Starting phenix.real_space_refine on Wed Mar 4 13:45:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cky_30394/03_2026/7cky_30394_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cky_30394/03_2026/7cky_30394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cky_30394/03_2026/7cky_30394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cky_30394/03_2026/7cky_30394.map" model { file = "/net/cci-nas-00/data/ceres_data/7cky_30394/03_2026/7cky_30394_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cky_30394/03_2026/7cky_30394_neut.cif" } resolution = 3.2 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= 0.005 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 7222 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 S 53 5.16 5 C 5171 2.51 5 N 1408 2.21 5 O 1494 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8128 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1906 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2587 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2171 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 266} Chain breaks: 3 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 1, 'G3U': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.89, per 1000 atoms: 0.23 Number of scatterers: 8128 At special positions: 0 Unit cell: (90, 86, 123, 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 53 16.00 F 2 9.00 O 1494 8.00 N 1408 7.00 C 5171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=1.96 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=1.44 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " 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: 0.73 Conformation dependent library (CDL) restraints added in 299.7 milliseconds 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 10 sheets defined 43.0% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 14 through 40 removed outlier: 3.729A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.566A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.155A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 285 " --> pdb=" O LEU A 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 281 through 285' Processing helix chain 'A' and resid 293 through 304 removed outlier: 4.667A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.507A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.934A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 4.096A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.908A pdb=" N ILE B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.739A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.640A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 51 removed outlier: 3.505A pdb=" N PHE R 51 " --> pdb=" O ALA R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 77 removed outlier: 4.148A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (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 removed outlier: 3.728A pdb=" N ALA R 109 " --> pdb=" O MET R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 161 removed outlier: 4.576A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 191 through 203 removed outlier: 3.835A pdb=" N ILE R 196 " --> pdb=" O ARG R 192 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE R 201 " --> pdb=" O SER R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 237 removed outlier: 3.956A pdb=" N ALA R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 295 removed outlier: 3.798A pdb=" N LYS R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL R 270 " --> pdb=" O ARG R 266 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 4.079A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 332 removed outlier: 4.075A pdb=" N VAL R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASN R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 344 removed outlier: 3.822A pdb=" N ALA R 340 " --> pdb=" O ASP R 336 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR R 343 " --> pdb=" O LYS R 339 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 214 removed outlier: 3.523A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.738A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.611A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.989A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.893A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.672A 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: 6.855A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.142A 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: 3.809A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.228A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.763A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1152 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: 1.46 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1308 1.31 - 1.44: 2328 1.44 - 1.56: 4591 1.56 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 8299 Sorted by residual: bond pdb=" C15 G3U R 502 " pdb=" C19 G3U R 502 " ideal model delta sigma weight residual 1.484 1.386 0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C24 G3U R 502 " pdb=" C26 G3U R 502 " ideal model delta sigma weight residual 1.449 1.372 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C24 G3U R 502 " pdb=" N23 G3U R 502 " ideal model delta sigma weight residual 1.379 1.316 0.063 2.00e-02 2.50e+03 9.85e+00 bond pdb=" C10 G3U R 502 " pdb=" O11 G3U R 502 " ideal model delta sigma weight residual 1.347 1.406 -0.059 2.00e-02 2.50e+03 8.56e+00 bond pdb=" C19 G3U R 502 " pdb=" N20 G3U R 502 " ideal model delta sigma weight residual 1.382 1.329 0.053 2.00e-02 2.50e+03 7.01e+00 ... (remaining 8294 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 10992 1.35 - 2.70: 227 2.70 - 4.06: 29 4.06 - 5.41: 12 5.41 - 6.76: 3 Bond angle restraints: 11263 Sorted by residual: angle pdb=" C TYR R 214 " pdb=" CA TYR R 214 " pdb=" CB TYR R 214 " ideal model delta sigma weight residual 110.67 115.79 -5.12 1.92e+00 2.71e-01 7.12e+00 angle pdb=" N SER B 227 " pdb=" CA SER B 227 " pdb=" C SER B 227 " ideal model delta sigma weight residual 108.34 111.69 -3.35 1.31e+00 5.83e-01 6.55e+00 angle pdb=" CA ASP B 186 " pdb=" C ASP B 186 " pdb=" O ASP B 186 " ideal model delta sigma weight residual 120.92 118.22 2.70 1.14e+00 7.69e-01 5.62e+00 angle pdb=" N ASN R 292 " pdb=" CA ASN R 292 " pdb=" C ASN R 292 " ideal model delta sigma weight residual 111.75 108.76 2.99 1.28e+00 6.10e-01 5.47e+00 angle pdb=" C21 G3U R 502 " pdb=" N23 G3U R 502 " pdb=" C24 G3U R 502 " ideal model delta sigma weight residual 127.77 121.01 6.76 3.00e+00 1.11e-01 5.08e+00 ... (remaining 11258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 4401 17.06 - 34.13: 462 34.13 - 51.19: 77 51.19 - 68.26: 24 68.26 - 85.32: 10 Dihedral angle restraints: 4974 sinusoidal: 1949 harmonic: 3025 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 60.49 32.51 1 1.00e+01 1.00e-02 1.50e+01 dihedral pdb=" CA ASP R 70 " pdb=" CB ASP R 70 " pdb=" CG ASP R 70 " pdb=" OD1 ASP R 70 " ideal model delta sinusoidal sigma weight residual -30.00 -86.03 56.03 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" C TYR R 214 " pdb=" N TYR R 214 " pdb=" CA TYR R 214 " pdb=" CB TYR R 214 " ideal model delta harmonic sigma weight residual -122.60 -130.64 8.04 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 4971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 976 0.042 - 0.084: 236 0.084 - 0.127: 66 0.127 - 0.169: 2 0.169 - 0.211: 1 Chirality restraints: 1281 Sorted by residual: chirality pdb=" CA TYR R 214 " pdb=" N TYR R 214 " pdb=" C TYR R 214 " pdb=" CB TYR R 214 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA LEU R 190 " pdb=" N LEU R 190 " pdb=" C LEU R 190 " pdb=" CB LEU R 190 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.62e-01 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 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1278 not shown) Planarity restraints: 1423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 205 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO R 206 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO R 206 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 206 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 327 " -0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO R 328 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO R 328 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 328 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.016 5.00e-02 4.00e+02 2.43e-02 9.44e-01 pdb=" N PRO N 88 " 0.042 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.014 5.00e-02 4.00e+02 ... (remaining 1420 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 290 2.70 - 3.25: 8429 3.25 - 3.80: 14553 3.80 - 4.35: 18657 4.35 - 4.90: 30677 Nonbonded interactions: 72606 Sorted by model distance: nonbonded pdb=" O PRO R 137 " pdb=" CD2 PHE R 141 " model vdw 2.154 3.340 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.186 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR R 108 " pdb=" OG SER R 202 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR R 59 " pdb=" OD2 ASP R 120 " model vdw 2.282 3.040 ... (remaining 72601 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.470 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4872 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 : 0.007 0.587 8303 Z= 0.367 Angle : 0.648 34.720 11271 Z= 0.352 Chirality : 0.039 0.211 1281 Planarity : 0.003 0.041 1423 Dihedral : 14.493 85.325 2996 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.51 % Allowed : 13.24 % Favored : 85.25 % 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: -2.84 (0.24), residues: 1018 helix: -0.77 (0.23), residues: 395 sheet: -2.80 (0.33), residues: 192 loop : -2.40 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.014 0.001 TYR R 214 PHE 0.006 0.001 PHE B 235 TRP 0.009 0.001 TRP A 234 HIS 0.002 0.000 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8299) covalent geometry : angle 0.47847 (11263) SS BOND : bond 0.29564 ( 4) SS BOND : angle 16.39717 ( 8) hydrogen bonds : bond 0.18297 ( 406) hydrogen bonds : angle 7.76411 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.1995 (t80) cc_final: 0.1395 (t80) REVERT: A 343 ASP cc_start: 0.4753 (m-30) cc_final: 0.4338 (m-30) REVERT: B 153 ASP cc_start: 0.6151 (p0) cc_final: 0.5784 (p0) REVERT: B 196 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7917 (m) REVERT: R 136 THR cc_start: 0.7920 (p) cc_final: 0.7611 (p) outliers start: 13 outliers final: 5 residues processed: 200 average time/residue: 0.1104 time to fit residues: 28.7702 Evaluate side-chains 153 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 120 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 267 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 371 ASN A 377 ASN A 390 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 110 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN N 13 GLN N 39 GLN R 60 ASN R 323 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4725 r_free = 0.4725 target = 0.255451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.224892 restraints weight = 9961.911| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 2.20 r_work: 0.4293 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8303 Z= 0.168 Angle : 0.581 8.584 11271 Z= 0.308 Chirality : 0.042 0.151 1281 Planarity : 0.004 0.031 1423 Dihedral : 5.243 47.991 1210 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.32 % Allowed : 17.89 % Favored : 79.79 % 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: -1.70 (0.26), residues: 1018 helix: 0.41 (0.26), residues: 391 sheet: -2.26 (0.37), residues: 170 loop : -2.03 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 389 TYR 0.016 0.002 TYR N 94 PHE 0.028 0.002 PHE R 141 TRP 0.020 0.002 TRP A 277 HIS 0.013 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 8299) covalent geometry : angle 0.58028 (11263) SS BOND : bond 0.00320 ( 4) SS BOND : angle 1.48152 ( 8) hydrogen bonds : bond 0.03869 ( 406) hydrogen bonds : angle 5.65883 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.3086 (t80) cc_final: 0.2407 (t80) REVERT: B 105 TYR cc_start: 0.8155 (t80) cc_final: 0.7946 (t80) REVERT: B 153 ASP cc_start: 0.7029 (p0) cc_final: 0.6690 (p0) REVERT: B 188 MET cc_start: 0.4789 (tpt) cc_final: 0.4353 (tpt) REVERT: R 136 THR cc_start: 0.8293 (p) cc_final: 0.8083 (p) REVERT: R 205 ILE cc_start: 0.7827 (mt) cc_final: 0.7524 (mt) outliers start: 20 outliers final: 7 residues processed: 175 average time/residue: 0.0900 time to fit residues: 21.7111 Evaluate side-chains 148 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 164 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 59 optimal weight: 0.0370 chunk 84 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 371 ASN B 17 GLN B 110 ASN B 125 ASN B 268 ASN N 123 GLN R 53 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.221042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.184463 restraints weight = 9150.120| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 2.11 r_work: 0.3944 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 8303 Z= 0.282 Angle : 0.740 8.272 11271 Z= 0.394 Chirality : 0.047 0.178 1281 Planarity : 0.005 0.053 1423 Dihedral : 5.672 57.803 1205 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.53 % Allowed : 18.82 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.26), residues: 1018 helix: 0.55 (0.26), residues: 390 sheet: -2.54 (0.36), residues: 168 loop : -2.08 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 118 TYR 0.018 0.003 TYR B 145 PHE 0.027 0.003 PHE R 141 TRP 0.026 0.003 TRP B 297 HIS 0.016 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00648 ( 8299) covalent geometry : angle 0.73958 (11263) SS BOND : bond 0.00666 ( 4) SS BOND : angle 1.53528 ( 8) hydrogen bonds : bond 0.05030 ( 406) hydrogen bonds : angle 6.02912 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 180 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5113 (t80) cc_final: 0.4491 (t80) REVERT: A 239 ASN cc_start: 0.8031 (OUTLIER) cc_final: 0.7579 (t0) REVERT: B 198 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7715 (pp) REVERT: B 234 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.8086 (t80) REVERT: B 339 TRP cc_start: 0.8283 (m100) cc_final: 0.7861 (m100) REVERT: G 38 MET cc_start: 0.8475 (tmm) cc_final: 0.8179 (tmm) REVERT: R 43 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7697 (mp) REVERT: R 52 ARG cc_start: 0.7363 (tpp-160) cc_final: 0.7134 (tpp-160) outliers start: 39 outliers final: 16 residues processed: 205 average time/residue: 0.0868 time to fit residues: 24.7001 Evaluate side-chains 170 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 298 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 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 278 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 295 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.223725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.186050 restraints weight = 9451.285| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.26 r_work: 0.3925 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8303 Z= 0.160 Angle : 0.587 7.768 11271 Z= 0.305 Chirality : 0.043 0.134 1281 Planarity : 0.004 0.044 1423 Dihedral : 5.265 55.856 1205 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.60 % Allowed : 21.25 % Favored : 75.15 % 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: -1.38 (0.26), residues: 1018 helix: 0.84 (0.26), residues: 387 sheet: -2.41 (0.34), residues: 185 loop : -1.80 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 336 TYR 0.016 0.002 TYR B 289 PHE 0.018 0.001 PHE R 141 TRP 0.014 0.002 TRP B 99 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8299) covalent geometry : angle 0.58657 (11263) SS BOND : bond 0.00510 ( 4) SS BOND : angle 0.85297 ( 8) hydrogen bonds : bond 0.03909 ( 406) hydrogen bonds : angle 5.57715 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5029 (t80) cc_final: 0.4466 (t80) REVERT: A 356 ARG cc_start: 0.8085 (mmt180) cc_final: 0.7811 (mmt-90) REVERT: B 37 ILE cc_start: 0.3068 (OUTLIER) cc_final: 0.2200 (mt) REVERT: B 43 ILE cc_start: 0.3956 (OUTLIER) cc_final: 0.3490 (pt) REVERT: B 65 THR cc_start: 0.7948 (p) cc_final: 0.7602 (p) REVERT: B 234 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.8129 (t80) REVERT: B 273 ILE cc_start: 0.7915 (mt) cc_final: 0.7534 (mt) REVERT: G 38 MET cc_start: 0.8449 (tmm) cc_final: 0.7933 (ttm) REVERT: N 34 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6412 (mtm) REVERT: N 35 ASN cc_start: 0.7448 (p0) cc_final: 0.6326 (p0) REVERT: N 120 GLN cc_start: 0.4429 (OUTLIER) cc_final: 0.3401 (tt0) REVERT: R 61 PHE cc_start: 0.8313 (m-10) cc_final: 0.8111 (m-10) REVERT: R 78 MET cc_start: 0.8091 (mmt) cc_final: 0.7623 (mmt) REVERT: R 141 PHE cc_start: 0.7698 (m-80) cc_final: 0.7417 (m-80) outliers start: 31 outliers final: 20 residues processed: 204 average time/residue: 0.0877 time to fit residues: 24.8727 Evaluate side-chains 186 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 298 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 42 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 63 optimal weight: 0.0470 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 17 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 230 ASN B 268 ASN B 293 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.223366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.185735 restraints weight = 9320.898| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.21 r_work: 0.3925 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.6974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8303 Z= 0.154 Angle : 0.568 6.703 11271 Z= 0.299 Chirality : 0.042 0.139 1281 Planarity : 0.004 0.056 1423 Dihedral : 5.069 54.963 1205 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.07 % Allowed : 24.51 % Favored : 71.43 % 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: -1.06 (0.27), residues: 1018 helix: 1.01 (0.27), residues: 390 sheet: -2.08 (0.35), residues: 199 loop : -1.58 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 304 TYR 0.013 0.002 TYR N 115 PHE 0.015 0.001 PHE R 141 TRP 0.013 0.002 TRP R 99 HIS 0.009 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8299) covalent geometry : angle 0.56733 (11263) SS BOND : bond 0.00434 ( 4) SS BOND : angle 0.92320 ( 8) hydrogen bonds : bond 0.03889 ( 406) hydrogen bonds : angle 5.45056 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.4940 (t80) cc_final: 0.4404 (t80) REVERT: A 356 ARG cc_start: 0.8151 (mmt180) cc_final: 0.7872 (mmt-90) REVERT: B 37 ILE cc_start: 0.3578 (OUTLIER) cc_final: 0.2152 (mt) REVERT: B 43 ILE cc_start: 0.4197 (OUTLIER) cc_final: 0.3897 (pt) REVERT: B 221 THR cc_start: 0.6702 (m) cc_final: 0.6475 (m) REVERT: B 234 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8164 (t80) REVERT: B 273 ILE cc_start: 0.7979 (mt) cc_final: 0.7758 (mt) REVERT: G 38 MET cc_start: 0.8381 (tmm) cc_final: 0.8030 (ttm) REVERT: N 120 GLN cc_start: 0.4703 (OUTLIER) cc_final: 0.3745 (tp40) REVERT: R 150 LEU cc_start: 0.8027 (tp) cc_final: 0.7700 (tp) outliers start: 35 outliers final: 23 residues processed: 197 average time/residue: 0.0746 time to fit residues: 21.1841 Evaluate side-chains 178 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 211 ILE Chi-restraints excluded: chain R residue 278 MET Chi-restraints excluded: chain R residue 298 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 25 optimal weight: 0.0970 chunk 10 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 96 optimal weight: 0.0980 chunk 61 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 230 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.225373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.189895 restraints weight = 9239.598| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 2.08 r_work: 0.3935 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.7310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8303 Z= 0.135 Angle : 0.563 6.678 11271 Z= 0.295 Chirality : 0.042 0.158 1281 Planarity : 0.004 0.038 1423 Dihedral : 4.983 52.589 1205 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.30 % Allowed : 24.04 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.27), residues: 1018 helix: 1.04 (0.27), residues: 390 sheet: -2.01 (0.35), residues: 200 loop : -1.43 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.011 0.001 TYR N 115 PHE 0.014 0.001 PHE B 292 TRP 0.013 0.002 TRP R 99 HIS 0.008 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8299) covalent geometry : angle 0.56228 (11263) SS BOND : bond 0.00347 ( 4) SS BOND : angle 0.99815 ( 8) hydrogen bonds : bond 0.03749 ( 406) hydrogen bonds : angle 5.40161 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 166 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.4829 (t80) cc_final: 0.4387 (t80) REVERT: A 239 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7518 (t0) REVERT: A 356 ARG cc_start: 0.8128 (mmt180) cc_final: 0.7891 (mmt-90) REVERT: B 43 ILE cc_start: 0.4154 (OUTLIER) cc_final: 0.3945 (pt) REVERT: B 221 THR cc_start: 0.6697 (m) cc_final: 0.6486 (m) REVERT: B 234 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.8199 (t80) REVERT: B 273 ILE cc_start: 0.8007 (mt) cc_final: 0.7732 (mt) REVERT: B 280 LYS cc_start: 0.8048 (mmmm) cc_final: 0.7824 (mmmm) REVERT: B 323 ASP cc_start: 0.7927 (p0) cc_final: 0.7713 (p0) REVERT: G 38 MET cc_start: 0.8437 (tmm) cc_final: 0.8114 (mtt) REVERT: N 34 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6713 (mtm) REVERT: R 78 MET cc_start: 0.8017 (mmt) cc_final: 0.7508 (mmt) REVERT: R 150 LEU cc_start: 0.8031 (tp) cc_final: 0.7700 (tp) outliers start: 37 outliers final: 24 residues processed: 189 average time/residue: 0.0849 time to fit residues: 22.4620 Evaluate side-chains 181 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 278 MET Chi-restraints excluded: chain R residue 298 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.0770 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 0.0060 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 52 optimal weight: 5.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 125 ASN B 230 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.224519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.188478 restraints weight = 9331.190| |-----------------------------------------------------------------------------| r_work (start): 0.4100 rms_B_bonded: 2.10 r_work: 0.3947 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.7547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8303 Z= 0.129 Angle : 0.555 6.349 11271 Z= 0.291 Chirality : 0.042 0.157 1281 Planarity : 0.004 0.046 1423 Dihedral : 4.944 51.226 1204 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.48 % Allowed : 24.97 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.27), residues: 1018 helix: 1.08 (0.27), residues: 392 sheet: -1.77 (0.36), residues: 188 loop : -1.41 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 228 TYR 0.011 0.001 TYR N 95 PHE 0.013 0.001 PHE R 141 TRP 0.013 0.002 TRP R 99 HIS 0.007 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8299) covalent geometry : angle 0.55330 (11263) SS BOND : bond 0.00571 ( 4) SS BOND : angle 1.77878 ( 8) hydrogen bonds : bond 0.03611 ( 406) hydrogen bonds : angle 5.30529 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.4777 (t80) cc_final: 0.4374 (t80) REVERT: A 239 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7516 (t0) REVERT: B 234 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.8137 (t80) REVERT: B 251 ARG cc_start: 0.7570 (tpp80) cc_final: 0.6852 (tpp-160) REVERT: B 273 ILE cc_start: 0.7838 (mt) cc_final: 0.7526 (mt) REVERT: N 34 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6708 (mtm) REVERT: R 150 LEU cc_start: 0.7968 (tp) cc_final: 0.7627 (tp) outliers start: 30 outliers final: 23 residues processed: 176 average time/residue: 0.0869 time to fit residues: 21.4663 Evaluate side-chains 177 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 278 MET Chi-restraints excluded: chain R residue 298 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 53 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.0570 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 75 GLN B 110 ASN B 230 ASN ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.214781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.176417 restraints weight = 9163.175| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.20 r_work: 0.3822 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.8325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8303 Z= 0.181 Angle : 0.594 7.017 11271 Z= 0.312 Chirality : 0.044 0.144 1281 Planarity : 0.004 0.041 1423 Dihedral : 5.099 50.546 1204 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 3.60 % Allowed : 24.62 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.27), residues: 1018 helix: 1.15 (0.27), residues: 392 sheet: -1.79 (0.37), residues: 190 loop : -1.32 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 389 TYR 0.011 0.002 TYR N 95 PHE 0.015 0.002 PHE B 253 TRP 0.020 0.002 TRP B 99 HIS 0.008 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 8299) covalent geometry : angle 0.59190 (11263) SS BOND : bond 0.00385 ( 4) SS BOND : angle 1.98929 ( 8) hydrogen bonds : bond 0.03943 ( 406) hydrogen bonds : angle 5.44693 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5035 (t80) cc_final: 0.4721 (t80) REVERT: A 239 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7520 (t0) REVERT: B 99 TRP cc_start: 0.7046 (m-90) cc_final: 0.6766 (m100) REVERT: B 188 MET cc_start: 0.7200 (mmm) cc_final: 0.6935 (mmm) REVERT: B 234 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8146 (t80) REVERT: B 273 ILE cc_start: 0.8223 (mt) cc_final: 0.7948 (mt) REVERT: N 34 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7081 (mtp) REVERT: R 150 LEU cc_start: 0.7932 (tp) cc_final: 0.7583 (tp) outliers start: 31 outliers final: 17 residues processed: 197 average time/residue: 0.0790 time to fit residues: 21.9802 Evaluate side-chains 179 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 278 MET Chi-restraints excluded: chain R residue 298 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 66 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 23 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 41 ASN ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.215029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.177449 restraints weight = 9178.790| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.17 r_work: 0.3837 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.8662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8303 Z= 0.156 Angle : 0.608 7.638 11271 Z= 0.319 Chirality : 0.043 0.141 1281 Planarity : 0.004 0.032 1423 Dihedral : 5.074 52.396 1204 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.79 % Allowed : 25.90 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.27), residues: 1018 helix: 1.13 (0.26), residues: 393 sheet: -1.72 (0.37), residues: 190 loop : -1.28 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 67 TYR 0.017 0.001 TYR G 40 PHE 0.011 0.001 PHE R 141 TRP 0.017 0.002 TRP B 169 HIS 0.007 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8299) covalent geometry : angle 0.60521 (11263) SS BOND : bond 0.00124 ( 4) SS BOND : angle 2.07183 ( 8) hydrogen bonds : bond 0.03783 ( 406) hydrogen bonds : angle 5.35745 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5052 (t80) cc_final: 0.4552 (t80) REVERT: A 265 ARG cc_start: 0.7594 (mmm-85) cc_final: 0.7354 (mmm-85) REVERT: B 234 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8181 (t80) REVERT: B 273 ILE cc_start: 0.8096 (mt) cc_final: 0.7820 (mt) REVERT: N 3 GLN cc_start: 0.6432 (mp10) cc_final: 0.6116 (mp10) REVERT: N 34 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7026 (mtm) REVERT: R 150 LEU cc_start: 0.7944 (tp) cc_final: 0.7621 (tp) outliers start: 24 outliers final: 18 residues processed: 187 average time/residue: 0.0821 time to fit residues: 21.6404 Evaluate side-chains 181 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 298 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 96 optimal weight: 0.7980 chunk 84 optimal weight: 0.4980 chunk 57 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 74 ASN ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.204525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.165163 restraints weight = 8929.954| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.20 r_work: 0.3712 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.9500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 8303 Z= 0.240 Angle : 0.696 9.069 11271 Z= 0.364 Chirality : 0.046 0.153 1281 Planarity : 0.004 0.034 1423 Dihedral : 5.359 50.022 1204 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.67 % Allowed : 26.95 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.27), residues: 1018 helix: 0.92 (0.26), residues: 397 sheet: -1.90 (0.39), residues: 171 loop : -1.48 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 67 TYR 0.044 0.002 TYR B 264 PHE 0.012 0.002 PHE B 151 TRP 0.030 0.003 TRP B 169 HIS 0.006 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 8299) covalent geometry : angle 0.69274 (11263) SS BOND : bond 0.00165 ( 4) SS BOND : angle 2.45206 ( 8) hydrogen bonds : bond 0.04414 ( 406) hydrogen bonds : angle 5.66309 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2036 Ramachandran restraints generated. 1018 Oldfield, 0 Emsley, 1018 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5233 (t80) cc_final: 0.4691 (t80) REVERT: B 38 ASP cc_start: 0.6890 (p0) cc_final: 0.6121 (m-30) REVERT: B 99 TRP cc_start: 0.7163 (m-90) cc_final: 0.6905 (m100) REVERT: B 234 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8173 (t80) REVERT: B 323 ASP cc_start: 0.8219 (p0) cc_final: 0.7896 (p0) REVERT: N 29 PHE cc_start: 0.8657 (t80) cc_final: 0.8364 (t80) REVERT: N 34 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7449 (mtp) REVERT: R 123 TRP cc_start: 0.7396 (m100) cc_final: 0.6856 (m100) REVERT: R 150 LEU cc_start: 0.7969 (tp) cc_final: 0.7594 (tp) outliers start: 23 outliers final: 17 residues processed: 195 average time/residue: 0.0804 time to fit residues: 22.2248 Evaluate side-chains 186 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 167 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 359 CYS Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 164 HIS Chi-restraints excluded: chain R residue 298 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 23 ASN A 278 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN ** R 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.209231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.171115 restraints weight = 8776.287| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.20 r_work: 0.3785 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.9647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8303 Z= 0.165 Angle : 0.634 7.314 11271 Z= 0.333 Chirality : 0.044 0.149 1281 Planarity : 0.004 0.035 1423 Dihedral : 5.237 55.270 1204 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.32 % Allowed : 27.41 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.27), residues: 1018 helix: 0.94 (0.26), residues: 399 sheet: -1.66 (0.37), residues: 189 loop : -1.24 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 389 TYR 0.038 0.002 TYR B 264 PHE 0.011 0.001 PHE B 253 TRP 0.025 0.002 TRP B 169 HIS 0.007 0.002 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8299) covalent geometry : angle 0.63198 (11263) SS BOND : bond 0.00196 ( 4) SS BOND : angle 2.09287 ( 8) hydrogen bonds : bond 0.03982 ( 406) hydrogen bonds : angle 5.45412 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1968.51 seconds wall clock time: 34 minutes 36.74 seconds (2076.74 seconds total)