Starting phenix.real_space_refine on Wed Sep 17 19:04:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6os9_20180/09_2025/6os9_20180.cif Found real_map, /net/cci-nas-00/data/ceres_data/6os9_20180/09_2025/6os9_20180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6os9_20180/09_2025/6os9_20180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6os9_20180/09_2025/6os9_20180.map" model { file = "/net/cci-nas-00/data/ceres_data/6os9_20180/09_2025/6os9_20180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6os9_20180/09_2025/6os9_20180.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2127 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: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5711 2.51 5 N 1528 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8969 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2415 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 53 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2584 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} 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: "D" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 1.92, per 1000 atoms: 0.21 Number of scatterers: 8969 At special positions: 0 Unit cell: (102.82, 121.9, 119.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 61 16.00 O 1669 8.00 N 1528 7.00 C 5711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.05 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 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: 0.84 Conformation dependent library (CDL) restraints added in 332.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 14 sheets defined 39.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'R' and resid 51 through 55 removed outlier: 3.607A pdb=" N LEU R 54 " --> pdb=" O SER R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 91 Processing helix chain 'R' and resid 97 through 128 removed outlier: 4.228A pdb=" N VAL R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Proline residue: R 121 - end of helix removed outlier: 3.620A pdb=" N TYR R 125 " --> pdb=" O PRO R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 removed outlier: 3.514A pdb=" N GLY R 140 " --> pdb=" O PHE R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 181 through 199 Processing helix chain 'R' and resid 201 through 206 removed outlier: 4.131A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 201 through 206' Processing helix chain 'R' and resid 229 through 245 removed outlier: 4.185A pdb=" N VAL R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 272 Processing helix chain 'R' and resid 295 through 329 removed outlier: 3.568A pdb=" N ARG R 299 " --> pdb=" O VAL R 295 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG R 306 " --> pdb=" O VAL R 302 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 366 Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 367 through 369 No H-bonds generated for 'chain 'R' and resid 367 through 369' Processing helix chain 'R' and resid 370 through 375 removed outlier: 4.507A pdb=" N ILE R 374 " --> pdb=" O ASN R 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.946A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.720A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.365A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 295 through 308 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.855A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.622A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.694A pdb=" N SER D 55 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 52 through 56' Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing sheet with id=AA1, first strand: chain 'R' and resid 209 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.960A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.862A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.701A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.654A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.588A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.590A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 5.979A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.688A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.700A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.700A pdb=" N GLY D 10 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 130 removed outlier: 3.702A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.692A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1314 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: 1.62 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2828 1.34 - 1.46: 2369 1.46 - 1.59: 3873 1.59 - 1.72: 0 1.72 - 1.84: 90 Bond restraints: 9160 Sorted by residual: bond pdb=" C MET R 120 " pdb=" N PRO R 121 " ideal model delta sigma weight residual 1.336 1.376 -0.041 1.23e-02 6.61e+03 1.09e+01 bond pdb=" CG1 ILE B 80 " pdb=" CD1 ILE B 80 " ideal model delta sigma weight residual 1.513 1.422 0.091 3.90e-02 6.57e+02 5.48e+00 bond pdb=" CB VAL R 159 " pdb=" CG1 VAL R 159 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.02e+00 bond pdb=" CG LEU B 146 " pdb=" CD1 LEU B 146 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.15e+00 bond pdb=" CB VAL R 313 " pdb=" CG2 VAL R 313 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.98e+00 ... (remaining 9155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 12071 2.73 - 5.46: 297 5.46 - 8.20: 36 8.20 - 10.93: 8 10.93 - 13.66: 7 Bond angle restraints: 12419 Sorted by residual: angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 135.20 -13.66 1.91e+00 2.74e-01 5.11e+01 angle pdb=" C SER B 227 " pdb=" N ASP B 228 " pdb=" CA ASP B 228 " ideal model delta sigma weight residual 120.90 127.76 -6.86 1.41e+00 5.03e-01 2.37e+01 angle pdb=" C HIS B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta sigma weight residual 122.46 129.15 -6.69 1.41e+00 5.03e-01 2.25e+01 angle pdb=" CA ARG D 206 " pdb=" CB ARG D 206 " pdb=" CG ARG D 206 " ideal model delta sigma weight residual 114.10 123.03 -8.93 2.00e+00 2.50e-01 1.99e+01 angle pdb=" C TYR D 178 " pdb=" N ARG D 179 " pdb=" CA ARG D 179 " ideal model delta sigma weight residual 122.19 127.99 -5.80 1.41e+00 5.03e-01 1.69e+01 ... (remaining 12414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 5128 16.05 - 32.10: 236 32.10 - 48.16: 42 48.16 - 64.21: 4 64.21 - 80.26: 7 Dihedral angle restraints: 5417 sinusoidal: 2069 harmonic: 3348 Sorted by residual: dihedral pdb=" CB CYS R 141 " pdb=" SG CYS R 141 " pdb=" SG CYS R 224 " pdb=" CB CYS R 224 " ideal model delta sinusoidal sigma weight residual -86.00 -166.26 80.26 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 165.73 -72.73 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 5414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1091 0.068 - 0.136: 282 0.136 - 0.204: 32 0.204 - 0.272: 9 0.272 - 0.340: 4 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CG LEU D 162 " pdb=" CB LEU D 162 " pdb=" CD1 LEU D 162 " pdb=" CD2 LEU D 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CB VAL B 90 " pdb=" CA VAL B 90 " pdb=" CG1 VAL B 90 " pdb=" CG2 VAL B 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB ILE D 100 " pdb=" CA ILE D 100 " pdb=" CG1 ILE D 100 " pdb=" CG2 ILE D 100 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 1415 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 142 " 0.026 2.00e-02 2.50e+03 2.67e-02 1.07e+01 pdb=" CG HIS B 142 " -0.055 2.00e-02 2.50e+03 pdb=" ND1 HIS B 142 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS B 142 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS B 142 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS B 142 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 111 " -0.023 2.00e-02 2.50e+03 1.75e-02 7.67e+00 pdb=" CG TRP D 111 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP D 111 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP D 111 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 111 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 111 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 111 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 111 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 111 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 111 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 227 " -0.006 2.00e-02 2.50e+03 1.71e-02 5.13e+00 pdb=" CG PHE D 227 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE D 227 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 PHE D 227 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 227 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE D 227 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 227 " -0.002 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1880 2.77 - 3.30: 7993 3.30 - 3.84: 14878 3.84 - 4.37: 17205 4.37 - 4.90: 30523 Nonbonded interactions: 72479 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.240 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR D 163 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.270 3.040 nonbonded pdb=" O ILE D 126 " pdb=" OG1 THR D 226 " model vdw 2.286 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.290 3.040 ... (remaining 72474 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=0.00 max=1.00 mean=0.99 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.310 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.010 0.091 9163 Z= 0.427 Angle : 1.084 13.659 12425 Z= 0.579 Chirality : 0.062 0.340 1418 Planarity : 0.006 0.051 1566 Dihedral : 10.142 77.253 3248 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.21 % Allowed : 4.13 % Favored : 95.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -2.70 (0.21), residues: 1132 helix: -1.48 (0.20), residues: 391 sheet: -1.61 (0.28), residues: 286 loop : -2.01 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 314 TYR 0.036 0.004 TYR B 111 PHE 0.037 0.004 PHE A 199 TRP 0.047 0.004 TRP D 111 HIS 0.028 0.004 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.01020 ( 9160) covalent geometry : angle 1.08283 (12419) SS BOND : bond 0.01086 ( 3) SS BOND : angle 2.77691 ( 6) hydrogen bonds : bond 0.17672 ( 457) hydrogen bonds : angle 7.33075 ( 1314) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 223 time to evaluate : 0.362 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 205 PHE cc_start: 0.7011 (p90) cc_final: 0.6554 (m-80) REVERT: R 210 GLN cc_start: 0.8365 (tt0) cc_final: 0.8126 (tt0) REVERT: R 232 THR cc_start: 0.7968 (m) cc_final: 0.7465 (m) REVERT: R 325 MET cc_start: 0.8262 (ttm) cc_final: 0.8001 (ttm) REVERT: A 49 ILE cc_start: 0.8426 (mt) cc_final: 0.8222 (OUTLIER) REVERT: B 12 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8271 (tp30) REVERT: B 170 ASP cc_start: 0.7912 (t70) cc_final: 0.7592 (t70) REVERT: B 188 MET cc_start: 0.8426 (mmm) cc_final: 0.8154 (mmp) REVERT: D 46 GLU cc_start: 0.8046 (tt0) cc_final: 0.7838 (tt0) outliers start: 2 outliers final: 4 residues processed: 225 average time/residue: 0.5856 time to fit residues: 139.8766 Evaluate side-chains 151 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 148 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 24 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.0000 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 255 ASN A 306 GLN B 88 ASN B 91 HIS B 259 GLN B 311 HIS D 130 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.140367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.107208 restraints weight = 13348.898| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.53 r_work: 0.3518 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9163 Z= 0.133 Angle : 0.637 8.291 12425 Z= 0.335 Chirality : 0.043 0.135 1418 Planarity : 0.004 0.043 1566 Dihedral : 5.050 25.791 1252 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.61 % Allowed : 13.21 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -1.06 (0.24), residues: 1132 helix: 0.51 (0.25), residues: 392 sheet: -1.00 (0.28), residues: 292 loop : -1.50 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 13 TYR 0.018 0.002 TYR A 296 PHE 0.012 0.001 PHE R 188 TRP 0.014 0.001 TRP B 99 HIS 0.013 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9160) covalent geometry : angle 0.63722 (12419) SS BOND : bond 0.00458 ( 3) SS BOND : angle 1.03554 ( 6) hydrogen bonds : bond 0.04499 ( 457) hydrogen bonds : angle 5.10715 ( 1314) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.342 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 124 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8386 (mm) REVERT: R 215 ASP cc_start: 0.7266 (t0) cc_final: 0.7052 (p0) REVERT: A 24 ARG cc_start: 0.8142 (mtt180) cc_final: 0.7216 (mtm110) REVERT: A 49 ILE cc_start: 0.8201 (mt) cc_final: 0.7843 (mp) REVERT: A 51 LYS cc_start: 0.8169 (tttt) cc_final: 0.7805 (mmtt) REVERT: A 53 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6799 (mpt) REVERT: B 10 GLU cc_start: 0.7125 (tp30) cc_final: 0.6901 (tp30) REVERT: B 12 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8450 (tm-30) REVERT: B 226 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: B 280 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7980 (tttp) REVERT: C 20 LYS cc_start: 0.8491 (ptmt) cc_final: 0.8094 (pttt) REVERT: D 46 GLU cc_start: 0.8565 (tt0) cc_final: 0.8128 (tt0) REVERT: D 76 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7978 (mptt) outliers start: 35 outliers final: 9 residues processed: 201 average time/residue: 0.5298 time to fit residues: 113.5916 Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 186 LYS Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 96 optimal weight: 0.0870 chunk 34 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 17 optimal weight: 0.0570 chunk 101 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.9678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.138764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.106952 restraints weight = 13228.229| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.45 r_work: 0.3432 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9163 Z= 0.140 Angle : 0.608 8.668 12425 Z= 0.316 Chirality : 0.043 0.154 1418 Planarity : 0.004 0.040 1566 Dihedral : 4.749 26.681 1252 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.92 % Allowed : 15.58 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -0.39 (0.25), residues: 1132 helix: 1.20 (0.26), residues: 395 sheet: -0.84 (0.28), residues: 299 loop : -1.09 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 87 TYR 0.015 0.002 TYR A 296 PHE 0.023 0.002 PHE D 68 TRP 0.011 0.001 TRP B 339 HIS 0.015 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9160) covalent geometry : angle 0.60742 (12419) SS BOND : bond 0.00442 ( 3) SS BOND : angle 1.04870 ( 6) hydrogen bonds : bond 0.04151 ( 457) hydrogen bonds : angle 4.80997 ( 1314) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.216 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: R 102 HIS cc_start: 0.7659 (m90) cc_final: 0.7194 (m90) REVERT: R 354 TYR cc_start: 0.7845 (m-10) cc_final: 0.7630 (m-10) REVERT: A 51 LYS cc_start: 0.8263 (tttt) cc_final: 0.7786 (mmtt) REVERT: A 53 MET cc_start: 0.7279 (mpt) cc_final: 0.6831 (mpt) REVERT: A 205 ARG cc_start: 0.8403 (ttp80) cc_final: 0.8066 (pmm150) REVERT: B 12 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8512 (tm-30) REVERT: B 217 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.7406 (pmm) REVERT: B 219 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.7895 (ttm110) REVERT: B 280 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7885 (tttp) REVERT: C 13 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8084 (ptp90) REVERT: C 20 LYS cc_start: 0.8475 (ptmt) cc_final: 0.8102 (pttt) REVERT: D 46 GLU cc_start: 0.8440 (tt0) cc_final: 0.8028 (tt0) REVERT: D 76 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7953 (mptt) outliers start: 38 outliers final: 11 residues processed: 182 average time/residue: 0.5745 time to fit residues: 110.9536 Evaluate side-chains 151 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 76 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 68 optimal weight: 0.0070 chunk 33 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 294 ASN A 306 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.140226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.108985 restraints weight = 13405.612| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.40 r_work: 0.3468 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9163 Z= 0.121 Angle : 0.596 8.299 12425 Z= 0.305 Chirality : 0.042 0.203 1418 Planarity : 0.003 0.043 1566 Dihedral : 4.525 25.323 1252 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.10 % Allowed : 17.96 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.02 (0.25), residues: 1132 helix: 1.63 (0.26), residues: 394 sheet: -0.65 (0.29), residues: 301 loop : -0.92 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 87 TYR 0.016 0.001 TYR A 296 PHE 0.012 0.001 PHE D 68 TRP 0.010 0.001 TRP B 339 HIS 0.011 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9160) covalent geometry : angle 0.59544 (12419) SS BOND : bond 0.00382 ( 3) SS BOND : angle 0.89198 ( 6) hydrogen bonds : bond 0.03766 ( 457) hydrogen bonds : angle 4.61622 ( 1314) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.319 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 102 HIS cc_start: 0.7667 (m90) cc_final: 0.7146 (m90) REVERT: A 205 ARG cc_start: 0.8363 (ttp80) cc_final: 0.8067 (pmm-80) REVERT: A 244 HIS cc_start: 0.8227 (t70) cc_final: 0.6907 (m90) REVERT: A 336 PHE cc_start: 0.8077 (m-10) cc_final: 0.7752 (m-10) REVERT: B 12 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8533 (tm-30) REVERT: B 217 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7543 (pmm) REVERT: B 219 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.8046 (ttm110) REVERT: B 226 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: B 280 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7789 (tttp) REVERT: B 323 ASP cc_start: 0.8837 (t0) cc_final: 0.8612 (t0) REVERT: C 13 ARG cc_start: 0.8532 (ttm110) cc_final: 0.8265 (ttm110) REVERT: C 20 LYS cc_start: 0.8396 (ptmt) cc_final: 0.7974 (pttt) REVERT: D 46 GLU cc_start: 0.8432 (tt0) cc_final: 0.8021 (tt0) outliers start: 30 outliers final: 12 residues processed: 174 average time/residue: 0.5527 time to fit residues: 102.3796 Evaluate side-chains 161 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 51 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN B 16 ASN ** B 75 GLN ** 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 = 0.3816 r_free = 0.3816 target = 0.131153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.097162 restraints weight = 13814.962| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.53 r_work: 0.3341 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 9163 Z= 0.253 Angle : 0.692 9.500 12425 Z= 0.354 Chirality : 0.046 0.197 1418 Planarity : 0.004 0.048 1566 Dihedral : 4.861 38.155 1252 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.33 % Allowed : 18.27 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: -0.04 (0.25), residues: 1132 helix: 1.43 (0.26), residues: 400 sheet: -0.56 (0.30), residues: 287 loop : -0.93 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 87 TYR 0.025 0.002 TYR B 105 PHE 0.021 0.002 PHE D 68 TRP 0.008 0.001 TRP B 297 HIS 0.017 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 9160) covalent geometry : angle 0.69157 (12419) SS BOND : bond 0.00629 ( 3) SS BOND : angle 1.61075 ( 6) hydrogen bonds : bond 0.04564 ( 457) hydrogen bonds : angle 4.71568 ( 1314) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.341 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 102 HIS cc_start: 0.7787 (m90) cc_final: 0.7035 (m90) REVERT: A 244 HIS cc_start: 0.8276 (OUTLIER) cc_final: 0.6991 (m90) REVERT: A 255 ASN cc_start: 0.8189 (m-40) cc_final: 0.7960 (m110) REVERT: B 142 HIS cc_start: 0.8744 (OUTLIER) cc_final: 0.8471 (t70) REVERT: B 217 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.7614 (pmm) REVERT: B 226 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: B 266 HIS cc_start: 0.8674 (t-90) cc_final: 0.8320 (t-90) REVERT: B 280 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8044 (tttp) REVERT: B 323 ASP cc_start: 0.8945 (t0) cc_final: 0.8615 (t0) REVERT: C 14 LYS cc_start: 0.8296 (tmtp) cc_final: 0.7742 (mtmm) REVERT: C 20 LYS cc_start: 0.8368 (ptmt) cc_final: 0.7999 (pttt) REVERT: D 46 GLU cc_start: 0.8484 (tt0) cc_final: 0.8072 (tt0) outliers start: 42 outliers final: 18 residues processed: 176 average time/residue: 0.5384 time to fit residues: 101.0919 Evaluate side-chains 159 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 314 VAL Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 172 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.136077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.102905 restraints weight = 13642.619| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.51 r_work: 0.3405 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9163 Z= 0.125 Angle : 0.626 9.555 12425 Z= 0.316 Chirality : 0.042 0.255 1418 Planarity : 0.004 0.058 1566 Dihedral : 4.494 27.402 1250 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.10 % Allowed : 20.95 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.26 (0.26), residues: 1132 helix: 1.80 (0.26), residues: 398 sheet: -0.43 (0.30), residues: 297 loop : -0.85 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 13 TYR 0.018 0.001 TYR A 296 PHE 0.012 0.001 PHE D 68 TRP 0.010 0.001 TRP B 99 HIS 0.011 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9160) covalent geometry : angle 0.62571 (12419) SS BOND : bond 0.00409 ( 3) SS BOND : angle 0.94293 ( 6) hydrogen bonds : bond 0.03719 ( 457) hydrogen bonds : angle 4.52101 ( 1314) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.440 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 244 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.6873 (m90) REVERT: A 253 ILE cc_start: 0.8675 (tp) cc_final: 0.8244 (pp) REVERT: B 13 GLN cc_start: 0.8627 (tp40) cc_final: 0.8405 (tp40) REVERT: B 217 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7540 (pmm) REVERT: B 219 ARG cc_start: 0.8264 (mtt-85) cc_final: 0.7977 (ttm110) REVERT: B 226 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: B 280 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7773 (tttp) REVERT: B 323 ASP cc_start: 0.8875 (t0) cc_final: 0.8575 (t0) REVERT: C 11 GLN cc_start: 0.6658 (pm20) cc_final: 0.6386 (pm20) REVERT: C 13 ARG cc_start: 0.8441 (ttm110) cc_final: 0.7991 (mtt180) REVERT: C 14 LYS cc_start: 0.8250 (tmtp) cc_final: 0.7747 (mtmm) REVERT: C 20 LYS cc_start: 0.8343 (ptmt) cc_final: 0.7958 (pttt) REVERT: C 46 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8593 (mmpt) REVERT: D 46 GLU cc_start: 0.8465 (tt0) cc_final: 0.8025 (tt0) outliers start: 30 outliers final: 13 residues processed: 171 average time/residue: 0.5955 time to fit residues: 108.4067 Evaluate side-chains 159 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 306 GLN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.133562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099852 restraints weight = 13779.135| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.55 r_work: 0.3384 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9163 Z= 0.178 Angle : 0.655 8.899 12425 Z= 0.334 Chirality : 0.043 0.182 1418 Planarity : 0.004 0.057 1566 Dihedral : 4.585 33.014 1250 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.10 % Allowed : 22.08 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.28 (0.26), residues: 1132 helix: 1.71 (0.26), residues: 399 sheet: -0.36 (0.30), residues: 303 loop : -0.79 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 13 TYR 0.024 0.002 TYR A 296 PHE 0.014 0.002 PHE D 68 TRP 0.008 0.001 TRP B 339 HIS 0.018 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 9160) covalent geometry : angle 0.65504 (12419) SS BOND : bond 0.00505 ( 3) SS BOND : angle 1.28556 ( 6) hydrogen bonds : bond 0.04008 ( 457) hydrogen bonds : angle 4.53830 ( 1314) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.305 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 102 HIS cc_start: 0.7589 (m90) cc_final: 0.7090 (m90) REVERT: R 210 GLN cc_start: 0.7737 (tt0) cc_final: 0.7239 (tt0) REVERT: A 244 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.6864 (m90) REVERT: A 253 ILE cc_start: 0.8736 (tp) cc_final: 0.8213 (pp) REVERT: B 217 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7628 (pmm) REVERT: B 219 ARG cc_start: 0.8233 (mtt-85) cc_final: 0.7819 (ttm110) REVERT: B 226 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: B 280 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7907 (tttp) REVERT: C 11 GLN cc_start: 0.6625 (pm20) cc_final: 0.6322 (pm20) REVERT: C 14 LYS cc_start: 0.8303 (tmtp) cc_final: 0.7768 (mtmm) REVERT: C 20 LYS cc_start: 0.8349 (ptmt) cc_final: 0.7974 (pttt) REVERT: C 46 LYS cc_start: 0.8940 (mmmm) cc_final: 0.8589 (mmpt) REVERT: C 48 ASP cc_start: 0.8605 (t0) cc_final: 0.8377 (t0) REVERT: D 46 GLU cc_start: 0.8470 (tt0) cc_final: 0.8061 (tt0) outliers start: 30 outliers final: 18 residues processed: 165 average time/residue: 0.5866 time to fit residues: 102.8917 Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 0.0670 chunk 75 optimal weight: 2.9990 chunk 90 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.136363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.103015 restraints weight = 13695.148| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.56 r_work: 0.3382 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9163 Z= 0.133 Angle : 0.634 10.423 12425 Z= 0.322 Chirality : 0.042 0.164 1418 Planarity : 0.004 0.056 1566 Dihedral : 4.406 27.314 1250 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.89 % Allowed : 22.39 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.41 (0.26), residues: 1132 helix: 1.83 (0.26), residues: 398 sheet: -0.18 (0.31), residues: 292 loop : -0.80 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 148 TYR 0.021 0.001 TYR A 296 PHE 0.014 0.001 PHE R 74 TRP 0.009 0.001 TRP B 339 HIS 0.012 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9160) covalent geometry : angle 0.63375 (12419) SS BOND : bond 0.00400 ( 3) SS BOND : angle 0.96359 ( 6) hydrogen bonds : bond 0.03698 ( 457) hydrogen bonds : angle 4.48238 ( 1314) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.339 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 210 GLN cc_start: 0.7638 (tt0) cc_final: 0.7164 (tt0) REVERT: R 358 THR cc_start: 0.8863 (m) cc_final: 0.8660 (m) REVERT: A 205 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8086 (pmm150) REVERT: A 244 HIS cc_start: 0.8146 (OUTLIER) cc_final: 0.6788 (m90) REVERT: A 253 ILE cc_start: 0.8688 (tp) cc_final: 0.8245 (pp) REVERT: B 13 GLN cc_start: 0.8689 (tp40) cc_final: 0.8472 (tp40) REVERT: B 146 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8627 (mp) REVERT: B 215 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7306 (pt0) REVERT: B 217 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7789 (pmm) REVERT: B 219 ARG cc_start: 0.8275 (mtt-85) cc_final: 0.8002 (mtt-85) REVERT: B 226 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8274 (mt-10) REVERT: B 280 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7785 (tttp) REVERT: C 13 ARG cc_start: 0.8210 (ttm-80) cc_final: 0.7914 (mtt180) REVERT: C 14 LYS cc_start: 0.8292 (tmtp) cc_final: 0.7741 (mtmm) REVERT: C 20 LYS cc_start: 0.8276 (ptmt) cc_final: 0.7863 (pttp) REVERT: C 46 LYS cc_start: 0.8874 (mmmm) cc_final: 0.8501 (mmpt) REVERT: C 48 ASP cc_start: 0.8586 (t0) cc_final: 0.8342 (t0) REVERT: D 11 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7244 (mp) REVERT: D 46 GLU cc_start: 0.8422 (tt0) cc_final: 0.8003 (tt0) outliers start: 28 outliers final: 19 residues processed: 170 average time/residue: 0.5630 time to fit residues: 101.9798 Evaluate side-chains 168 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 24 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 306 GLN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.135976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102611 restraints weight = 13710.165| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.56 r_work: 0.3427 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9163 Z= 0.142 Angle : 0.665 11.510 12425 Z= 0.334 Chirality : 0.043 0.233 1418 Planarity : 0.004 0.060 1566 Dihedral : 4.401 28.877 1250 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.89 % Allowed : 23.22 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.44 (0.26), residues: 1132 helix: 1.84 (0.26), residues: 398 sheet: -0.15 (0.31), residues: 292 loop : -0.78 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 148 TYR 0.019 0.001 TYR A 296 PHE 0.018 0.001 PHE R 74 TRP 0.012 0.001 TRP R 316 HIS 0.012 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9160) covalent geometry : angle 0.66519 (12419) SS BOND : bond 0.00439 ( 3) SS BOND : angle 1.02967 ( 6) hydrogen bonds : bond 0.03740 ( 457) hydrogen bonds : angle 4.49026 ( 1314) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.361 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: R 210 GLN cc_start: 0.7488 (tt0) cc_final: 0.7046 (tt0) REVERT: A 205 ARG cc_start: 0.8379 (ttp80) cc_final: 0.8049 (pmm150) REVERT: A 244 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.6701 (m90) REVERT: A 253 ILE cc_start: 0.8647 (tp) cc_final: 0.8163 (pp) REVERT: B 146 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8568 (mp) REVERT: B 219 ARG cc_start: 0.8241 (mtt-85) cc_final: 0.7852 (ttm110) REVERT: B 226 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: B 266 HIS cc_start: 0.8679 (t-90) cc_final: 0.8326 (t-90) REVERT: B 280 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7767 (tttp) REVERT: C 13 ARG cc_start: 0.8280 (ttm-80) cc_final: 0.7907 (mtt180) REVERT: C 14 LYS cc_start: 0.8300 (tmtp) cc_final: 0.7762 (mtmm) REVERT: C 20 LYS cc_start: 0.8270 (ptmt) cc_final: 0.7928 (pttt) REVERT: C 46 LYS cc_start: 0.8893 (mmmm) cc_final: 0.8527 (mmpt) REVERT: C 48 ASP cc_start: 0.8667 (t0) cc_final: 0.8436 (t0) REVERT: D 11 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7180 (mp) REVERT: D 46 GLU cc_start: 0.8377 (tt0) cc_final: 0.7911 (tt0) outliers start: 28 outliers final: 18 residues processed: 162 average time/residue: 0.5790 time to fit residues: 99.8540 Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 144 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.1980 chunk 94 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 60 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.138738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.105763 restraints weight = 13604.404| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.56 r_work: 0.3469 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9163 Z= 0.122 Angle : 0.657 12.943 12425 Z= 0.329 Chirality : 0.042 0.200 1418 Planarity : 0.004 0.064 1566 Dihedral : 4.193 24.074 1248 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.27 % Allowed : 23.63 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.54 (0.26), residues: 1132 helix: 1.93 (0.26), residues: 398 sheet: -0.01 (0.32), residues: 285 loop : -0.80 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 148 TYR 0.015 0.001 TYR A 296 PHE 0.012 0.001 PHE R 74 TRP 0.013 0.001 TRP R 316 HIS 0.010 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9160) covalent geometry : angle 0.65676 (12419) SS BOND : bond 0.00392 ( 3) SS BOND : angle 0.88241 ( 6) hydrogen bonds : bond 0.03520 ( 457) hydrogen bonds : angle 4.40968 ( 1314) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.377 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: R 210 GLN cc_start: 0.7485 (tt0) cc_final: 0.6945 (tt0) REVERT: A 205 ARG cc_start: 0.8305 (ttp80) cc_final: 0.8050 (pmm150) REVERT: A 244 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.6585 (m90) REVERT: A 253 ILE cc_start: 0.8628 (tp) cc_final: 0.8167 (pp) REVERT: B 158 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8156 (p) REVERT: B 219 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7892 (ttm110) REVERT: B 266 HIS cc_start: 0.8676 (t-90) cc_final: 0.8293 (t-90) REVERT: C 13 ARG cc_start: 0.8332 (ttm-80) cc_final: 0.7941 (mtt180) REVERT: C 14 LYS cc_start: 0.8306 (tmtp) cc_final: 0.7764 (mtmm) REVERT: C 20 LYS cc_start: 0.8199 (ptmt) cc_final: 0.7725 (pttp) REVERT: C 46 LYS cc_start: 0.8852 (mmmm) cc_final: 0.8488 (mmpt) REVERT: D 11 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7186 (mp) REVERT: D 46 GLU cc_start: 0.8315 (tt0) cc_final: 0.7811 (tt0) outliers start: 22 outliers final: 16 residues processed: 168 average time/residue: 0.5168 time to fit residues: 92.8528 Evaluate side-chains 161 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 211 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9980 chunk 96 optimal weight: 0.0070 chunk 83 optimal weight: 4.9990 chunk 105 optimal weight: 0.0000 chunk 106 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 79 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 HIS R 229 HIS A 255 ASN A 306 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.139015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.105994 restraints weight = 13418.874| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.56 r_work: 0.3467 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9163 Z= 0.124 Angle : 0.666 13.217 12425 Z= 0.332 Chirality : 0.042 0.160 1418 Planarity : 0.004 0.061 1566 Dihedral : 4.129 24.176 1248 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.58 % Allowed : 24.46 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 aren not related in a simple way. whole: 0.56 (0.26), residues: 1132 helix: 1.88 (0.26), residues: 398 sheet: 0.02 (0.33), residues: 276 loop : -0.71 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 87 TYR 0.014 0.001 TYR A 296 PHE 0.013 0.001 PHE R 74 TRP 0.012 0.001 TRP R 316 HIS 0.009 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9160) covalent geometry : angle 0.66545 (12419) SS BOND : bond 0.00360 ( 3) SS BOND : angle 0.89537 ( 6) hydrogen bonds : bond 0.03565 ( 457) hydrogen bonds : angle 4.40690 ( 1314) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3543.76 seconds wall clock time: 61 minutes 9.49 seconds (3669.49 seconds total)