Starting phenix.real_space_refine on Sun May 3 03:52:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izf_61031/05_2026/9izf_61031_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izf_61031/05_2026/9izf_61031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9izf_61031/05_2026/9izf_61031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izf_61031/05_2026/9izf_61031.map" model { file = "/net/cci-nas-00/data/ceres_data/9izf_61031/05_2026/9izf_61031_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izf_61031/05_2026/9izf_61031_neut.cif" } resolution = 3.14 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= -0.002 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2193 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 71 5.16 5 C 5568 2.51 5 N 1491 2.21 5 O 1580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8711 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2305 Classifications: {'peptide': 291} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1651 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 1, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 7, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2549 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'GLN:plan1': 1, 'ASN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1742 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'NKP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.43, per 1000 atoms: 0.28 Number of scatterers: 8711 At special positions: 0 Unit cell: (89.25, 121.5, 126.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 71 16.00 P 1 15.00 O 1580 8.00 N 1491 7.00 C 5568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 188 " - pdb=" SG CYS R 195 " distance=2.03 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 287 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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: 0.82 Conformation dependent library (CDL) restraints added in 351.1 milliseconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 15 sheets defined 35.5% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'R' and resid 30 through 38 removed outlier: 3.630A pdb=" N TYR R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG R 36 " --> pdb=" O PHE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 77 removed outlier: 4.206A pdb=" N THR R 58 " --> pdb=" O GLY R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 81 removed outlier: 3.558A pdb=" N HIS R 81 " --> pdb=" O ARG R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 78 through 81' Processing helix chain 'R' and resid 82 through 107 removed outlier: 3.747A pdb=" N LEU R 87 " --> pdb=" O PRO R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 113 Proline residue: R 111 - end of helix No H-bonds generated for 'chain 'R' and resid 108 through 113' Processing helix chain 'R' and resid 117 through 152 removed outlier: 3.507A pdb=" N LEU R 132 " --> pdb=" O ILE R 128 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER R 135 " --> pdb=" O SER R 131 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE R 151 " --> pdb=" O HIS R 147 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG R 152 " --> pdb=" O ILE R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 181 removed outlier: 3.896A pdb=" N VAL R 167 " --> pdb=" O ARG R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 237 removed outlier: 3.547A pdb=" N PHE R 229 " --> pdb=" O TYR R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 270 removed outlier: 4.563A pdb=" N PHE R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 281 Processing helix chain 'R' and resid 290 through 311 removed outlier: 4.321A pdb=" N LYS R 294 " --> pdb=" O LEU R 290 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N PHE R 295 " --> pdb=" O ALA R 291 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU R 298 " --> pdb=" O LYS R 294 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N SER R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 315 through 327 Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.900A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 329 through 351 removed outlier: 4.349A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.692A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 187 removed outlier: 5.833A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.545A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.247A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.735A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.607A 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 151 removed outlier: 3.541A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.692A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.650A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 5.543A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.535A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET S 83 " --> pdb=" O ARG S 18 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'S' and resid 34 through 39 removed outlier: 6.654A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 93 through 94 Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.699A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.612A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR S 231 " --> pdb=" O TYR S 215 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 174 through 177 removed outlier: 6.652A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1131 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: 1.43 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1484 1.32 - 1.45: 2414 1.45 - 1.57: 4884 1.57 - 1.69: 1 1.69 - 1.82: 107 Bond restraints: 8890 Sorted by residual: bond pdb=" OAD NKP R 601 " pdb=" PAC NKP R 601 " ideal model delta sigma weight residual 1.696 1.512 0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" OAB NKP R 601 " pdb=" PAC NKP R 601 " ideal model delta sigma weight residual 1.683 1.515 0.168 2.00e-02 2.50e+03 7.05e+01 bond pdb=" OAA NKP R 601 " pdb=" PAC NKP R 601 " ideal model delta sigma weight residual 1.472 1.514 -0.042 2.00e-02 2.50e+03 4.42e+00 bond pdb=" CAH NKP R 601 " pdb=" OBC NKP R 601 " ideal model delta sigma weight residual 1.468 1.429 0.039 2.00e-02 2.50e+03 3.90e+00 bond pdb=" CAK NKP R 601 " pdb=" OAJ NKP R 601 " ideal model delta sigma weight residual 1.380 1.343 0.037 2.00e-02 2.50e+03 3.46e+00 ... (remaining 8885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.97: 12054 11.97 - 23.95: 1 23.95 - 35.92: 0 35.92 - 47.90: 0 47.90 - 59.87: 1 Bond angle restraints: 12056 Sorted by residual: angle pdb=" OAB NKP R 601 " pdb=" PAC NKP R 601 " pdb=" OAD NKP R 601 " ideal model delta sigma weight residual 53.21 113.08 -59.87 3.00e+00 1.11e-01 3.98e+02 angle pdb=" OAA NKP R 601 " pdb=" PAC NKP R 601 " pdb=" OAB NKP R 601 " ideal model delta sigma weight residual 128.27 112.71 15.56 3.00e+00 1.11e-01 2.69e+01 angle pdb=" OAB NKP R 601 " pdb=" PAC NKP R 601 " pdb=" OAF NKP R 601 " ideal model delta sigma weight residual 115.22 105.81 9.41 3.00e+00 1.11e-01 9.83e+00 angle pdb=" C LYS B 280 " pdb=" N SER B 281 " pdb=" CA SER B 281 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.32e+00 angle pdb=" OAA NKP R 601 " pdb=" PAC NKP R 601 " pdb=" OAF NKP R 601 " ideal model delta sigma weight residual 115.02 105.89 9.13 3.00e+00 1.11e-01 9.27e+00 ... (remaining 12051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4482 17.89 - 35.79: 594 35.79 - 53.68: 143 53.68 - 71.58: 23 71.58 - 89.47: 5 Dihedral angle restraints: 5247 sinusoidal: 1950 harmonic: 3297 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 57.46 35.54 1 1.00e+01 1.00e-02 1.79e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 160.56 19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CB CYS R 284 " pdb=" SG CYS R 284 " pdb=" SG CYS R 287 " pdb=" CB CYS R 287 " ideal model delta sinusoidal sigma weight residual 93.00 62.86 30.14 1 1.00e+01 1.00e-02 1.30e+01 ... (remaining 5244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1328 0.090 - 0.179: 66 0.179 - 0.269: 0 0.269 - 0.358: 0 0.358 - 0.448: 1 Chirality restraints: 1395 Sorted by residual: chirality pdb=" CAH NKP R 601 " pdb=" CAG NKP R 601 " pdb=" CAI NKP R 601 " pdb=" OBC NKP R 601 " both_signs ideal model delta sigma weight residual False -2.84 -2.40 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.35e-01 chirality pdb=" CB ILE S 100 " pdb=" CA ILE S 100 " pdb=" CG1 ILE S 100 " pdb=" CG2 ILE S 100 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 1392 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 96 " 0.014 2.00e-02 2.50e+03 1.59e-02 4.41e+00 pdb=" CG PHE R 96 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE R 96 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE R 96 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE R 96 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 96 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE R 96 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 237 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" CG ASN B 237 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 237 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 237 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR R 272 " 0.026 5.00e-02 4.00e+02 3.86e-02 2.38e+00 pdb=" N PRO R 273 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 273 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 273 " 0.022 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 280 2.70 - 3.25: 8432 3.25 - 3.80: 14601 3.80 - 4.35: 19098 4.35 - 4.90: 31924 Nonbonded interactions: 74335 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.147 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.202 3.040 nonbonded pdb=" O ILE S 100 " pdb=" OG SER S 105 " model vdw 2.250 3.040 nonbonded pdb=" O ILE S 145 " pdb=" OG1 THR S 201 " model vdw 2.251 3.040 ... (remaining 74330 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.230 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 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 : 0.004 0.184 8893 Z= 0.199 Angle : 0.829 59.871 12062 Z= 0.356 Chirality : 0.043 0.448 1395 Planarity : 0.004 0.039 1508 Dihedral : 16.858 89.469 3110 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.33 % Allowed : 29.41 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.90 (0.24), residues: 1118 helix: -1.65 (0.23), residues: 380 sheet: -1.16 (0.34), residues: 246 loop : -0.75 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 79 TYR 0.010 0.001 TYR R 231 PHE 0.037 0.002 PHE R 96 TRP 0.017 0.001 TRP R 271 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 8890) covalent geometry : angle 0.82890 (12056) SS BOND : bond 0.00167 ( 3) SS BOND : angle 0.92441 ( 6) hydrogen bonds : bond 0.26034 ( 398) hydrogen bonds : angle 9.25269 ( 1131) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.245 Fit side-chains REVERT: A 251 ASP cc_start: 0.7614 (t0) cc_final: 0.7394 (m-30) REVERT: B 264 TYR cc_start: 0.7591 (m-80) cc_final: 0.7287 (m-10) outliers start: 3 outliers final: 1 residues processed: 150 average time/residue: 0.0955 time to fit residues: 19.8110 Evaluate side-chains 143 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.0470 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.183578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145391 restraints weight = 9672.963| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.16 r_work: 0.3527 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8893 Z= 0.137 Angle : 0.515 5.283 12062 Z= 0.276 Chirality : 0.040 0.156 1395 Planarity : 0.004 0.038 1508 Dihedral : 6.645 67.038 1257 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.08 % Allowed : 27.97 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.97 (0.25), residues: 1118 helix: 0.04 (0.26), residues: 375 sheet: -1.25 (0.34), residues: 236 loop : -0.71 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG S 72 TYR 0.012 0.001 TYR B 264 PHE 0.012 0.001 PHE B 235 TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8890) covalent geometry : angle 0.51463 (12056) SS BOND : bond 0.00250 ( 3) SS BOND : angle 0.70160 ( 6) hydrogen bonds : bond 0.04276 ( 398) hydrogen bonds : angle 5.37896 ( 1131) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.311 Fit side-chains REVERT: R 88 MET cc_start: 0.6547 (mtt) cc_final: 0.6331 (mtp) REVERT: R 178 MET cc_start: 0.7265 (ttm) cc_final: 0.7000 (ttm) REVERT: B 59 TYR cc_start: 0.8401 (m-80) cc_final: 0.8165 (m-80) REVERT: B 212 ASP cc_start: 0.7493 (t70) cc_final: 0.7173 (t0) REVERT: B 264 TYR cc_start: 0.7694 (m-80) cc_final: 0.7374 (m-80) REVERT: S 82 GLN cc_start: 0.7254 (tp40) cc_final: 0.7027 (tp40) outliers start: 28 outliers final: 14 residues processed: 176 average time/residue: 0.0924 time to fit residues: 22.8619 Evaluate side-chains 159 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 161 ASN Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.0060 chunk 77 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.184724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.146873 restraints weight = 9601.472| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.15 r_work: 0.3533 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8893 Z= 0.114 Angle : 0.487 8.252 12062 Z= 0.258 Chirality : 0.040 0.154 1395 Planarity : 0.003 0.038 1508 Dihedral : 6.479 59.869 1254 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.30 % Allowed : 28.30 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 (0.25), residues: 1118 helix: 0.67 (0.27), residues: 379 sheet: -1.29 (0.33), residues: 236 loop : -0.71 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 79 TYR 0.009 0.001 TYR R 231 PHE 0.011 0.001 PHE B 235 TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 8890) covalent geometry : angle 0.48670 (12056) SS BOND : bond 0.00205 ( 3) SS BOND : angle 0.92154 ( 6) hydrogen bonds : bond 0.03801 ( 398) hydrogen bonds : angle 4.92344 ( 1131) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.377 Fit side-chains REVERT: R 178 MET cc_start: 0.7322 (ttm) cc_final: 0.6919 (ttm) REVERT: A 306 GLN cc_start: 0.7920 (tp40) cc_final: 0.7531 (mm-40) REVERT: B 209 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7870 (mttm) REVERT: B 212 ASP cc_start: 0.7455 (t70) cc_final: 0.7166 (t0) REVERT: B 246 ASP cc_start: 0.8878 (m-30) cc_final: 0.8502 (m-30) REVERT: B 267 ASP cc_start: 0.7839 (m-30) cc_final: 0.7424 (m-30) outliers start: 30 outliers final: 16 residues processed: 172 average time/residue: 0.0897 time to fit residues: 21.7605 Evaluate side-chains 161 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 161 ASN Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.2980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.183325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144561 restraints weight = 9679.839| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.18 r_work: 0.3533 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8893 Z= 0.142 Angle : 0.504 9.730 12062 Z= 0.264 Chirality : 0.041 0.154 1395 Planarity : 0.003 0.036 1508 Dihedral : 6.311 58.787 1254 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.19 % Allowed : 27.86 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.25), residues: 1118 helix: 0.92 (0.27), residues: 377 sheet: -1.36 (0.33), residues: 238 loop : -0.69 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 79 TYR 0.009 0.001 TYR B 264 PHE 0.012 0.001 PHE B 235 TRP 0.012 0.001 TRP R 271 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8890) covalent geometry : angle 0.50341 (12056) SS BOND : bond 0.00158 ( 3) SS BOND : angle 0.74184 ( 6) hydrogen bonds : bond 0.03639 ( 398) hydrogen bonds : angle 4.78246 ( 1131) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.379 Fit side-chains REVERT: R 178 MET cc_start: 0.7432 (ttm) cc_final: 0.7046 (ttm) REVERT: A 308 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7126 (mt-10) REVERT: B 209 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7953 (mttm) REVERT: B 212 ASP cc_start: 0.7484 (t70) cc_final: 0.7176 (t0) outliers start: 38 outliers final: 23 residues processed: 171 average time/residue: 0.0824 time to fit residues: 20.1587 Evaluate side-chains 164 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 161 ASN Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.180954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.141064 restraints weight = 9618.903| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.19 r_work: 0.3454 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8893 Z= 0.179 Angle : 0.535 10.605 12062 Z= 0.279 Chirality : 0.042 0.147 1395 Planarity : 0.003 0.038 1508 Dihedral : 6.000 59.236 1254 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.96 % Allowed : 26.98 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.53 (0.25), residues: 1118 helix: 1.10 (0.27), residues: 367 sheet: -1.46 (0.33), residues: 241 loop : -0.77 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 79 TYR 0.011 0.001 TYR B 264 PHE 0.012 0.001 PHE B 235 TRP 0.014 0.001 TRP R 271 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 8890) covalent geometry : angle 0.53542 (12056) SS BOND : bond 0.00092 ( 3) SS BOND : angle 0.66278 ( 6) hydrogen bonds : bond 0.03639 ( 398) hydrogen bonds : angle 4.74663 ( 1131) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 145 time to evaluate : 0.261 Fit side-chains REVERT: B 209 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8010 (mttm) REVERT: B 212 ASP cc_start: 0.7473 (t70) cc_final: 0.7136 (t0) REVERT: B 262 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7350 (mpp) outliers start: 45 outliers final: 26 residues processed: 175 average time/residue: 0.0852 time to fit residues: 21.3561 Evaluate side-chains 170 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 105 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 0.0980 chunk 21 optimal weight: 0.2980 chunk 98 optimal weight: 0.0070 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 0.0670 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.187140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.148977 restraints weight = 9570.645| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.18 r_work: 0.3588 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8893 Z= 0.096 Angle : 0.480 10.942 12062 Z= 0.251 Chirality : 0.039 0.150 1395 Planarity : 0.003 0.036 1508 Dihedral : 5.446 57.966 1254 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.19 % Allowed : 29.85 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.28 (0.25), residues: 1118 helix: 1.44 (0.27), residues: 367 sheet: -1.27 (0.33), residues: 232 loop : -0.79 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 79 TYR 0.011 0.001 TYR S 60 PHE 0.013 0.001 PHE R 96 TRP 0.015 0.001 TRP R 271 HIS 0.003 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 8890) covalent geometry : angle 0.47990 (12056) SS BOND : bond 0.00314 ( 3) SS BOND : angle 0.97569 ( 6) hydrogen bonds : bond 0.03142 ( 398) hydrogen bonds : angle 4.46361 ( 1131) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 141 time to evaluate : 0.321 Fit side-chains REVERT: R 88 MET cc_start: 0.6404 (mtt) cc_final: 0.6204 (mtp) REVERT: R 178 MET cc_start: 0.7326 (ttm) cc_final: 0.6969 (ttm) REVERT: R 210 TRP cc_start: 0.6310 (OUTLIER) cc_final: 0.5241 (t60) REVERT: B 145 TYR cc_start: 0.8565 (p90) cc_final: 0.8277 (p90) REVERT: B 212 ASP cc_start: 0.7449 (t70) cc_final: 0.7135 (t0) REVERT: B 262 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7387 (mpp) outliers start: 29 outliers final: 22 residues processed: 162 average time/residue: 0.0897 time to fit residues: 20.5042 Evaluate side-chains 158 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 52 optimal weight: 0.1980 chunk 77 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 16 optimal weight: 0.0020 chunk 42 optimal weight: 4.9990 overall best weight: 1.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.180733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.140568 restraints weight = 9673.999| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.21 r_work: 0.3485 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 8893 Z= 0.189 Angle : 0.549 10.885 12062 Z= 0.283 Chirality : 0.042 0.146 1395 Planarity : 0.003 0.034 1508 Dihedral : 5.298 57.131 1254 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.30 % Allowed : 28.52 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.38 (0.25), residues: 1118 helix: 1.28 (0.27), residues: 375 sheet: -1.46 (0.32), residues: 241 loop : -0.72 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 79 TYR 0.012 0.001 TYR S 60 PHE 0.013 0.001 PHE R 96 TRP 0.022 0.002 TRP R 271 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 8890) covalent geometry : angle 0.54893 (12056) SS BOND : bond 0.00182 ( 3) SS BOND : angle 0.92331 ( 6) hydrogen bonds : bond 0.03507 ( 398) hydrogen bonds : angle 4.60515 ( 1131) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.313 Fit side-chains REVERT: R 210 TRP cc_start: 0.6495 (OUTLIER) cc_final: 0.5323 (t60) REVERT: A 18 MET cc_start: 0.7696 (ttm) cc_final: 0.7366 (mtt) REVERT: B 212 ASP cc_start: 0.7467 (t70) cc_final: 0.7115 (t0) REVERT: B 262 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7571 (mpp) outliers start: 39 outliers final: 29 residues processed: 166 average time/residue: 0.0886 time to fit residues: 20.8490 Evaluate side-chains 164 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 133 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 161 ASN Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.0170 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 29 optimal weight: 0.6980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.186060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.147377 restraints weight = 9556.132| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.18 r_work: 0.3569 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8893 Z= 0.103 Angle : 0.493 12.023 12062 Z= 0.254 Chirality : 0.040 0.152 1395 Planarity : 0.003 0.034 1508 Dihedral : 4.803 49.225 1254 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.74 % Allowed : 29.19 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.13 (0.25), residues: 1118 helix: 1.56 (0.27), residues: 373 sheet: -1.28 (0.33), residues: 233 loop : -0.66 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 79 TYR 0.011 0.001 TYR S 60 PHE 0.013 0.001 PHE R 96 TRP 0.021 0.001 TRP R 271 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8890) covalent geometry : angle 0.49310 (12056) SS BOND : bond 0.00261 ( 3) SS BOND : angle 0.78870 ( 6) hydrogen bonds : bond 0.03073 ( 398) hydrogen bonds : angle 4.40917 ( 1131) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.314 Fit side-chains REVERT: R 64 MET cc_start: 0.7886 (mtp) cc_final: 0.6954 (mmt) REVERT: R 178 MET cc_start: 0.7326 (ttm) cc_final: 0.6889 (ttm) REVERT: R 210 TRP cc_start: 0.6284 (OUTLIER) cc_final: 0.5143 (t60) REVERT: B 212 ASP cc_start: 0.7486 (t70) cc_final: 0.7159 (t0) REVERT: B 262 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7264 (mpp) outliers start: 34 outliers final: 26 residues processed: 166 average time/residue: 0.0898 time to fit residues: 21.3213 Evaluate side-chains 164 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 161 ASN Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 87 optimal weight: 0.0270 chunk 3 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.184300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.145297 restraints weight = 9613.422| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.19 r_work: 0.3559 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8893 Z= 0.117 Angle : 0.503 11.810 12062 Z= 0.259 Chirality : 0.040 0.150 1395 Planarity : 0.003 0.033 1508 Dihedral : 4.642 48.794 1254 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.41 % Allowed : 29.19 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.11 (0.25), residues: 1118 helix: 1.56 (0.27), residues: 373 sheet: -1.21 (0.33), residues: 233 loop : -0.66 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 79 TYR 0.011 0.001 TYR S 60 PHE 0.013 0.001 PHE B 292 TRP 0.028 0.001 TRP R 271 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8890) covalent geometry : angle 0.50295 (12056) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.80715 ( 6) hydrogen bonds : bond 0.03064 ( 398) hydrogen bonds : angle 4.42351 ( 1131) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.378 Fit side-chains REVERT: R 178 MET cc_start: 0.7368 (ttm) cc_final: 0.7009 (ttm) REVERT: R 210 TRP cc_start: 0.6276 (OUTLIER) cc_final: 0.5165 (t60) REVERT: A 18 MET cc_start: 0.7359 (mtt) cc_final: 0.6989 (ttm) REVERT: B 212 ASP cc_start: 0.7482 (t70) cc_final: 0.7156 (t0) REVERT: B 262 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7368 (mpp) outliers start: 31 outliers final: 26 residues processed: 163 average time/residue: 0.0901 time to fit residues: 20.7864 Evaluate side-chains 164 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 161 ASN Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 104 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 0.4980 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 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 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.183037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.143204 restraints weight = 9623.128| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.21 r_work: 0.3516 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8893 Z= 0.158 Angle : 0.531 11.973 12062 Z= 0.274 Chirality : 0.041 0.149 1395 Planarity : 0.003 0.032 1508 Dihedral : 4.730 47.343 1254 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.63 % Allowed : 29.19 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.25), residues: 1118 helix: 1.49 (0.27), residues: 373 sheet: -1.35 (0.33), residues: 237 loop : -0.67 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 79 TYR 0.011 0.001 TYR S 60 PHE 0.013 0.001 PHE R 96 TRP 0.038 0.002 TRP R 271 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8890) covalent geometry : angle 0.53095 (12056) SS BOND : bond 0.00168 ( 3) SS BOND : angle 0.82287 ( 6) hydrogen bonds : bond 0.03231 ( 398) hydrogen bonds : angle 4.51209 ( 1131) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 133 time to evaluate : 0.322 Fit side-chains REVERT: R 210 TRP cc_start: 0.6352 (OUTLIER) cc_final: 0.5190 (t60) REVERT: A 18 MET cc_start: 0.7451 (mtt) cc_final: 0.7082 (ttm) REVERT: B 212 ASP cc_start: 0.7482 (t70) cc_final: 0.7144 (t0) REVERT: B 262 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7493 (mpp) outliers start: 33 outliers final: 30 residues processed: 158 average time/residue: 0.0928 time to fit residues: 20.4848 Evaluate side-chains 164 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 161 ASN Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 210 TRP Chi-restraints excluded: chain R residue 261 VAL Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 224 CYS Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 88 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 214 VAL Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 101 optimal weight: 30.0000 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.183171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.143344 restraints weight = 9624.603| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.20 r_work: 0.3502 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.223 8893 Z= 0.189 Angle : 0.863 59.198 12062 Z= 0.516 Chirality : 0.046 0.781 1395 Planarity : 0.003 0.032 1508 Dihedral : 4.776 47.334 1254 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.85 % Allowed : 28.96 % Favored : 67.18 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.70 % 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: -0.23 (0.25), residues: 1118 helix: 1.44 (0.27), residues: 373 sheet: -1.35 (0.33), residues: 237 loop : -0.67 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 79 TYR 0.010 0.001 TYR S 178 PHE 0.013 0.001 PHE R 96 TRP 0.032 0.002 TRP R 271 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 8890) covalent geometry : angle 0.86303 (12056) SS BOND : bond 0.00171 ( 3) SS BOND : angle 0.78198 ( 6) hydrogen bonds : bond 0.03230 ( 398) hydrogen bonds : angle 4.52071 ( 1131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2535.26 seconds wall clock time: 44 minutes 16.14 seconds (2656.14 seconds total)