Starting phenix.real_space_refine on Fri Feb 14 20:40:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6os9_20180/02_2025/6os9_20180.cif Found real_map, /net/cci-nas-00/data/ceres_data/6os9_20180/02_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_20180/02_2025/6os9_20180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6os9_20180/02_2025/6os9_20180.map" model { file = "/net/cci-nas-00/data/ceres_data/6os9_20180/02_2025/6os9_20180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6os9_20180/02_2025/6os9_20180.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.34, per 1000 atoms: 0.60 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: 2.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.98 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: 2.42 Time building geometry restraints manager: 2.42 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: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.730 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.580 ------------------------------------------------------------------------------- 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 9160 Z= 0.668 Angle : 1.083 13.659 12419 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 : 5.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.047 0.004 TRP D 111 HIS 0.028 0.004 HIS B 142 PHE 0.037 0.004 PHE A 199 TYR 0.036 0.004 TYR B 111 ARG 0.010 0.001 ARG B 314 *********************** 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 : 1.033 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: 0.8125 (tt0) REVERT: R 232 THR cc_start: 0.7968 (m) cc_final: 0.7466 (m) REVERT: R 325 MET cc_start: 0.8262 (ttm) cc_final: 0.8000 (ttm) REVERT: A 49 ILE cc_start: 0.8426 (mt) cc_final: 0.8223 (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: 0.8158 (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: 1.2504 time to fit residues: 300.0444 Evaluate side-chains 152 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3998 r_free = 0.3998 target = 0.139357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.106137 restraints weight = 13281.734| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.52 r_work: 0.3439 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9160 Z= 0.199 Angle : 0.644 8.119 12419 Z= 0.339 Chirality : 0.043 0.138 1418 Planarity : 0.004 0.042 1566 Dihedral : 5.088 25.857 1252 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.51 % Allowed : 13.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1132 helix: 0.46 (0.25), residues: 392 sheet: -1.02 (0.28), residues: 292 loop : -1.51 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 111 HIS 0.014 0.001 HIS B 142 PHE 0.012 0.002 PHE R 188 TYR 0.017 0.002 TYR A 296 ARG 0.011 0.001 ARG C 13 *********************** 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 216 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.994 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 124 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8382 (mm) REVERT: R 215 ASP cc_start: 0.7368 (t0) cc_final: 0.7132 (p0) REVERT: A 24 ARG cc_start: 0.8174 (mtt180) cc_final: 0.7253 (mtm110) REVERT: A 49 ILE cc_start: 0.8205 (mt) cc_final: 0.7831 (mp) REVERT: A 51 LYS cc_start: 0.8160 (tttt) cc_final: 0.7769 (mmtt) REVERT: A 53 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6784 (mpt) REVERT: A 298 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7336 (tm-30) REVERT: B 8 ARG cc_start: 0.8334 (mmm-85) cc_final: 0.7949 (mpt180) REVERT: B 10 GLU cc_start: 0.7106 (tp30) cc_final: 0.6850 (tp30) REVERT: B 12 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8453 (tm-30) REVERT: B 226 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: B 280 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8048 (tttp) REVERT: B 294 CYS cc_start: 0.8640 (m) cc_final: 0.8369 (t) REVERT: C 13 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8109 (ptp90) REVERT: C 20 LYS cc_start: 0.8491 (ptmt) cc_final: 0.8109 (pttt) REVERT: D 46 GLU cc_start: 0.8569 (tt0) cc_final: 0.8183 (tt0) REVERT: D 76 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7981 (mptt) outliers start: 34 outliers final: 10 residues processed: 195 average time/residue: 1.2373 time to fit residues: 257.4067 Evaluate side-chains 160 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 311 ASN 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 86 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 85 optimal weight: 0.0870 overall best weight: 1.0162 ------------------------------------------------------------------------------- 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 = 0.138626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.105209 restraints weight = 13383.369| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.51 r_work: 0.3425 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9160 Z= 0.216 Angle : 0.609 8.593 12419 Z= 0.317 Chirality : 0.043 0.152 1418 Planarity : 0.004 0.041 1566 Dihedral : 4.769 27.578 1252 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.82 % Allowed : 15.58 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.25), residues: 1132 helix: 1.20 (0.26), residues: 395 sheet: -0.85 (0.29), residues: 299 loop : -1.09 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 111 HIS 0.016 0.001 HIS B 142 PHE 0.022 0.002 PHE D 68 TYR 0.015 0.001 TYR A 296 ARG 0.008 0.001 ARG D 87 *********************** 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 197 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 1.011 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: 0.7675 (m90) cc_final: 0.7213 (m90) REVERT: R 333 GLN cc_start: 0.8424 (mp10) cc_final: 0.8201 (pm20) REVERT: A 51 LYS cc_start: 0.8271 (tttt) cc_final: 0.7811 (mmtt) REVERT: A 53 MET cc_start: 0.7297 (mpt) cc_final: 0.6850 (mpt) REVERT: A 205 ARG cc_start: 0.8413 (ttp80) cc_final: 0.8075 (pmm150) REVERT: B 12 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8511 (tm-30) REVERT: B 217 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7418 (pmm) REVERT: B 219 ARG cc_start: 0.8277 (mtt-85) cc_final: 0.7899 (ttm110) REVERT: B 280 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7886 (tttp) REVERT: C 13 ARG cc_start: 0.8523 (ttm110) cc_final: 0.8066 (ptp90) REVERT: C 20 LYS cc_start: 0.8484 (ptmt) cc_final: 0.8072 (pttt) REVERT: D 46 GLU cc_start: 0.8467 (tt0) cc_final: 0.8060 (tt0) REVERT: D 76 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7959 (mptt) REVERT: D 90 ASP cc_start: 0.8246 (m-30) cc_final: 0.8030 (m-30) outliers start: 37 outliers final: 9 residues processed: 178 average time/residue: 1.3148 time to fit residues: 248.7437 Evaluate side-chains 149 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 54 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 99 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.138449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.107075 restraints weight = 13257.886| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.37 r_work: 0.3434 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9160 Z= 0.220 Angle : 0.608 8.334 12419 Z= 0.313 Chirality : 0.043 0.150 1418 Planarity : 0.003 0.043 1566 Dihedral : 4.626 28.813 1252 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.51 % Allowed : 17.34 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1132 helix: 1.55 (0.26), residues: 394 sheet: -0.71 (0.29), residues: 301 loop : -0.94 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 111 HIS 0.013 0.001 HIS B 142 PHE 0.015 0.001 PHE D 68 TYR 0.015 0.001 TYR A 296 ARG 0.009 0.001 ARG D 87 *********************** 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 193 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 1.183 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: 0.7770 (m90) cc_final: 0.7197 (m90) REVERT: R 123 GLU cc_start: 0.8039 (tt0) cc_final: 0.7834 (tt0) REVERT: R 188 PHE cc_start: 0.7569 (t80) cc_final: 0.7341 (t80) REVERT: A 51 LYS cc_start: 0.8139 (tttt) cc_final: 0.7645 (mmtt) REVERT: A 205 ARG cc_start: 0.8418 (ttp80) cc_final: 0.8054 (pmm-80) REVERT: A 244 HIS cc_start: 0.8210 (t70) cc_final: 0.6916 (m90) REVERT: B 12 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8482 (tm-30) REVERT: B 217 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7547 (pmm) REVERT: B 219 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7979 (ttm110) REVERT: B 226 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: B 266 HIS cc_start: 0.8713 (t-90) cc_final: 0.8345 (t-90) REVERT: B 280 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7891 (tttp) REVERT: B 323 ASP cc_start: 0.8880 (t0) cc_final: 0.8631 (t0) REVERT: C 13 ARG cc_start: 0.8523 (ttm110) cc_final: 0.8013 (ptp90) REVERT: C 20 LYS cc_start: 0.8390 (ptmt) cc_final: 0.7974 (pttt) REVERT: C 48 ASP cc_start: 0.8472 (t0) cc_final: 0.8236 (t0) REVERT: D 46 GLU cc_start: 0.8464 (tt0) cc_final: 0.8041 (tt0) outliers start: 34 outliers final: 10 residues processed: 176 average time/residue: 1.2154 time to fit residues: 228.3206 Evaluate side-chains 158 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 274 THR Chi-restraints excluded: chain B residue 280 LYS 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 69 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 294 ASN A 306 GLN B 16 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.132436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098594 restraints weight = 13696.550| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.54 r_work: 0.3358 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9160 Z= 0.322 Angle : 0.663 9.377 12419 Z= 0.338 Chirality : 0.045 0.198 1418 Planarity : 0.004 0.046 1566 Dihedral : 4.733 35.257 1250 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.23 % Allowed : 17.65 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1132 helix: 1.49 (0.26), residues: 399 sheet: -0.56 (0.30), residues: 288 loop : -0.88 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 111 HIS 0.015 0.001 HIS B 142 PHE 0.021 0.002 PHE D 68 TYR 0.020 0.002 TYR B 105 ARG 0.010 0.001 ARG D 87 *********************** 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: 41 poor density : 154 time to evaluate : 1.095 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: 0.7742 (m90) cc_final: 0.7010 (m90) REVERT: R 188 PHE cc_start: 0.7586 (t80) cc_final: 0.7291 (t80) REVERT: R 209 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8006 (tm-30) REVERT: A 51 LYS cc_start: 0.8173 (tttt) cc_final: 0.7678 (mmtt) REVERT: A 192 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7890 (mtmm) REVERT: A 244 HIS cc_start: 0.8209 (OUTLIER) cc_final: 0.6915 (m90) REVERT: A 255 ASN cc_start: 0.8165 (m-40) cc_final: 0.7962 (m110) REVERT: B 217 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.7600 (pmm) REVERT: B 219 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.7877 (ttm110) REVERT: B 226 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8260 (mt-10) REVERT: B 266 HIS cc_start: 0.8716 (t-90) cc_final: 0.8289 (t-90) REVERT: B 280 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.8025 (tttp) REVERT: B 323 ASP cc_start: 0.8945 (t0) cc_final: 0.8616 (t0) REVERT: C 14 LYS cc_start: 0.8223 (tmtp) cc_final: 0.7710 (mtmm) REVERT: C 20 LYS cc_start: 0.8339 (ptmt) cc_final: 0.7962 (pttt) REVERT: C 48 ASP cc_start: 0.8670 (t0) cc_final: 0.8449 (t0) REVERT: D 46 GLU cc_start: 0.8498 (tt0) cc_final: 0.8082 (tt0) outliers start: 41 outliers final: 14 residues processed: 177 average time/residue: 1.2406 time to fit residues: 234.5843 Evaluate side-chains 160 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 192 LYS 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 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 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 103 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 0.0980 chunk 106 optimal weight: 0.0170 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 67 optimal weight: 0.2980 overall best weight: 0.4822 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.137093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.103826 restraints weight = 13552.950| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.53 r_work: 0.3397 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9160 Z= 0.173 Angle : 0.618 10.138 12419 Z= 0.312 Chirality : 0.042 0.128 1418 Planarity : 0.004 0.053 1566 Dihedral : 4.386 25.221 1250 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.79 % Allowed : 20.33 % Favored : 76.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.26), residues: 1132 helix: 1.84 (0.26), residues: 398 sheet: -0.39 (0.30), residues: 302 loop : -0.84 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.011 0.001 HIS B 142 PHE 0.013 0.001 PHE D 68 TYR 0.019 0.001 TYR A 296 ARG 0.015 0.001 ARG C 13 *********************** 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 187 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 1.036 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 188 PHE cc_start: 0.7406 (t80) cc_final: 0.7065 (t80) REVERT: A 205 ARG cc_start: 0.8386 (ttp80) cc_final: 0.8073 (pmm150) REVERT: A 244 HIS cc_start: 0.8182 (OUTLIER) cc_final: 0.6866 (m90) REVERT: A 253 ILE cc_start: 0.8637 (tp) cc_final: 0.8234 (pp) REVERT: B 13 GLN cc_start: 0.8629 (tp40) cc_final: 0.8404 (tp40) REVERT: B 217 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7535 (pmm) REVERT: B 219 ARG cc_start: 0.8240 (mtt-85) cc_final: 0.7843 (ttm110) REVERT: B 226 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: B 280 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7767 (tttp) REVERT: B 323 ASP cc_start: 0.8857 (t0) cc_final: 0.8562 (t0) REVERT: C 11 GLN cc_start: 0.6661 (pm20) cc_final: 0.6383 (pm20) REVERT: C 13 ARG cc_start: 0.8464 (ttm110) cc_final: 0.8021 (mtt180) REVERT: C 14 LYS cc_start: 0.8261 (tmtp) cc_final: 0.7727 (mtmm) REVERT: C 20 LYS cc_start: 0.8298 (ptmt) cc_final: 0.7916 (pttt) REVERT: C 46 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8531 (mmpt) REVERT: D 46 GLU cc_start: 0.8455 (tt0) cc_final: 0.7984 (tt0) outliers start: 27 outliers final: 11 residues processed: 173 average time/residue: 1.2524 time to fit residues: 231.0408 Evaluate side-chains 159 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 355 VAL Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain B residue 43 ILE 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 217 MET Chi-restraints excluded: chain B residue 226 GLU 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 51 ILE 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 96 optimal weight: 1.9990 chunk 37 optimal weight: 0.0670 chunk 48 optimal weight: 3.9990 chunk 102 optimal weight: 20.0000 chunk 45 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.136189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.102758 restraints weight = 13670.839| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.56 r_work: 0.3376 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9160 Z= 0.202 Angle : 0.636 12.214 12419 Z= 0.320 Chirality : 0.043 0.294 1418 Planarity : 0.004 0.057 1566 Dihedral : 4.284 28.396 1248 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.20 % Allowed : 20.43 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 1132 helix: 1.83 (0.26), residues: 399 sheet: -0.21 (0.32), residues: 283 loop : -0.76 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.012 0.001 HIS B 142 PHE 0.013 0.001 PHE D 68 TYR 0.022 0.001 TYR A 296 ARG 0.012 0.001 ARG C 13 *********************** 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 181 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 1.027 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 188 PHE cc_start: 0.7374 (t80) cc_final: 0.7047 (t80) REVERT: R 210 GLN cc_start: 0.7591 (tt0) cc_final: 0.7084 (tt0) REVERT: R 358 THR cc_start: 0.8876 (m) cc_final: 0.8662 (m) REVERT: A 205 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8065 (pmm150) REVERT: A 244 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.6818 (m90) REVERT: A 253 ILE cc_start: 0.8662 (tp) cc_final: 0.8196 (pp) REVERT: B 146 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8618 (mp) REVERT: B 217 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7546 (pmm) REVERT: B 219 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7849 (ttm110) REVERT: B 226 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8238 (mt-10) REVERT: B 280 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7741 (tttp) REVERT: C 13 ARG cc_start: 0.8425 (ttm110) cc_final: 0.7966 (mtt180) REVERT: C 14 LYS cc_start: 0.8323 (tmtp) cc_final: 0.7816 (mtmm) REVERT: C 20 LYS cc_start: 0.8288 (ptmt) cc_final: 0.7867 (pttp) REVERT: C 46 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8543 (mmpt) REVERT: C 48 ASP cc_start: 0.8561 (t0) cc_final: 0.8346 (t0) REVERT: D 46 GLU cc_start: 0.8426 (tt0) cc_final: 0.7940 (tt0) outliers start: 31 outliers final: 18 residues processed: 171 average time/residue: 1.2534 time to fit residues: 228.5219 Evaluate side-chains 165 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 117 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 327 THR Chi-restraints excluded: chain B residue 6 GLN 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 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 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 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 84 optimal weight: 0.7980 chunk 17 optimal weight: 0.0040 chunk 111 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 90 optimal weight: 0.1980 chunk 54 optimal weight: 0.4980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.3901 r_free = 0.3901 target = 0.138208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.105050 restraints weight = 13799.161| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.58 r_work: 0.3437 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9160 Z= 0.178 Angle : 0.631 9.693 12419 Z= 0.317 Chirality : 0.042 0.143 1418 Planarity : 0.004 0.055 1566 Dihedral : 4.171 24.865 1248 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.30 % Allowed : 21.47 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1132 helix: 1.93 (0.26), residues: 398 sheet: -0.06 (0.32), residues: 281 loop : -0.75 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.012 0.001 HIS B 142 PHE 0.014 0.001 PHE R 74 TYR 0.021 0.001 TYR A 296 ARG 0.013 0.001 ARG D 148 *********************** 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: 32 poor density : 149 time to evaluate : 1.035 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 188 PHE cc_start: 0.7362 (t80) cc_final: 0.7055 (t80) REVERT: R 210 GLN cc_start: 0.7670 (tt0) cc_final: 0.7194 (tt0) REVERT: A 205 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7947 (pmm-80) REVERT: A 244 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.6800 (m90) REVERT: A 253 ILE cc_start: 0.8667 (tp) cc_final: 0.8270 (pp) REVERT: B 13 GLN cc_start: 0.8654 (tp40) cc_final: 0.8441 (tp40) REVERT: B 217 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.7620 (pmm) REVERT: B 219 ARG cc_start: 0.8298 (mtt-85) cc_final: 0.8003 (ttm110) REVERT: B 226 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: B 266 HIS cc_start: 0.8728 (t-90) cc_final: 0.8376 (t-90) REVERT: C 11 GLN cc_start: 0.6213 (pm20) cc_final: 0.6007 (pm20) REVERT: C 13 ARG cc_start: 0.8442 (ttm110) cc_final: 0.7925 (mtt180) REVERT: C 14 LYS cc_start: 0.8320 (tmtp) cc_final: 0.7807 (mtmm) REVERT: C 20 LYS cc_start: 0.8234 (ptmt) cc_final: 0.7860 (pttp) REVERT: C 46 LYS cc_start: 0.8936 (mmmm) cc_final: 0.8564 (mmpt) REVERT: D 11 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7198 (mp) REVERT: D 46 GLU cc_start: 0.8362 (tt0) cc_final: 0.7870 (tt0) REVERT: D 76 LYS cc_start: 0.8487 (mtmm) cc_final: 0.7841 (pmtt) outliers start: 32 outliers final: 17 residues processed: 168 average time/residue: 1.1976 time to fit residues: 215.2561 Evaluate side-chains 160 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 6 GLN 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 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 274 THR 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 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 11 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.136031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102496 restraints weight = 13681.574| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.59 r_work: 0.3417 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9160 Z= 0.226 Angle : 0.662 11.963 12419 Z= 0.330 Chirality : 0.044 0.274 1418 Planarity : 0.004 0.053 1566 Dihedral : 4.284 30.734 1248 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.51 % Allowed : 21.88 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1132 helix: 1.90 (0.26), residues: 399 sheet: -0.04 (0.32), residues: 290 loop : -0.75 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 339 HIS 0.011 0.001 HIS B 142 PHE 0.015 0.001 PHE R 74 TYR 0.029 0.001 TYR A 296 ARG 0.013 0.001 ARG D 87 *********************** 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 175 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 1.064 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: R 120 MET cc_start: 0.8342 (tpt) cc_final: 0.8039 (tpt) REVERT: R 188 PHE cc_start: 0.7414 (t80) cc_final: 0.7091 (t80) REVERT: R 210 GLN cc_start: 0.7665 (tt0) cc_final: 0.7054 (tt0) REVERT: R 222 LEU cc_start: 0.7862 (mm) cc_final: 0.7549 (mt) REVERT: A 205 ARG cc_start: 0.8348 (ttp80) cc_final: 0.8051 (pmm-80) REVERT: A 244 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.6749 (m90) REVERT: A 253 ILE cc_start: 0.8707 (tp) cc_final: 0.8232 (pp) REVERT: B 13 GLN cc_start: 0.8712 (tp40) cc_final: 0.8469 (tp40) REVERT: B 217 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7517 (pmm) REVERT: B 219 ARG cc_start: 0.8269 (mtt-85) cc_final: 0.7948 (ttm110) REVERT: B 226 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8201 (mt-10) REVERT: B 266 HIS cc_start: 0.8773 (t-90) cc_final: 0.8384 (t-90) REVERT: B 280 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7741 (tttp) REVERT: C 13 ARG cc_start: 0.8410 (ttm110) cc_final: 0.7972 (mtt180) REVERT: C 20 LYS cc_start: 0.8298 (ptmt) cc_final: 0.7947 (pttt) REVERT: C 46 LYS cc_start: 0.8933 (mmmm) cc_final: 0.8560 (mmpt) REVERT: D 11 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7174 (mp) REVERT: D 46 GLU cc_start: 0.8399 (tt0) cc_final: 0.7921 (tt0) REVERT: D 76 LYS cc_start: 0.8521 (mtmm) cc_final: 0.7880 (pmtt) outliers start: 34 outliers final: 21 residues processed: 162 average time/residue: 1.3281 time to fit residues: 230.8913 Evaluate side-chains 162 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 225 THR Chi-restraints excluded: chain R residue 238 GLN 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 283 LEU Chi-restraints excluded: chain B residue 6 GLN 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 234 PHE 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 Chi-restraints excluded: chain D residue 172 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 29 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 60 optimal weight: 0.0570 chunk 12 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 72 optimal weight: 0.0770 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 104 HIS A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.139124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.106023 restraints weight = 13676.494| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.57 r_work: 0.3473 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9160 Z= 0.179 Angle : 0.640 12.584 12419 Z= 0.321 Chirality : 0.042 0.128 1418 Planarity : 0.004 0.061 1566 Dihedral : 4.115 23.455 1248 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.79 % Allowed : 22.60 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1132 helix: 2.00 (0.26), residues: 398 sheet: 0.16 (0.34), residues: 264 loop : -0.73 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 316 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE R 74 TYR 0.025 0.001 TYR A 296 ARG 0.014 0.001 ARG D 148 ********************** 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 180 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.105 Fit side-chains TARDY: cannot create tardy model for: "LYS L 8 " (corrupted residue). Skipping it. REVERT: R 86 PHE cc_start: 0.6701 (t80) cc_final: 0.6489 (t80) REVERT: R 165 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6959 (mt-10) REVERT: R 188 PHE cc_start: 0.7225 (t80) cc_final: 0.6877 (t80) REVERT: R 210 GLN cc_start: 0.7504 (tt0) cc_final: 0.6966 (tt0) REVERT: R 222 LEU cc_start: 0.7567 (mm) cc_final: 0.7362 (tp) REVERT: R 243 MET cc_start: 0.9002 (tpp) cc_final: 0.8790 (tpp) REVERT: R 358 THR cc_start: 0.8832 (m) cc_final: 0.8618 (m) REVERT: A 205 ARG cc_start: 0.8292 (ttp80) cc_final: 0.8055 (pmm-80) REVERT: A 244 HIS cc_start: 0.7941 (OUTLIER) cc_final: 0.6638 (m90) REVERT: A 253 ILE cc_start: 0.8607 (tp) cc_final: 0.8178 (pp) REVERT: B 13 GLN cc_start: 0.8751 (tp40) cc_final: 0.8502 (tp40) REVERT: B 217 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7437 (pmm) REVERT: B 219 ARG cc_start: 0.8266 (mtt-85) cc_final: 0.7895 (ttm110) REVERT: B 266 HIS cc_start: 0.8678 (t-90) cc_final: 0.8249 (t-90) REVERT: B 280 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7482 (tttp) REVERT: B 294 CYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8100 (p) REVERT: C 14 LYS cc_start: 0.8067 (tptp) cc_final: 0.7543 (mtmm) REVERT: C 20 LYS cc_start: 0.8131 (ptmt) cc_final: 0.7717 (pttt) REVERT: C 46 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8521 (mmpt) REVERT: C 48 ASP cc_start: 0.8532 (t0) cc_final: 0.8301 (t0) REVERT: D 6 GLU cc_start: 0.8284 (mp0) cc_final: 0.6984 (mt-10) REVERT: D 11 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7168 (mp) REVERT: D 46 GLU cc_start: 0.8188 (tt0) cc_final: 0.7780 (tt0) outliers start: 27 outliers final: 19 residues processed: 170 average time/residue: 1.1366 time to fit residues: 207.1656 Evaluate side-chains 167 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 R residue 362 ILE Chi-restraints excluded: chain A residue 244 HIS Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 6 GLN 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 234 PHE 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 294 CYS Chi-restraints excluded: chain C residue 16 VAL 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 86 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 229 HIS A 255 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 = 0.3883 r_free = 0.3883 target = 0.136441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.102870 restraints weight = 13745.720| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.57 r_work: 0.3427 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9160 Z= 0.236 Angle : 0.677 10.858 12419 Z= 0.339 Chirality : 0.043 0.193 1418 Planarity : 0.004 0.063 1566 Dihedral : 4.245 31.625 1248 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1132 helix: 1.89 (0.26), residues: 399 sheet: 0.02 (0.32), residues: 290 loop : -0.68 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE D 68 TYR 0.020 0.001 TYR A 296 ARG 0.014 0.001 ARG D 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7602.19 seconds wall clock time: 134 minutes 33.86 seconds (8073.86 seconds total)