Starting phenix.real_space_refine on Tue Feb 3 22:54:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xjh_33227/02_2026/7xjh_33227.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xjh_33227/02_2026/7xjh_33227.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/7xjh_33227/02_2026/7xjh_33227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xjh_33227/02_2026/7xjh_33227.map" model { file = "/net/cci-nas-00/data/ceres_data/7xjh_33227/02_2026/7xjh_33227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xjh_33227/02_2026/7xjh_33227.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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 4962 2.51 5 N 1378 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7832 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2543 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2047 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 4, 'GLU:plan': 1, 'HIS:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'5FW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.15, per 1000 atoms: 0.27 Number of scatterers: 7832 At special positions: 0 Unit cell: (96.3829, 120.479, 86.5255, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1446 8.00 N 1378 7.00 C 4962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 189 " - pdb=" SG CYS R 195 " distance=2.03 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: 0.74 Conformation dependent library (CDL) restraints added in 299.7 milliseconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 43.7% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.699A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 302 through 308 removed outlier: 3.662A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 307 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 341 Processing helix chain 'A' and resid 360 through 381 removed outlier: 3.888A pdb=" N ARG A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.644A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 11 through 23 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.674A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 64 removed outlier: 3.513A pdb=" N ALA R 42 " --> pdb=" O ALA R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 69 Processing helix chain 'R' and resid 70 through 90 removed outlier: 3.528A pdb=" N VAL R 74 " --> pdb=" O THR R 70 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE R 75 " --> pdb=" O MET R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 100 Processing helix chain 'R' and resid 106 through 141 removed outlier: 3.784A pdb=" N SER R 124 " --> pdb=" O CYS R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 149 Processing helix chain 'R' and resid 150 through 170 Processing helix chain 'R' and resid 170 through 175 removed outlier: 3.549A pdb=" N MET R 174 " --> pdb=" O PHE R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 192 Processing helix chain 'R' and resid 201 through 213 Processing helix chain 'R' and resid 213 through 243 Processing helix chain 'R' and resid 288 through 318 removed outlier: 3.900A pdb=" N ARG R 292 " --> pdb=" O HIS R 288 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP R 305 " --> pdb=" O PHE R 301 " (cutoff:3.500A) Proline residue: R 307 - end of helix Processing helix chain 'R' and resid 324 through 342 Processing helix chain 'R' and resid 343 through 345 No H-bonds generated for 'chain 'R' and resid 343 through 345' Processing helix chain 'R' and resid 349 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.319A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.631A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.674A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.043A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150 removed outlier: 4.053A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.684A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.036A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.259A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.244A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1200 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: 1.33 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2581 1.34 - 1.46: 1625 1.46 - 1.58: 3719 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 7986 Sorted by residual: bond pdb=" CA SER N 21 " pdb=" CB SER N 21 " ideal model delta sigma weight residual 1.532 1.486 0.046 1.74e-02 3.30e+03 6.99e+00 bond pdb=" CAO 5FW R 401 " pdb=" OAC 5FW R 401 " ideal model delta sigma weight residual 1.351 1.400 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" CAM 5FW R 401 " pdb=" OAB 5FW R 401 " ideal model delta sigma weight residual 1.353 1.401 -0.048 2.00e-02 2.50e+03 5.66e+00 bond pdb=" C LEU R 306 " pdb=" N PRO R 307 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.30e-02 5.92e+03 2.00e+00 bond pdb=" N SER N 21 " pdb=" CA SER N 21 " ideal model delta sigma weight residual 1.454 1.470 -0.016 1.19e-02 7.06e+03 1.79e+00 ... (remaining 7981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 10580 1.53 - 3.07: 224 3.07 - 4.60: 38 4.60 - 6.13: 13 6.13 - 7.67: 3 Bond angle restraints: 10858 Sorted by residual: angle pdb=" N PHE A 222 " pdb=" CA PHE A 222 " pdb=" C PHE A 222 " ideal model delta sigma weight residual 108.55 113.15 -4.60 1.62e+00 3.81e-01 8.07e+00 angle pdb=" N GLU A 16 " pdb=" CA GLU A 16 " pdb=" CB GLU A 16 " ideal model delta sigma weight residual 110.28 114.64 -4.36 1.55e+00 4.16e-01 7.90e+00 angle pdb=" CA SER N 21 " pdb=" C SER N 21 " pdb=" O SER N 21 " ideal model delta sigma weight residual 121.16 118.03 3.13 1.13e+00 7.83e-01 7.66e+00 angle pdb=" C LEU N 20 " pdb=" N SER N 21 " pdb=" CA SER N 21 " ideal model delta sigma weight residual 122.87 118.94 3.93 1.61e+00 3.86e-01 5.95e+00 angle pdb=" C LEU R 89 " pdb=" N VAL R 90 " pdb=" CA VAL R 90 " ideal model delta sigma weight residual 122.63 119.81 2.82 1.19e+00 7.06e-01 5.60e+00 ... (remaining 10853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4301 17.97 - 35.93: 382 35.93 - 53.90: 58 53.90 - 71.87: 9 71.87 - 89.83: 8 Dihedral angle restraints: 4758 sinusoidal: 1782 harmonic: 2976 Sorted by residual: dihedral pdb=" CB CYS R 189 " pdb=" SG CYS R 189 " pdb=" SG CYS R 195 " pdb=" CB CYS R 195 " ideal model delta sinusoidal sigma weight residual -86.00 -133.54 47.54 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 134.21 -41.21 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 4755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 967 0.045 - 0.090: 220 0.090 - 0.134: 67 0.134 - 0.179: 2 0.179 - 0.224: 2 Chirality restraints: 1258 Sorted by residual: chirality pdb=" CAE 5FW R 401 " pdb=" CAF 5FW R 401 " pdb=" CAH 5FW R 401 " pdb=" OAA 5FW R 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.52 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB THR A 315 " pdb=" CA THR A 315 " pdb=" OG1 THR A 315 " pdb=" CG2 THR A 315 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1255 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 215 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO R 216 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO R 216 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 216 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 323 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO R 324 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO R 324 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 324 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 192 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO R 193 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO R 193 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 193 " 0.022 5.00e-02 4.00e+02 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1016 2.75 - 3.29: 7524 3.29 - 3.83: 13177 3.83 - 4.36: 15228 4.36 - 4.90: 27153 Nonbonded interactions: 64098 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.218 3.040 nonbonded pdb=" OD2 ASP A 33 " pdb=" NZ LYS B 78 " model vdw 2.223 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.226 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.228 3.040 nonbonded pdb=" O GLU B 226 " pdb=" NH2 ARG N 98 " model vdw 2.252 3.120 ... (remaining 64093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.840 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:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7990 Z= 0.142 Angle : 0.586 7.667 10866 Z= 0.316 Chirality : 0.042 0.224 1258 Planarity : 0.004 0.045 1390 Dihedral : 14.021 89.834 2820 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.45 (0.27), residues: 1011 helix: 2.43 (0.26), residues: 377 sheet: -0.72 (0.33), residues: 212 loop : -1.14 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 19 TYR 0.011 0.001 TYR B 59 PHE 0.023 0.002 PHE A 222 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7986) covalent geometry : angle 0.58361 (10858) SS BOND : bond 0.00112 ( 4) SS BOND : angle 1.83083 ( 8) hydrogen bonds : bond 0.09914 ( 425) hydrogen bonds : angle 4.87998 ( 1200) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7055 (mtmt) cc_final: 0.6774 (mtmt) REVERT: A 32 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7353 (mtpt) REVERT: A 34 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7769 (tttt) REVERT: A 213 GLN cc_start: 0.7742 (tt0) cc_final: 0.7514 (tt0) REVERT: A 252 ASP cc_start: 0.7055 (t70) cc_final: 0.6826 (t70) REVERT: A 304 GLU cc_start: 0.7674 (pm20) cc_final: 0.7462 (pm20) REVERT: B 42 ARG cc_start: 0.7577 (tmt170) cc_final: 0.6922 (tpt170) REVERT: B 175 GLN cc_start: 0.7772 (mt0) cc_final: 0.7544 (mt0) REVERT: B 226 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8450 (mt-10) REVERT: N 20 LEU cc_start: 0.8028 (mt) cc_final: 0.7764 (mt) REVERT: N 21 SER cc_start: 0.8305 (m) cc_final: 0.7963 (p) REVERT: N 77 ASN cc_start: 0.6830 (m-40) cc_final: 0.6525 (m-40) REVERT: R 236 ARG cc_start: 0.6685 (mtm110) cc_final: 0.6406 (mtm110) REVERT: R 240 ARG cc_start: 0.7363 (tmm-80) cc_final: 0.7003 (ttm170) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1226 time to fit residues: 25.9136 Evaluate side-chains 129 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.5980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 284 GLN B 220 GLN N 31 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.150490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.116777 restraints weight = 9099.675| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.73 r_work: 0.3100 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7990 Z= 0.199 Angle : 0.609 7.983 10866 Z= 0.319 Chirality : 0.044 0.163 1258 Planarity : 0.005 0.055 1390 Dihedral : 4.585 30.277 1122 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.35 % Allowed : 8.10 % Favored : 90.55 % 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: 0.37 (0.26), residues: 1011 helix: 2.13 (0.26), residues: 381 sheet: -0.61 (0.34), residues: 206 loop : -1.07 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 19 TYR 0.014 0.002 TYR A 329 PHE 0.017 0.002 PHE R 309 TRP 0.012 0.002 TRP B 63 HIS 0.007 0.002 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 7986) covalent geometry : angle 0.60846 (10858) SS BOND : bond 0.00147 ( 4) SS BOND : angle 1.31730 ( 8) hydrogen bonds : bond 0.04809 ( 425) hydrogen bonds : angle 4.64081 ( 1200) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7788 (mtpt) REVERT: A 34 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8203 (tttt) REVERT: A 252 ASP cc_start: 0.7599 (t70) cc_final: 0.7323 (t70) REVERT: A 342 SER cc_start: 0.8101 (t) cc_final: 0.7901 (p) REVERT: B 42 ARG cc_start: 0.7636 (tmt170) cc_final: 0.6888 (tpt170) REVERT: B 175 GLN cc_start: 0.8163 (mt0) cc_final: 0.7958 (mt0) REVERT: B 259 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7931 (mm-40) REVERT: N 20 LEU cc_start: 0.8161 (mt) cc_final: 0.7892 (mt) REVERT: N 46 GLU cc_start: 0.8523 (pt0) cc_final: 0.8197 (pt0) REVERT: N 65 LYS cc_start: 0.6675 (ttmm) cc_final: 0.6433 (tptp) REVERT: N 77 ASN cc_start: 0.7043 (m-40) cc_final: 0.6803 (m110) REVERT: R 126 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8424 (mm-30) REVERT: R 240 ARG cc_start: 0.7503 (tmm-80) cc_final: 0.6974 (tmm-80) outliers start: 11 outliers final: 9 residues processed: 134 average time/residue: 0.1144 time to fit residues: 19.9163 Evaluate side-chains 129 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 338 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 23 optimal weight: 30.0000 chunk 88 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 74 optimal weight: 0.3980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.152980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.119545 restraints weight = 8979.117| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.78 r_work: 0.3144 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7990 Z= 0.120 Angle : 0.525 8.601 10866 Z= 0.274 Chirality : 0.041 0.150 1258 Planarity : 0.004 0.048 1390 Dihedral : 4.310 29.278 1122 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.10 % Allowed : 11.41 % Favored : 87.48 % 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: 0.58 (0.27), residues: 1011 helix: 2.35 (0.26), residues: 383 sheet: -0.46 (0.34), residues: 214 loop : -1.04 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 19 TYR 0.012 0.001 TYR A 37 PHE 0.014 0.001 PHE A 212 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 7986) covalent geometry : angle 0.52515 (10858) SS BOND : bond 0.00091 ( 4) SS BOND : angle 0.70773 ( 8) hydrogen bonds : bond 0.04188 ( 425) hydrogen bonds : angle 4.42060 ( 1200) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.359 Fit side-chains REVERT: A 32 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7742 (mtpt) REVERT: A 34 LYS cc_start: 0.8369 (ttpp) cc_final: 0.8138 (tttt) REVERT: A 252 ASP cc_start: 0.7517 (t70) cc_final: 0.7200 (t70) REVERT: A 308 TYR cc_start: 0.7901 (t80) cc_final: 0.7176 (t80) REVERT: A 342 SER cc_start: 0.8011 (t) cc_final: 0.7776 (p) REVERT: B 42 ARG cc_start: 0.7658 (tmt170) cc_final: 0.6892 (tpt170) REVERT: B 175 GLN cc_start: 0.8117 (mt0) cc_final: 0.7907 (mt0) REVERT: B 256 ARG cc_start: 0.7878 (mtm110) cc_final: 0.7030 (mtm110) REVERT: B 259 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7930 (mm-40) REVERT: N 20 LEU cc_start: 0.8147 (mt) cc_final: 0.7886 (mt) REVERT: N 46 GLU cc_start: 0.8545 (pt0) cc_final: 0.8211 (pt0) REVERT: N 65 LYS cc_start: 0.6637 (ttmm) cc_final: 0.6384 (tptp) REVERT: R 68 LEU cc_start: 0.7640 (mt) cc_final: 0.7433 (mt) REVERT: R 211 VAL cc_start: 0.8467 (t) cc_final: 0.8252 (t) REVERT: R 240 ARG cc_start: 0.7409 (tmm-80) cc_final: 0.6877 (tmm-80) outliers start: 9 outliers final: 5 residues processed: 135 average time/residue: 0.1148 time to fit residues: 20.3238 Evaluate side-chains 131 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 65 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.150262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.115868 restraints weight = 9133.903| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.85 r_work: 0.3100 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7990 Z= 0.166 Angle : 0.559 8.430 10866 Z= 0.292 Chirality : 0.042 0.153 1258 Planarity : 0.004 0.051 1390 Dihedral : 4.425 29.609 1122 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.82 % Allowed : 12.52 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.26), residues: 1011 helix: 2.15 (0.26), residues: 388 sheet: -0.53 (0.34), residues: 205 loop : -1.13 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 98 TYR 0.013 0.002 TYR A 37 PHE 0.025 0.002 PHE N 108 TRP 0.011 0.001 TRP B 99 HIS 0.006 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 7986) covalent geometry : angle 0.55924 (10858) SS BOND : bond 0.00165 ( 4) SS BOND : angle 0.81827 ( 8) hydrogen bonds : bond 0.04521 ( 425) hydrogen bonds : angle 4.49426 ( 1200) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.296 Fit side-chains REVERT: A 32 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7778 (mtpt) REVERT: A 34 LYS cc_start: 0.8396 (ttpp) cc_final: 0.8169 (tttt) REVERT: A 230 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 252 ASP cc_start: 0.7533 (t70) cc_final: 0.7215 (t70) REVERT: A 342 SER cc_start: 0.7960 (t) cc_final: 0.7663 (p) REVERT: B 42 ARG cc_start: 0.7616 (tmt170) cc_final: 0.6788 (tpt170) REVERT: B 175 GLN cc_start: 0.8141 (mt0) cc_final: 0.7921 (mt0) REVERT: B 256 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7193 (mtm110) REVERT: B 259 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7955 (mm-40) REVERT: N 20 LEU cc_start: 0.8119 (mt) cc_final: 0.7846 (mt) REVERT: N 46 GLU cc_start: 0.8581 (pt0) cc_final: 0.8335 (pt0) REVERT: N 65 LYS cc_start: 0.6722 (ttmm) cc_final: 0.6446 (tptp) REVERT: N 108 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8311 (t80) outliers start: 23 outliers final: 16 residues processed: 139 average time/residue: 0.1132 time to fit residues: 20.7443 Evaluate side-chains 136 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 59 ASN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.152104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118123 restraints weight = 8986.407| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.80 r_work: 0.3126 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7990 Z= 0.129 Angle : 0.522 8.805 10866 Z= 0.273 Chirality : 0.041 0.144 1258 Planarity : 0.004 0.048 1390 Dihedral : 4.279 28.895 1122 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.70 % Allowed : 13.50 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.27), residues: 1011 helix: 2.30 (0.26), residues: 390 sheet: -0.42 (0.33), residues: 213 loop : -1.09 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 98 TYR 0.013 0.001 TYR A 37 PHE 0.015 0.001 PHE R 308 TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7986) covalent geometry : angle 0.52218 (10858) SS BOND : bond 0.00121 ( 4) SS BOND : angle 0.77067 ( 8) hydrogen bonds : bond 0.04181 ( 425) hydrogen bonds : angle 4.36748 ( 1200) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.305 Fit side-chains REVERT: A 32 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7755 (mtpt) REVERT: A 34 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8140 (tttt) REVERT: A 230 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7772 (mt-10) REVERT: A 252 ASP cc_start: 0.7520 (t70) cc_final: 0.7185 (t70) REVERT: A 329 TYR cc_start: 0.8675 (m-80) cc_final: 0.8306 (m-80) REVERT: A 342 SER cc_start: 0.7947 (t) cc_final: 0.7598 (p) REVERT: B 42 ARG cc_start: 0.7629 (tmt170) cc_final: 0.6783 (tpt170) REVERT: B 256 ARG cc_start: 0.7886 (mtm110) cc_final: 0.7170 (mtm110) REVERT: B 259 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8090 (mm-40) REVERT: N 20 LEU cc_start: 0.8145 (mt) cc_final: 0.7832 (mt) REVERT: N 65 LYS cc_start: 0.6784 (ttmm) cc_final: 0.6416 (tptp) outliers start: 22 outliers final: 16 residues processed: 137 average time/residue: 0.1126 time to fit residues: 20.2443 Evaluate side-chains 135 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 303 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 97 optimal weight: 0.0470 chunk 91 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.152646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118584 restraints weight = 8959.355| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.77 r_work: 0.3134 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7990 Z= 0.118 Angle : 0.517 8.840 10866 Z= 0.269 Chirality : 0.041 0.359 1258 Planarity : 0.004 0.047 1390 Dihedral : 4.184 28.173 1122 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.94 % Allowed : 14.23 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.27), residues: 1011 helix: 2.38 (0.26), residues: 390 sheet: -0.43 (0.33), residues: 213 loop : -1.06 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 98 TYR 0.013 0.001 TYR A 37 PHE 0.014 0.001 PHE R 308 TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7986) covalent geometry : angle 0.51719 (10858) SS BOND : bond 0.00092 ( 4) SS BOND : angle 0.72883 ( 8) hydrogen bonds : bond 0.04021 ( 425) hydrogen bonds : angle 4.30837 ( 1200) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 0.340 Fit side-chains REVERT: A 32 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7742 (mtpt) REVERT: A 34 LYS cc_start: 0.8342 (ttpp) cc_final: 0.8130 (tttt) REVERT: A 252 ASP cc_start: 0.7572 (t70) cc_final: 0.7156 (t70) REVERT: A 329 TYR cc_start: 0.8632 (m-80) cc_final: 0.8280 (m-80) REVERT: A 342 SER cc_start: 0.7844 (t) cc_final: 0.7543 (p) REVERT: B 42 ARG cc_start: 0.7652 (tmt170) cc_final: 0.6802 (tpt170) REVERT: B 256 ARG cc_start: 0.7886 (mtm110) cc_final: 0.7177 (mtm110) REVERT: B 259 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8108 (mm-40) REVERT: B 298 ASP cc_start: 0.8301 (t70) cc_final: 0.8083 (t70) REVERT: N 20 LEU cc_start: 0.8108 (mt) cc_final: 0.7805 (mt) REVERT: N 61 THR cc_start: 0.9064 (t) cc_final: 0.8717 (p) REVERT: N 65 LYS cc_start: 0.6759 (ttmm) cc_final: 0.6416 (tptp) REVERT: R 345 ILE cc_start: 0.8464 (mt) cc_final: 0.8250 (mt) outliers start: 24 outliers final: 18 residues processed: 142 average time/residue: 0.1083 time to fit residues: 20.3144 Evaluate side-chains 142 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 303 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN N 77 ASN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.148108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.113211 restraints weight = 9049.287| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.85 r_work: 0.3059 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7990 Z= 0.212 Angle : 0.606 8.320 10866 Z= 0.316 Chirality : 0.045 0.389 1258 Planarity : 0.004 0.051 1390 Dihedral : 4.585 31.806 1122 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.07 % Allowed : 14.23 % Favored : 82.70 % 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: 0.36 (0.26), residues: 1011 helix: 2.07 (0.26), residues: 389 sheet: -0.52 (0.34), residues: 205 loop : -1.13 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 98 TYR 0.015 0.002 TYR R 145 PHE 0.020 0.002 PHE R 308 TRP 0.013 0.002 TRP B 99 HIS 0.007 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00504 ( 7986) covalent geometry : angle 0.60582 (10858) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.98731 ( 8) hydrogen bonds : bond 0.04871 ( 425) hydrogen bonds : angle 4.62151 ( 1200) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.367 Fit side-chains REVERT: A 32 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7832 (mtpt) REVERT: A 34 LYS cc_start: 0.8470 (ttpp) cc_final: 0.8240 (tttt) REVERT: A 209 GLU cc_start: 0.6990 (tp30) cc_final: 0.6654 (tp30) REVERT: A 252 ASP cc_start: 0.7653 (t70) cc_final: 0.7290 (t70) REVERT: A 342 SER cc_start: 0.7870 (t) cc_final: 0.7596 (p) REVERT: B 42 ARG cc_start: 0.7650 (tmt170) cc_final: 0.6828 (tpt170) REVERT: B 256 ARG cc_start: 0.7971 (mtm110) cc_final: 0.7260 (mtm110) REVERT: B 259 GLN cc_start: 0.8377 (mm-40) cc_final: 0.8142 (mm-40) REVERT: N 20 LEU cc_start: 0.8114 (mt) cc_final: 0.7824 (mt) REVERT: N 65 LYS cc_start: 0.6896 (ttmm) cc_final: 0.6558 (tptp) REVERT: N 108 PHE cc_start: 0.8862 (OUTLIER) cc_final: 0.7885 (t80) outliers start: 25 outliers final: 19 residues processed: 136 average time/residue: 0.1087 time to fit residues: 19.3589 Evaluate side-chains 138 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 93 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN N 123 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.151724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.116570 restraints weight = 9107.958| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.94 r_work: 0.3104 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7990 Z= 0.130 Angle : 0.543 9.041 10866 Z= 0.282 Chirality : 0.042 0.376 1258 Planarity : 0.004 0.049 1390 Dihedral : 4.324 29.166 1122 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.82 % Allowed : 14.85 % Favored : 82.33 % 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: 0.49 (0.27), residues: 1011 helix: 2.18 (0.26), residues: 390 sheet: -0.45 (0.33), residues: 210 loop : -1.09 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 98 TYR 0.014 0.001 TYR A 37 PHE 0.015 0.001 PHE R 308 TRP 0.012 0.001 TRP B 99 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7986) covalent geometry : angle 0.54246 (10858) SS BOND : bond 0.00066 ( 4) SS BOND : angle 0.76571 ( 8) hydrogen bonds : bond 0.04211 ( 425) hydrogen bonds : angle 4.41716 ( 1200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.314 Fit side-chains REVERT: A 32 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7805 (mtpt) REVERT: A 34 LYS cc_start: 0.8399 (ttpp) cc_final: 0.8198 (tttt) REVERT: A 209 GLU cc_start: 0.6860 (tp30) cc_final: 0.6557 (tp30) REVERT: A 252 ASP cc_start: 0.7692 (t70) cc_final: 0.7305 (t70) REVERT: A 342 SER cc_start: 0.7943 (t) cc_final: 0.7631 (p) REVERT: A 346 ARG cc_start: 0.7579 (mtm180) cc_final: 0.7308 (mtm-85) REVERT: B 42 ARG cc_start: 0.7672 (tmt170) cc_final: 0.6839 (tpt170) REVERT: B 256 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7231 (mtm110) REVERT: B 259 GLN cc_start: 0.8377 (mm-40) cc_final: 0.7911 (mm-40) REVERT: B 298 ASP cc_start: 0.8342 (t0) cc_final: 0.8120 (t70) REVERT: N 20 LEU cc_start: 0.8127 (mt) cc_final: 0.7840 (mt) REVERT: N 60 TYR cc_start: 0.8737 (m-80) cc_final: 0.8477 (m-80) REVERT: N 65 LYS cc_start: 0.6837 (ttmm) cc_final: 0.6488 (tptp) REVERT: R 345 ILE cc_start: 0.8466 (mt) cc_final: 0.8259 (mt) outliers start: 23 outliers final: 16 residues processed: 137 average time/residue: 0.0982 time to fit residues: 17.9455 Evaluate side-chains 135 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 0.0170 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN R 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.119698 restraints weight = 8969.858| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.79 r_work: 0.3144 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7990 Z= 0.109 Angle : 0.525 9.151 10866 Z= 0.274 Chirality : 0.041 0.354 1258 Planarity : 0.004 0.047 1390 Dihedral : 4.126 27.750 1122 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.84 % Allowed : 15.83 % Favored : 82.33 % 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: 0.60 (0.27), residues: 1011 helix: 2.30 (0.26), residues: 390 sheet: -0.39 (0.34), residues: 211 loop : -1.07 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 240 TYR 0.013 0.001 TYR A 37 PHE 0.014 0.001 PHE A 212 TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 7986) covalent geometry : angle 0.52455 (10858) SS BOND : bond 0.00065 ( 4) SS BOND : angle 0.65945 ( 8) hydrogen bonds : bond 0.03919 ( 425) hydrogen bonds : angle 4.27291 ( 1200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.257 Fit side-chains REVERT: A 32 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7763 (mtpt) REVERT: A 252 ASP cc_start: 0.7520 (t70) cc_final: 0.7027 (t0) REVERT: A 308 TYR cc_start: 0.7862 (t80) cc_final: 0.7324 (t80) REVERT: A 329 TYR cc_start: 0.8610 (m-80) cc_final: 0.8282 (m-80) REVERT: A 342 SER cc_start: 0.7872 (t) cc_final: 0.7558 (p) REVERT: B 42 ARG cc_start: 0.7679 (tmt170) cc_final: 0.6914 (tpt170) REVERT: B 137 ARG cc_start: 0.8209 (mmt180) cc_final: 0.8003 (tpt170) REVERT: B 256 ARG cc_start: 0.7862 (mtm110) cc_final: 0.7151 (mtm110) REVERT: B 259 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8005 (mm-40) REVERT: B 298 ASP cc_start: 0.8314 (t0) cc_final: 0.8061 (t70) REVERT: N 20 LEU cc_start: 0.8145 (mt) cc_final: 0.7850 (mt) REVERT: N 65 LYS cc_start: 0.6769 (ttmm) cc_final: 0.6480 (tptp) REVERT: N 108 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.7854 (t80) outliers start: 15 outliers final: 12 residues processed: 139 average time/residue: 0.1028 time to fit residues: 18.6843 Evaluate side-chains 141 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 45 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.152339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.117830 restraints weight = 8981.994| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.85 r_work: 0.3118 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7990 Z= 0.132 Angle : 0.551 8.917 10866 Z= 0.285 Chirality : 0.043 0.455 1258 Planarity : 0.004 0.048 1390 Dihedral : 4.200 28.386 1122 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.09 % Allowed : 15.95 % Favored : 81.96 % 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: 0.59 (0.27), residues: 1011 helix: 2.30 (0.26), residues: 390 sheet: -0.41 (0.33), residues: 215 loop : -1.06 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 240 TYR 0.014 0.001 TYR A 37 PHE 0.015 0.001 PHE R 308 TRP 0.010 0.001 TRP B 99 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7986) covalent geometry : angle 0.55070 (10858) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.72208 ( 8) hydrogen bonds : bond 0.04131 ( 425) hydrogen bonds : angle 4.29111 ( 1200) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.212 Fit side-chains REVERT: A 32 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7781 (mtpt) REVERT: A 209 GLU cc_start: 0.6965 (tp30) cc_final: 0.6679 (tp30) REVERT: A 252 ASP cc_start: 0.7523 (t70) cc_final: 0.7135 (t70) REVERT: A 329 TYR cc_start: 0.8689 (m-80) cc_final: 0.8341 (m-80) REVERT: A 342 SER cc_start: 0.7890 (t) cc_final: 0.7586 (p) REVERT: B 42 ARG cc_start: 0.7677 (tmt170) cc_final: 0.6897 (tpt170) REVERT: B 137 ARG cc_start: 0.8183 (mmt180) cc_final: 0.7976 (tpt170) REVERT: B 256 ARG cc_start: 0.7850 (mtm110) cc_final: 0.7128 (mtm110) REVERT: B 259 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8018 (mm-40) REVERT: B 298 ASP cc_start: 0.8345 (t0) cc_final: 0.8089 (t70) REVERT: B 329 THR cc_start: 0.9138 (m) cc_final: 0.8889 (p) REVERT: N 20 LEU cc_start: 0.8124 (mt) cc_final: 0.7831 (mt) REVERT: N 60 TYR cc_start: 0.8741 (m-80) cc_final: 0.8434 (m-80) REVERT: N 108 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.7901 (t80) outliers start: 17 outliers final: 15 residues processed: 137 average time/residue: 0.0976 time to fit residues: 17.6189 Evaluate side-chains 141 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 108 PHE Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 131 LEU Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 30.0000 chunk 98 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 11 optimal weight: 0.0970 chunk 47 optimal weight: 6.9990 chunk 25 optimal weight: 40.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.154438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117846 restraints weight = 8957.071| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.02 r_work: 0.3129 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7990 Z= 0.114 Angle : 0.536 9.066 10866 Z= 0.277 Chirality : 0.042 0.421 1258 Planarity : 0.004 0.047 1390 Dihedral : 4.099 28.147 1122 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.21 % Allowed : 15.83 % Favored : 81.96 % 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: 1011 helix: 2.36 (0.26), residues: 390 sheet: -0.37 (0.33), residues: 215 loop : -1.00 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 240 TYR 0.013 0.001 TYR A 37 PHE 0.014 0.001 PHE A 212 TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7986) covalent geometry : angle 0.53622 (10858) SS BOND : bond 0.00073 ( 4) SS BOND : angle 0.66767 ( 8) hydrogen bonds : bond 0.03945 ( 425) hydrogen bonds : angle 4.22183 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2276.51 seconds wall clock time: 39 minutes 46.40 seconds (2386.40 seconds total)