc_final: 0.7325 (tpp80) REVERT: B 175 ASP cc_start: 0.7207 (m-30) cc_final: 0.6817 (m-30) REVERT: B 222 MET cc_start: 0.7474 (mmm) cc_final: 0.7218 (mmm) REVERT: B 233 ASP cc_start: 0.7347 (m-30) cc_final: 0.7111 (t0) REVERT: B 239 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: B 244 ASN cc_start: 0.8173 (m-40) cc_final: 0.7780 (t0) REVERT: B 255 CYS cc_start: 0.8245 (t) cc_final: 0.7794 (p) REVERT: B 256 ARG cc_start: 0.8185 (mtt-85) cc_final: 0.7642 (mtt90) REVERT: B 263 ASP cc_start: 0.7817 (t0) cc_final: 0.7484 (t70) REVERT: B 268 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8135 (t) REVERT: B 309 ARG cc_start: 0.8341 (mtm-85) cc_final: 0.8044 (mtm-85) REVERT: B 338 ASP cc_start: 0.7824 (p0) cc_final: 0.7546 (p0) REVERT: B 345 ASN cc_start: 0.7745 (t0) cc_final: 0.7209 (p0) REVERT: R 30 ILE cc_start: 0.7395 (OUTLIER) cc_final: 0.7183 (tp) REVERT: R 195 HIS cc_start: 0.8263 (OUTLIER) cc_final: 0.7232 (t70) REVERT: R 242 MET cc_start: 0.8372 (tmm) cc_final: 0.8088 (ttp) REVERT: R 245 CYS cc_start: 0.7698 (p) cc_final: 0.7449 (p) REVERT: R 266 MET cc_start: 0.8009 (mmm) cc_final: 0.7649 (mmm) outliers start: 38 outliers final: 26 residues processed: 267 average time/residue: 0.0980 time to fit residues: 33.3865 Evaluate side-chains 283 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 58 LEU Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 195 HIS Chi-restraints excluded: chain R residue 227 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 10 optimal weight: 0.3980 chunk 90 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 70 optimal weight: 0.0070 chunk 9 optimal weight: 0.0030 chunk 31 optimal weight: 0.0040 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.128165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.112770 restraints weight = 11936.108| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.24 r_work: 0.3315 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7823 Z= 0.118 Angle : 0.580 9.782 10589 Z= 0.304 Chirality : 0.042 0.189 1201 Planarity : 0.004 0.042 1339 Dihedral : 4.464 21.355 1053 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.08 % Allowed : 25.66 % Favored : 70.26 % 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: 0.91 (0.28), residues: 954 helix: 2.05 (0.25), residues: 421 sheet: -0.50 (0.39), residues: 175 loop : -0.52 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 232 TYR 0.010 0.001 TYR A 230 PHE 0.018 0.001 PHE A 189 TRP 0.020 0.002 TRP B 174 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 ( 7821) covalent geometry : angle 0.58010 / 0.30 (10585) SS BOND : bond 0.00506 / 0.26 ( 2) SS BOND : angle 1.00435 / 0.49 ( 4) hydrogen bonds : bond 0.03784 / 2.53 ( 415) hydrogen bonds : angle 4.66098 / 3.25 ( 1203) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 252 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8336 (tp) cc_final: 0.7863 (tp) REVERT: A 239 ASP cc_start: 0.8100 (m-30) cc_final: 0.7790 (t0) REVERT: A 260 LYS cc_start: 0.8703 (mtmp) cc_final: 0.7859 (mtmm) REVERT: A 267 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7872 (ttpt) REVERT: A 274 LYS cc_start: 0.8959 (mttt) cc_final: 0.8670 (mptt) REVERT: A 313 LEU cc_start: 0.8551 (mm) cc_final: 0.8134 (mt) REVERT: A 340 ARG cc_start: 0.8470 (tpp-160) cc_final: 0.8068 (tpt170) REVERT: A 347 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7638 (ttm-80) REVERT: B 104 TRP cc_start: 0.8520 (m100) cc_final: 0.8202 (m100) REVERT: B 115 ASN cc_start: 0.8569 (m110) cc_final: 0.8120 (m110) REVERT: B 116 TYR cc_start: 0.8429 (m-80) cc_final: 0.7834 (m-80) REVERT: B 117 VAL cc_start: 0.8726 (p) cc_final: 0.8514 (t) REVERT: B 142 ARG cc_start: 0.7893 (tpp80) cc_final: 0.7296 (tpp80) REVERT: B 175 ASP cc_start: 0.7177 (m-30) cc_final: 0.6827 (m-30) REVERT: B 222 MET cc_start: 0.7478 (mmm) cc_final: 0.7203 (mmm) REVERT: B 233 ASP cc_start: 0.7145 (m-30) cc_final: 0.6923 (t0) REVERT: B 239 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: B 244 ASN cc_start: 0.8167 (m-40) cc_final: 0.7539 (t0) REVERT: B 255 CYS cc_start: 0.8371 (t) cc_final: 0.7823 (p) REVERT: B 256 ARG cc_start: 0.8209 (mtt-85) cc_final: 0.7570 (mtt90) REVERT: B 263 ASP cc_start: 0.7775 (t0) cc_final: 0.7430 (t70) REVERT: B 268 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8236 (t) REVERT: B 280 SER cc_start: 0.8771 (t) cc_final: 0.8282 (p) REVERT: B 281 VAL cc_start: 0.8729 (p) cc_final: 0.8477 (t) REVERT: B 309 ARG cc_start: 0.8286 (mtm-85) cc_final: 0.7963 (mtm-85) REVERT: B 338 ASP cc_start: 0.7809 (p0) cc_final: 0.7557 (p0) REVERT: R 30 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.7009 (tp) REVERT: R 195 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7120 (t70) REVERT: R 242 MET cc_start: 0.8387 (tmm) cc_final: 0.8093 (ttp) REVERT: R 245 CYS cc_start: 0.7696 (p) cc_final: 0.7440 (p) REVERT: R 266 MET cc_start: 0.7927 (mmm) cc_final: 0.7589 (mmm) outliers start: 34 outliers final: 19 residues processed: 266 average time/residue: 0.0971 time to fit residues: 32.9291 Evaluate side-chains 276 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 251 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 89 MET Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 195 HIS Chi-restraints excluded: chain R residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 90 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 71 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.126953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111571 restraints weight = 11890.586| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.20 r_work: 0.3293 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7823 Z= 0.150 Angle : 0.610 10.393 10589 Z= 0.320 Chirality : 0.042 0.198 1201 Planarity : 0.004 0.042 1339 Dihedral : 4.534 20.236 1053 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.12 % Allowed : 27.10 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.28), residues: 954 helix: 1.96 (0.24), residues: 426 sheet: -0.36 (0.40), residues: 175 loop : -0.50 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 87 TYR 0.022 0.001 TYR A 230 PHE 0.021 0.001 PHE A 189 TRP 0.017 0.002 TRP A 211 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 7821) covalent geometry : angle 0.60976 / 0.32 (10585) SS BOND : bond 0.00350 / 0.18 ( 2) SS BOND : angle 0.79859 / 0.38 ( 4) hydrogen bonds : bond 0.03947 / 2.63 ( 415) hydrogen bonds : angle 4.66042 / 3.24 ( 1203) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1908 Ramachandran restraints generated. 954 Oldfield, 0 Emsley, 954 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 256 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8359 (tp) cc_final: 0.7905 (tp) REVERT: A 20 GLU cc_start: 0.7791 (tp30) cc_final: 0.7532 (tp30) REVERT: A 210 LYS cc_start: 0.8227 (mttm) cc_final: 0.7856 (mttm) REVERT: A 239 ASP cc_start: 0.8131 (m-30) cc_final: 0.7833 (t0) REVERT: A 260 LYS cc_start: 0.8687 (mtmp) cc_final: 0.7940 (mtmm) REVERT: A 267 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7983 (ttpt) REVERT: A 274 LYS cc_start: 0.9042 (mttt) cc_final: 0.8745 (mptt) REVERT: A 313 LEU cc_start: 0.8586 (mm) cc_final: 0.8187 (mt) REVERT: A 340 ARG cc_start: 0.8508 (tpp-160) cc_final: 0.8106 (tpt170) REVERT: A 347 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7732 (ttm-80) REVERT: B 64 TYR cc_start: 0.7850 (m-80) cc_final: 0.7303 (m-80) REVERT: B 79 SER cc_start: 0.8425 (p) cc_final: 0.7704 (p) REVERT: B 104 TRP cc_start: 0.8542 (m100) cc_final: 0.8133 (m100) REVERT: B 115 ASN cc_start: 0.8599 (m110) cc_final: 0.8109 (m110) REVERT: B 116 TYR cc_start: 0.8451 (m-80) cc_final: 0.7847 (m-80) REVERT: B 117 VAL cc_start: 0.8764 (p) cc_final: 0.8512 (t) REVERT: B 142 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7356 (tpp80) REVERT: B 175 ASP cc_start: 0.7176 (m-30) cc_final: 0.6812 (m-30) REVERT: B 222 MET cc_start: 0.7414 (mmm) cc_final: 0.7170 (mmm) REVERT: B 233 ASP cc_start: 0.7256 (m-30) cc_final: 0.7047 (t0) REVERT: B 239 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: B 244 ASN cc_start: 0.8191 (m-40) cc_final: 0.7568 (t0) REVERT: B 256 ARG cc_start: 0.8285 (mtt-85) cc_final: 0.7513 (mtt180) REVERT: B 263 ASP cc_start: 0.7869 (t0) cc_final: 0.7583 (t70) REVERT: B 280 SER cc_start: 0.8763 (t) cc_final: 0.8266 (p) REVERT: B 281 VAL cc_start: 0.8767 (p) cc_final: 0.8524 (t) REVERT: B 309 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.8004 (mtm-85) REVERT: B 336 SER cc_start: 0.8246 (t) cc_final: 0.7929 (t) REVERT: R 30 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.7030 (tp) REVERT: R 195 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7073 (t70) REVERT: R 242 MET cc_start: 0.8372 (tmm) cc_final: 0.8094 (ttp) REVERT: R 245 CYS cc_start: 0.7738 (p) cc_final: 0.7475 (p) outliers start: 26 outliers final: 17 residues processed: 271 average time/residue: 0.0895 time to fit residues: 31.0391 Evaluate side-chains 275 residues out of total 846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 110 TYR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 264 GLN Chi-restraints excluded: chain P residue 24 ILE Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 195 HIS Chi-restraints excluded: chain R residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 0.0000 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.126591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.111021 restraints weight = 11871.253| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.21 r_work: 0.3284 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7823 Z= 0.162 Angle : 0.639 12.493 10589 Z= 0.333 Chirality : 0.044 0.257 1201 Planarity : 0.004 0.042 1339 Dihedral : 4.621 22.860 1053 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.12 % Allowed : 27.94 % Favored : 68.94 % 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: 0.85 (0.28), residues: 954 helix: 1.90 (0.24), residues: 426 sheet: -0.40 (0.40), residues: 170 loop : -0.53 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 87 TYR 0.019 0.001 TYR A 230 PHE 0.021 0.002 PHE A 189 TRP 0.019 0.002 TRP B 87 HIS 0.005 0.001 HIS A 197 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 ( 7821) covalent geometry : angle 0.63880 / 0.33 (10585) SS BOND : bond 0.00369 / 0.19 ( 2) SS BOND : angle 0.68695 / 0.31 ( 4) hydrogen bonds : bond 0.03986 / 2.66 ( 415) hydrogen bonds : angle 4.73219 / 3.29 ( 1203) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1945.43 seconds wall clock time: 34 minutes 1.53 seconds (2041.53 seconds total)