Starting phenix.real_space_refine on Sun Apr 5 06:11:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lle_63199/04_2026/9lle_63199.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lle_63199/04_2026/9lle_63199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lle_63199/04_2026/9lle_63199.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lle_63199/04_2026/9lle_63199.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lle_63199/04_2026/9lle_63199.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lle_63199/04_2026/9lle_63199.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 5441 2.51 5 N 1478 2.21 5 O 1557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8527 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2104 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 3 Chain: "O" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 590 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2576 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "C" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1836 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.69, per 1000 atoms: 0.20 Number of scatterers: 8527 At special positions: 0 Unit cell: (82.77, 100.44, 127.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1557 8.00 N 1478 7.00 C 5441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 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 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: 0.75 Conformation dependent library (CDL) restraints added in 246.2 milliseconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 48.7% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'R' and resid 20 through 51 Processing helix chain 'R' and resid 51 through 56 removed outlier: 3.845A pdb=" N ARG R 55 " --> pdb=" O PHE R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 77 removed outlier: 3.911A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL R 77 " --> pdb=" O VAL R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' Processing helix chain 'R' and resid 95 through 127 Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 157 removed outlier: 3.585A pdb=" N SER R 155 " --> pdb=" O SER R 151 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 203 Processing helix chain 'R' and resid 203 through 234 removed outlier: 3.597A pdb=" N ILE R 217 " --> pdb=" O THR R 213 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 295 removed outlier: 3.857A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 296 through 298 No H-bonds generated for 'chain 'R' and resid 296 through 298' Processing helix chain 'R' and resid 309 through 322 Processing helix chain 'R' and resid 322 through 332 removed outlier: 3.527A pdb=" N LEU R 326 " --> pdb=" O ALA R 322 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'O' and resid 2 through 31 removed outlier: 3.699A pdb=" N ILE O 29 " --> pdb=" O MET O 25 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG O 30 " --> pdb=" O ARG O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 69 Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.698A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B 37 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 24 removed outlier: 3.683A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 removed outlier: 4.024A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'D' and resid 12 through 39 removed outlier: 3.892A pdb=" N GLU D 16 " --> pdb=" O GLN D 12 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA D 39 " --> pdb=" O GLN D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 239 removed outlier: 3.771A pdb=" N GLN D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 278 Processing helix chain 'D' and resid 279 through 283 removed outlier: 3.960A pdb=" N ARG D 283 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 304 Processing helix chain 'D' and resid 307 through 311 Processing helix chain 'D' and resid 312 through 318 removed outlier: 3.509A pdb=" N ALA D 316 " --> pdb=" O PRO D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 352 removed outlier: 3.705A pdb=" N ILE D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N SER D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 391 Processing sheet with id=AA1, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.554A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.775A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.148A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 5.897A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.227A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.588A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.779A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AA9, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.751A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 209 through 214 removed outlier: 3.827A pdb=" N ALA D 243 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE D 244 " --> pdb=" O ILE D 288 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE D 290 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE D 246 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASN D 292 " --> pdb=" O PHE D 246 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL D 248 " --> pdb=" O ASN D 292 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1401 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: 1.40 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: 1.18 - 1.31: 1368 1.31 - 1.43: 2344 1.43 - 1.56: 4915 1.56 - 1.68: 0 1.68 - 1.81: 68 Bond restraints: 8695 Sorted by residual: bond pdb=" C THR R 213 " pdb=" O THR R 213 " ideal model delta sigma weight residual 1.236 1.181 0.054 1.29e-02 6.01e+03 1.78e+01 bond pdb=" N ARG O 30 " pdb=" CA ARG O 30 " ideal model delta sigma weight residual 1.459 1.419 0.040 1.20e-02 6.94e+03 1.10e+01 bond pdb=" N ASP D 274 " pdb=" CA ASP D 274 " ideal model delta sigma weight residual 1.459 1.430 0.029 1.23e-02 6.61e+03 5.41e+00 bond pdb=" C PHE D 273 " pdb=" N ASP D 274 " ideal model delta sigma weight residual 1.335 1.303 0.032 1.36e-02 5.41e+03 5.39e+00 bond pdb=" C3 LDP R 701 " pdb=" O1 LDP R 701 " ideal model delta sigma weight residual 1.353 1.399 -0.046 2.00e-02 2.50e+03 5.24e+00 ... (remaining 8690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 11529 1.24 - 2.47: 185 2.47 - 3.71: 46 3.71 - 4.95: 11 4.95 - 6.18: 6 Bond angle restraints: 11777 Sorted by residual: angle pdb=" N ASN D 239 " pdb=" CA ASN D 239 " pdb=" C ASN D 239 " ideal model delta sigma weight residual 113.01 118.33 -5.32 1.20e+00 6.94e-01 1.96e+01 angle pdb=" C GLY O 31 " pdb=" N LEU O 32 " pdb=" CA LEU O 32 " ideal model delta sigma weight residual 122.72 117.67 5.05 1.38e+00 5.25e-01 1.34e+01 angle pdb=" N ILE B 33 " pdb=" CA ILE B 33 " pdb=" C ILE B 33 " ideal model delta sigma weight residual 111.91 108.86 3.05 8.90e-01 1.26e+00 1.18e+01 angle pdb=" CA THR R 213 " pdb=" C THR R 213 " pdb=" N TYR R 214 " ideal model delta sigma weight residual 118.14 122.62 -4.48 1.31e+00 5.83e-01 1.17e+01 angle pdb=" N ARG O 30 " pdb=" CA ARG O 30 " pdb=" C ARG O 30 " ideal model delta sigma weight residual 111.24 107.03 4.21 1.29e+00 6.01e-01 1.06e+01 ... (remaining 11772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.82: 4931 15.82 - 31.64: 196 31.64 - 47.46: 39 47.46 - 63.28: 4 63.28 - 79.10: 3 Dihedral angle restraints: 5173 sinusoidal: 2019 harmonic: 3154 Sorted by residual: dihedral pdb=" CA MET B 45 " pdb=" C MET B 45 " pdb=" N ARG B 46 " pdb=" CA ARG B 46 " ideal model delta harmonic sigma weight residual -180.00 -164.53 -15.47 0 5.00e+00 4.00e-02 9.57e+00 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 165.05 14.95 0 5.00e+00 4.00e-02 8.95e+00 dihedral pdb=" CA PHE R 203 " pdb=" C PHE R 203 " pdb=" N TYR R 204 " pdb=" CA TYR R 204 " ideal model delta harmonic sigma weight residual -180.00 -165.33 -14.67 0 5.00e+00 4.00e-02 8.61e+00 ... (remaining 5170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1070 0.046 - 0.091: 223 0.091 - 0.137: 54 0.137 - 0.182: 3 0.182 - 0.228: 1 Chirality restraints: 1351 Sorted by residual: chirality pdb=" CA THR R 213 " pdb=" N THR R 213 " pdb=" C THR R 213 " pdb=" CB THR R 213 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB THR D 285 " pdb=" CA THR D 285 " pdb=" OG1 THR D 285 " pdb=" CG2 THR D 285 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA PHE D 238 " pdb=" N PHE D 238 " pdb=" C PHE D 238 " pdb=" CB PHE D 238 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 1348 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 283 " 0.008 2.00e-02 2.50e+03 1.49e-02 2.23e+00 pdb=" C ARG D 283 " -0.026 2.00e-02 2.50e+03 pdb=" O ARG D 283 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP D 284 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.022 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO B 236 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 205 " -0.018 5.00e-02 4.00e+02 2.78e-02 1.24e+00 pdb=" N PRO R 206 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO R 206 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO R 206 " -0.016 5.00e-02 4.00e+02 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 942 2.75 - 3.29: 8436 3.29 - 3.83: 14811 3.83 - 4.36: 16774 4.36 - 4.90: 29762 Nonbonded interactions: 70725 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.213 3.040 nonbonded pdb=" OG SER R 69 " pdb=" OD1 ASN R 113 " model vdw 2.241 3.040 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.276 3.040 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.276 3.120 nonbonded pdb=" O ALA R 322 " pdb=" OG SER R 325 " model vdw 2.277 3.040 ... (remaining 70720 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: 0.810 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: 8.560 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:9.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 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 0.054 8698 Z= 0.161 Angle : 0.466 6.185 11783 Z= 0.278 Chirality : 0.039 0.228 1351 Planarity : 0.003 0.034 1486 Dihedral : 9.056 79.099 3114 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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: 2.64 (0.27), residues: 1062 helix: 3.53 (0.23), residues: 451 sheet: 0.75 (0.34), residues: 238 loop : 0.19 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.008 0.001 TYR D 37 PHE 0.012 0.001 PHE R 61 TRP 0.009 0.001 TRP B 339 HIS 0.002 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8695) covalent geometry : angle 0.46617 (11777) SS BOND : bond 0.00130 ( 3) SS BOND : angle 0.45418 ( 6) hydrogen bonds : bond 0.16695 ( 497) hydrogen bonds : angle 5.41983 ( 1401) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 210 MET cc_start: 0.7579 (mtp) cc_final: 0.7355 (mtp) REVERT: O 26 ARG cc_start: 0.7288 (tpt170) cc_final: 0.6795 (ptt180) REVERT: B 209 LYS cc_start: 0.7565 (mmtt) cc_final: 0.6263 (mtmt) REVERT: D 223 ASP cc_start: 0.7678 (t0) cc_final: 0.7152 (m-30) REVERT: D 364 THR cc_start: 0.7325 (p) cc_final: 0.7072 (t) REVERT: D 377 ASN cc_start: 0.7977 (m-40) cc_final: 0.7776 (m-40) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.5400 time to fit residues: 92.9072 Evaluate side-chains 107 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN B 54 HIS B 110 ASN B 176 GLN B 220 GLN D 218 ASN ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.207154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.168307 restraints weight = 9087.959| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 2.11 r_work: 0.3940 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8698 Z= 0.155 Angle : 0.550 6.717 11783 Z= 0.295 Chirality : 0.043 0.279 1351 Planarity : 0.004 0.043 1486 Dihedral : 4.239 46.342 1180 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.50 % Allowed : 9.88 % Favored : 87.62 % 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: 2.40 (0.26), residues: 1062 helix: 3.06 (0.23), residues: 455 sheet: 0.92 (0.34), residues: 236 loop : 0.20 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 251 TYR 0.015 0.002 TYR D 391 PHE 0.021 0.002 PHE R 288 TRP 0.016 0.002 TRP D 234 HIS 0.004 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8695) covalent geometry : angle 0.54990 (11777) SS BOND : bond 0.00120 ( 3) SS BOND : angle 0.62506 ( 6) hydrogen bonds : bond 0.04434 ( 497) hydrogen bonds : angle 4.49262 ( 1401) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 26 ARG cc_start: 0.7391 (tpt170) cc_final: 0.6419 (ptt180) REVERT: C 46 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6705 (mptp) REVERT: D 221 MET cc_start: 0.8035 (tpp) cc_final: 0.7443 (tpp) REVERT: D 223 ASP cc_start: 0.7549 (t0) cc_final: 0.7273 (t70) REVERT: D 274 ASP cc_start: 0.7360 (t0) cc_final: 0.7025 (t0) REVERT: D 377 ASN cc_start: 0.7586 (m-40) cc_final: 0.7376 (m-40) REVERT: D 386 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6969 (ptt) outliers start: 23 outliers final: 9 residues processed: 128 average time/residue: 0.5202 time to fit residues: 71.3503 Evaluate side-chains 113 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 160 GLN Chi-restraints excluded: chain O residue 12 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain D residue 386 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 12 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN D 213 GLN ** D 220 HIS ** 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 = 0.4356 r_free = 0.4356 target = 0.206478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170088 restraints weight = 9014.309| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 1.89 r_work: 0.3956 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8698 Z= 0.127 Angle : 0.490 6.127 11783 Z= 0.265 Chirality : 0.041 0.227 1351 Planarity : 0.003 0.033 1486 Dihedral : 4.328 57.117 1180 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.82 % Allowed : 11.18 % Favored : 85.99 % 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: 2.44 (0.26), residues: 1062 helix: 3.24 (0.23), residues: 444 sheet: 0.79 (0.33), residues: 243 loop : 0.21 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 251 TYR 0.011 0.001 TYR D 37 PHE 0.026 0.002 PHE D 376 TRP 0.014 0.002 TRP R 99 HIS 0.003 0.001 HIS D 387 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8695) covalent geometry : angle 0.49027 (11777) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.43919 ( 6) hydrogen bonds : bond 0.04105 ( 497) hydrogen bonds : angle 4.22279 ( 1401) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 LEU cc_start: 0.5901 (mm) cc_final: 0.5606 (tt) REVERT: R 103 ASP cc_start: 0.7793 (t0) cc_final: 0.7381 (m-30) REVERT: R 134 LYS cc_start: 0.7122 (mtpt) cc_final: 0.6892 (mtpt) REVERT: R 226 ARG cc_start: 0.7135 (mtm-85) cc_final: 0.6777 (mmp-170) REVERT: O 26 ARG cc_start: 0.7405 (tpt170) cc_final: 0.6448 (ptt180) REVERT: O 49 LEU cc_start: 0.6761 (OUTLIER) cc_final: 0.6482 (mm) REVERT: B 228 ASP cc_start: 0.6540 (m-30) cc_final: 0.5968 (m-30) REVERT: D 221 MET cc_start: 0.7976 (tpp) cc_final: 0.7311 (tpp) REVERT: D 274 ASP cc_start: 0.7279 (t0) cc_final: 0.6993 (t0) REVERT: D 338 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7437 (ptmm) REVERT: D 377 ASN cc_start: 0.7600 (m-40) cc_final: 0.7369 (m-40) REVERT: D 386 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6893 (ptt) outliers start: 26 outliers final: 7 residues processed: 136 average time/residue: 0.4989 time to fit residues: 72.5856 Evaluate side-chains 123 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 338 LYS Chi-restraints excluded: chain D residue 386 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 99 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 0.0870 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 ASN B 176 GLN D 220 HIS D 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.207466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.171271 restraints weight = 9187.199| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.91 r_work: 0.3963 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8698 Z= 0.105 Angle : 0.473 8.673 11783 Z= 0.251 Chirality : 0.040 0.144 1351 Planarity : 0.003 0.031 1486 Dihedral : 4.225 57.730 1180 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.50 % Allowed : 13.14 % Favored : 84.36 % 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: 2.49 (0.26), residues: 1062 helix: 3.38 (0.23), residues: 444 sheet: 0.74 (0.33), residues: 240 loop : 0.16 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 150 TYR 0.017 0.001 TYR D 360 PHE 0.029 0.001 PHE D 376 TRP 0.012 0.001 TRP R 99 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8695) covalent geometry : angle 0.47251 (11777) SS BOND : bond 0.00065 ( 3) SS BOND : angle 0.69196 ( 6) hydrogen bonds : bond 0.03716 ( 497) hydrogen bonds : angle 4.07130 ( 1401) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 226 ARG cc_start: 0.7176 (mtm-85) cc_final: 0.6727 (mmp-170) REVERT: O 26 ARG cc_start: 0.7345 (tpt170) cc_final: 0.6378 (ptt180) REVERT: O 49 LEU cc_start: 0.6831 (OUTLIER) cc_final: 0.6559 (mm) REVERT: B 124 TYR cc_start: 0.7119 (m-80) cc_final: 0.6846 (m-80) REVERT: D 216 LYS cc_start: 0.6696 (tptp) cc_final: 0.6448 (tptp) REVERT: D 220 HIS cc_start: 0.6444 (OUTLIER) cc_final: 0.6101 (m170) REVERT: D 221 MET cc_start: 0.8102 (tpp) cc_final: 0.7496 (tpp) REVERT: D 338 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7466 (ptmm) REVERT: D 386 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6900 (ptt) outliers start: 23 outliers final: 10 residues processed: 127 average time/residue: 0.4678 time to fit residues: 63.7757 Evaluate side-chains 123 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 109 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 338 LYS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 386 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 220 GLN D 220 HIS D 371 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.202344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.163118 restraints weight = 9091.707| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.10 r_work: 0.3923 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3798 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8698 Z= 0.118 Angle : 0.480 6.218 11783 Z= 0.257 Chirality : 0.041 0.240 1351 Planarity : 0.003 0.030 1486 Dihedral : 4.266 59.312 1180 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.04 % Allowed : 13.36 % Favored : 83.60 % 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: 2.39 (0.26), residues: 1062 helix: 3.31 (0.23), residues: 443 sheet: 0.62 (0.33), residues: 244 loop : 0.16 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 389 TYR 0.013 0.001 TYR D 37 PHE 0.027 0.002 PHE D 376 TRP 0.012 0.002 TRP R 99 HIS 0.009 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8695) covalent geometry : angle 0.48011 (11777) SS BOND : bond 0.00346 ( 3) SS BOND : angle 0.94021 ( 6) hydrogen bonds : bond 0.03775 ( 497) hydrogen bonds : angle 4.06712 ( 1401) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 223 LYS cc_start: 0.7296 (mttp) cc_final: 0.7079 (mtmm) REVERT: R 226 ARG cc_start: 0.7207 (mtm-85) cc_final: 0.6758 (mmp-170) REVERT: O 26 ARG cc_start: 0.7379 (tpt170) cc_final: 0.6396 (ptt180) REVERT: O 49 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6678 (mm) REVERT: B 124 TYR cc_start: 0.7119 (m-80) cc_final: 0.6861 (m-80) REVERT: B 228 ASP cc_start: 0.6552 (m-30) cc_final: 0.6291 (m-30) REVERT: N 99 CYS cc_start: 0.6852 (t) cc_final: 0.6576 (t) REVERT: D 216 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.6358 (mtmt) REVERT: D 221 MET cc_start: 0.8084 (tpp) cc_final: 0.7551 (tpp) REVERT: D 338 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7503 (ptmm) REVERT: D 386 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.7040 (ptt) outliers start: 28 outliers final: 18 residues processed: 126 average time/residue: 0.5094 time to fit residues: 68.7119 Evaluate side-chains 127 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 338 LYS Chi-restraints excluded: chain D residue 364 THR Chi-restraints excluded: chain D residue 371 ASN Chi-restraints excluded: chain D residue 386 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 80 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 67 optimal weight: 0.0370 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 45 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 overall best weight: 1.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.197610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157862 restraints weight = 9091.330| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.11 r_work: 0.3870 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8698 Z= 0.163 Angle : 0.535 6.583 11783 Z= 0.287 Chirality : 0.043 0.269 1351 Planarity : 0.004 0.034 1486 Dihedral : 4.521 59.144 1180 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.04 % Allowed : 14.01 % Favored : 82.95 % 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: 2.03 (0.26), residues: 1062 helix: 2.86 (0.23), residues: 443 sheet: 0.49 (0.32), residues: 245 loop : 0.13 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 389 TYR 0.021 0.002 TYR D 360 PHE 0.021 0.002 PHE R 288 TRP 0.011 0.002 TRP D 281 HIS 0.004 0.001 HIS D 220 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 8695) covalent geometry : angle 0.53481 (11777) SS BOND : bond 0.00103 ( 3) SS BOND : angle 0.86040 ( 6) hydrogen bonds : bond 0.04349 ( 497) hydrogen bonds : angle 4.25337 ( 1401) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 111 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: R 25 LEU cc_start: 0.6059 (mm) cc_final: 0.5726 (tt) REVERT: R 30 LEU cc_start: 0.6724 (mt) cc_final: 0.6503 (mp) REVERT: R 223 LYS cc_start: 0.7245 (mttp) cc_final: 0.7025 (mtmm) REVERT: R 226 ARG cc_start: 0.7144 (mtm-85) cc_final: 0.6760 (mmp-170) REVERT: O 24 PHE cc_start: 0.5731 (t80) cc_final: 0.5067 (t80) REVERT: O 26 ARG cc_start: 0.7419 (tpt170) cc_final: 0.6416 (ptt180) REVERT: O 49 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6511 (mm) REVERT: C 46 LYS cc_start: 0.7041 (mttp) cc_final: 0.6813 (mptt) REVERT: D 220 HIS cc_start: 0.6694 (OUTLIER) cc_final: 0.6259 (m170) REVERT: D 221 MET cc_start: 0.7939 (tpp) cc_final: 0.7339 (tpp) REVERT: D 338 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7536 (ptmm) outliers start: 28 outliers final: 16 residues processed: 127 average time/residue: 0.4701 time to fit residues: 64.2182 Evaluate side-chains 119 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 338 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 19 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 220 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.202684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.164531 restraints weight = 9230.142| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.05 r_work: 0.3893 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8698 Z= 0.121 Angle : 0.498 6.293 11783 Z= 0.266 Chirality : 0.041 0.149 1351 Planarity : 0.004 0.034 1486 Dihedral : 4.412 58.491 1180 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.93 % Allowed : 14.88 % Favored : 82.19 % 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: 2.09 (0.26), residues: 1062 helix: 3.03 (0.23), residues: 447 sheet: 0.45 (0.32), residues: 245 loop : 0.01 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 38 TYR 0.015 0.001 TYR D 37 PHE 0.028 0.002 PHE D 376 TRP 0.012 0.002 TRP R 99 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8695) covalent geometry : angle 0.49727 (11777) SS BOND : bond 0.00100 ( 3) SS BOND : angle 1.14514 ( 6) hydrogen bonds : bond 0.03929 ( 497) hydrogen bonds : angle 4.13792 ( 1401) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 25 LEU cc_start: 0.5976 (mm) cc_final: 0.5671 (tt) REVERT: R 103 ASP cc_start: 0.7950 (t0) cc_final: 0.7576 (m-30) REVERT: R 223 LYS cc_start: 0.7242 (mttp) cc_final: 0.7035 (mtmm) REVERT: R 226 ARG cc_start: 0.7098 (mtm-85) cc_final: 0.6731 (mmp-170) REVERT: O 24 PHE cc_start: 0.5768 (t80) cc_final: 0.5130 (t80) REVERT: O 26 ARG cc_start: 0.7408 (tpt170) cc_final: 0.6409 (ptt180) REVERT: O 49 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6588 (mm) REVERT: D 38 ARG cc_start: 0.6629 (mmm160) cc_final: 0.5860 (mmt-90) REVERT: D 220 HIS cc_start: 0.6664 (OUTLIER) cc_final: 0.6246 (m170) REVERT: D 221 MET cc_start: 0.7966 (tpp) cc_final: 0.7334 (tpp) REVERT: D 338 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7436 (ptmm) outliers start: 27 outliers final: 17 residues processed: 119 average time/residue: 0.4810 time to fit residues: 61.4770 Evaluate side-chains 122 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 338 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 42 optimal weight: 4.9990 chunk 82 optimal weight: 0.0770 chunk 40 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN D 294 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.205271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.167222 restraints weight = 9039.616| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 2.00 r_work: 0.3921 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8698 Z= 0.120 Angle : 0.495 6.762 11783 Z= 0.266 Chirality : 0.042 0.288 1351 Planarity : 0.003 0.030 1486 Dihedral : 4.325 58.223 1180 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.61 % Allowed : 15.31 % Favored : 82.08 % 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: 2.10 (0.26), residues: 1062 helix: 2.99 (0.23), residues: 447 sheet: 0.49 (0.32), residues: 242 loop : 0.05 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 38 TYR 0.015 0.001 TYR D 37 PHE 0.019 0.001 PHE N 27 TRP 0.014 0.002 TRP R 318 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8695) covalent geometry : angle 0.49435 (11777) SS BOND : bond 0.00088 ( 3) SS BOND : angle 0.92380 ( 6) hydrogen bonds : bond 0.03879 ( 497) hydrogen bonds : angle 4.09958 ( 1401) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: R 103 ASP cc_start: 0.7876 (t0) cc_final: 0.7586 (m-30) REVERT: O 24 PHE cc_start: 0.5782 (t80) cc_final: 0.5055 (t80) REVERT: O 26 ARG cc_start: 0.7309 (tpt170) cc_final: 0.6459 (mtt180) REVERT: O 49 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6615 (mm) REVERT: B 45 MET cc_start: 0.7673 (mtm) cc_final: 0.7383 (mtt) REVERT: C 41 CYS cc_start: 0.6590 (p) cc_final: 0.6350 (m) REVERT: D 38 ARG cc_start: 0.6520 (mmm160) cc_final: 0.5820 (mmt-90) REVERT: D 220 HIS cc_start: 0.6578 (OUTLIER) cc_final: 0.6180 (m170) REVERT: D 221 MET cc_start: 0.7977 (tpp) cc_final: 0.7358 (tpp) REVERT: D 338 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7493 (ptmm) outliers start: 24 outliers final: 17 residues processed: 116 average time/residue: 0.4498 time to fit residues: 56.3148 Evaluate side-chains 120 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain D residue 54 ASN Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 338 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 86 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.200499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.161822 restraints weight = 9104.412| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.00 r_work: 0.3869 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3742 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8698 Z= 0.173 Angle : 0.564 7.500 11783 Z= 0.303 Chirality : 0.044 0.195 1351 Planarity : 0.004 0.035 1486 Dihedral : 4.704 59.239 1180 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.71 % Allowed : 15.09 % Favored : 82.19 % 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: 1.67 (0.26), residues: 1062 helix: 2.56 (0.23), residues: 446 sheet: 0.32 (0.32), residues: 245 loop : -0.08 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 38 TYR 0.021 0.002 TYR D 360 PHE 0.027 0.002 PHE D 376 TRP 0.015 0.002 TRP D 234 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00405 ( 8695) covalent geometry : angle 0.56287 (11777) SS BOND : bond 0.00297 ( 3) SS BOND : angle 1.44320 ( 6) hydrogen bonds : bond 0.04566 ( 497) hydrogen bonds : angle 4.31429 ( 1401) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 111 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: R 25 LEU cc_start: 0.6163 (mm) cc_final: 0.5819 (tt) REVERT: O 24 PHE cc_start: 0.5749 (OUTLIER) cc_final: 0.5019 (t80) REVERT: O 26 ARG cc_start: 0.7264 (tpt170) cc_final: 0.6418 (mtt180) REVERT: O 49 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6659 (mm) REVERT: C 41 CYS cc_start: 0.6930 (p) cc_final: 0.6491 (m) REVERT: N 99 CYS cc_start: 0.6911 (t) cc_final: 0.6627 (t) REVERT: D 38 ARG cc_start: 0.6702 (mmm160) cc_final: 0.5871 (mmt-90) REVERT: D 220 HIS cc_start: 0.6692 (OUTLIER) cc_final: 0.6253 (m170) REVERT: D 221 MET cc_start: 0.7874 (tpp) cc_final: 0.7313 (tpp) REVERT: D 338 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7591 (ptmm) outliers start: 25 outliers final: 18 residues processed: 124 average time/residue: 0.4330 time to fit residues: 57.9389 Evaluate side-chains 122 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 338 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 67 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN N 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.204950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.166581 restraints weight = 8990.296| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.03 r_work: 0.3909 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8698 Z= 0.126 Angle : 0.526 8.945 11783 Z= 0.283 Chirality : 0.042 0.343 1351 Planarity : 0.004 0.032 1486 Dihedral : 4.455 57.052 1180 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.17 % Allowed : 16.83 % Favored : 81.00 % 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: 1.94 (0.26), residues: 1062 helix: 2.88 (0.23), residues: 447 sheet: 0.35 (0.32), residues: 242 loop : 0.00 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 38 TYR 0.014 0.001 TYR N 60 PHE 0.020 0.002 PHE N 27 TRP 0.014 0.002 TRP D 234 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8695) covalent geometry : angle 0.52522 (11777) SS BOND : bond 0.00097 ( 3) SS BOND : angle 1.27133 ( 6) hydrogen bonds : bond 0.03924 ( 497) hydrogen bonds : angle 4.16592 ( 1401) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.7586 (mtp) cc_final: 0.7378 (mtp) REVERT: O 24 PHE cc_start: 0.5878 (OUTLIER) cc_final: 0.5096 (t80) REVERT: O 26 ARG cc_start: 0.7236 (tpt170) cc_final: 0.6423 (mtt180) REVERT: O 49 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6519 (mm) REVERT: B 128 THR cc_start: 0.7420 (m) cc_final: 0.7145 (p) REVERT: C 41 CYS cc_start: 0.6797 (p) cc_final: 0.6296 (m) REVERT: D 38 ARG cc_start: 0.6593 (mmm160) cc_final: 0.5767 (mmt-90) REVERT: D 220 HIS cc_start: 0.6548 (OUTLIER) cc_final: 0.6138 (m170) REVERT: D 221 MET cc_start: 0.7939 (tpp) cc_final: 0.7402 (tpp) REVERT: D 338 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7485 (ptmm) outliers start: 20 outliers final: 15 residues processed: 113 average time/residue: 0.4531 time to fit residues: 55.2004 Evaluate side-chains 118 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 49 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 220 HIS Chi-restraints excluded: chain D residue 229 ASP Chi-restraints excluded: chain D residue 338 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 67 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN D 371 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.206446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.168355 restraints weight = 8989.008| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.00 r_work: 0.3929 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3804 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8698 Z= 0.116 Angle : 0.519 9.000 11783 Z= 0.277 Chirality : 0.042 0.316 1351 Planarity : 0.003 0.028 1486 Dihedral : 4.343 56.053 1180 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.39 % Allowed : 16.83 % Favored : 80.78 % 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: 2.09 (0.26), residues: 1062 helix: 3.07 (0.23), residues: 447 sheet: 0.55 (0.33), residues: 232 loop : -0.11 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 38 TYR 0.016 0.001 TYR D 360 PHE 0.022 0.002 PHE D 376 TRP 0.013 0.002 TRP B 339 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 8695) covalent geometry : angle 0.51901 (11777) SS BOND : bond 0.00062 ( 3) SS BOND : angle 1.05018 ( 6) hydrogen bonds : bond 0.03696 ( 497) hydrogen bonds : angle 4.08129 ( 1401) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3017.98 seconds wall clock time: 52 minutes 8.85 seconds (3128.85 seconds total)