Starting phenix.real_space_refine on Thu Jul 2 14:52:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vax_64908/07_2026/9vax_64908.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vax_64908/07_2026/9vax_64908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vax_64908/07_2026/9vax_64908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vax_64908/07_2026/9vax_64908.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vax_64908/07_2026/9vax_64908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vax_64908/07_2026/9vax_64908.map" } resolution = 3.46 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= -0.008 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 61 5.16 5 C 5687 2.51 5 N 1522 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8936 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1747 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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 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: "R" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2386 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 296} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 1.77, per 1000 atoms: 0.20 Number of scatterers: 8936 At special positions: 0 Unit cell: (91.3, 123.117, 131.417, 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 1666 8.00 N 1522 7.00 C 5687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.73 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.51 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.84 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: 0.54 Conformation dependent library (CDL) restraints added in 464.0 milliseconds 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: 28 helices and 14 sheets defined 39.5% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.978A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 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: 3.624A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.371A 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 309 Processing helix chain 'A' and resid 328 through 352 removed outlier: 4.461A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.821A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.529A 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: 3.655A pdb=" N SER D 55 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 3.884A 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 helix chain 'R' and resid 51 through 55 removed outlier: 3.530A pdb=" N LEU R 54 " --> pdb=" O SER R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 91 removed outlier: 4.161A pdb=" N LYS R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 128 Proline residue: R 121 - end of helix removed outlier: 3.503A pdb=" N TYR R 125 " --> pdb=" O PRO R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 172 Processing helix chain 'R' and resid 172 through 180 Processing helix chain 'R' and resid 181 through 200 removed outlier: 3.634A pdb=" N ALA R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 201 through 207 removed outlier: 3.961A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET R 207 " --> pdb=" O MET R 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 201 through 207' Processing helix chain 'R' and resid 229 through 245 removed outlier: 3.888A pdb=" N VAL R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 273 removed outlier: 3.780A pdb=" N ALA R 271 " --> pdb=" O VAL R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 329 Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 365 Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 369 through 375 removed outlier: 4.051A pdb=" N HIS R 373 " --> pdb=" O ALA R 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 9.042A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.880A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.994A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.683A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.566A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.651A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.047A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.425A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.522A pdb=" N THR D 118 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.522A pdb=" N THR D 118 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 130 removed outlier: 3.540A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 136 removed outlier: 7.054A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 182 " --> pdb=" O TYR D 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 209 through 211 472 hydrogen bonds defined for protein. 1335 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: 1.20 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1738 1.33 - 1.45: 2386 1.45 - 1.57: 4908 1.57 - 1.69: 2 1.69 - 1.81: 90 Bond restraints: 9124 Sorted by residual: bond pdb=" CG PHE R 174 " pdb=" CD1 PHE R 174 " ideal model delta sigma weight residual 1.384 1.543 -0.159 2.10e-02 2.27e+03 5.71e+01 bond pdb=" CG PHE R 174 " pdb=" CD2 PHE R 174 " ideal model delta sigma weight residual 1.384 1.266 0.118 2.10e-02 2.27e+03 3.18e+01 bond pdb=" CB MET R 180 " pdb=" CG MET R 180 " ideal model delta sigma weight residual 1.520 1.362 0.158 3.00e-02 1.11e+03 2.78e+01 bond pdb=" CA SER B 161 " pdb=" CB SER B 161 " ideal model delta sigma weight residual 1.530 1.462 0.068 1.49e-02 4.50e+03 2.07e+01 bond pdb=" CA SER B 147 " pdb=" CB SER B 147 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.59e-02 3.96e+03 1.94e+01 ... (remaining 9119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 11462 2.72 - 5.44: 837 5.44 - 8.16: 65 8.16 - 10.88: 5 10.88 - 13.60: 4 Bond angle restraints: 12373 Sorted by residual: angle pdb=" N LEU R 97 " pdb=" CA LEU R 97 " pdb=" C LEU R 97 " ideal model delta sigma weight residual 111.07 99.69 11.38 1.07e+00 8.73e-01 1.13e+02 angle pdb=" N GLN R 95 " pdb=" CA GLN R 95 " pdb=" C GLN R 95 " ideal model delta sigma weight residual 111.69 99.55 12.14 1.23e+00 6.61e-01 9.73e+01 angle pdb=" N GLY A 352 " pdb=" CA GLY A 352 " pdb=" C GLY A 352 " ideal model delta sigma weight residual 115.43 103.74 11.69 1.41e+00 5.03e-01 6.87e+01 angle pdb=" N HIS R 104 " pdb=" CA HIS R 104 " pdb=" C HIS R 104 " ideal model delta sigma weight residual 111.28 103.25 8.03 1.09e+00 8.42e-01 5.43e+01 angle pdb=" CA MET R 180 " pdb=" CB MET R 180 " pdb=" CG MET R 180 " ideal model delta sigma weight residual 114.10 127.70 -13.60 2.00e+00 2.50e-01 4.62e+01 ... (remaining 12368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 5043 16.10 - 32.19: 288 32.19 - 48.29: 53 48.29 - 64.38: 8 64.38 - 80.48: 7 Dihedral angle restraints: 5399 sinusoidal: 2051 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 -164.24 78.24 1 1.00e+01 1.00e-02 7.64e+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 93.00 169.39 -76.39 1 1.00e+01 1.00e-02 7.34e+01 dihedral pdb=" C ARG D 206 " pdb=" N ARG D 206 " pdb=" CA ARG D 206 " pdb=" CB ARG D 206 " ideal model delta harmonic sigma weight residual -122.60 -133.70 11.10 0 2.50e+00 1.60e-01 1.97e+01 ... (remaining 5396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1037 0.096 - 0.192: 318 0.192 - 0.287: 51 0.287 - 0.383: 8 0.383 - 0.478: 3 Chirality restraints: 1417 Sorted by residual: chirality pdb=" CB ILE R 60 " pdb=" CA ILE R 60 " pdb=" CG1 ILE R 60 " pdb=" CG2 ILE R 60 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CG LEU R 71 " pdb=" CB LEU R 71 " pdb=" CD1 LEU R 71 " pdb=" CD2 LEU R 71 " both_signs ideal model delta sigma weight residual False -2.59 -3.06 0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA ASP R 149 " pdb=" N ASP R 149 " pdb=" C ASP R 149 " pdb=" CB ASP R 149 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 ... (remaining 1414 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 174 " -0.018 2.00e-02 2.50e+03 3.81e-02 2.53e+01 pdb=" CG PHE R 174 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 PHE R 174 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE R 174 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE R 174 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 174 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE R 174 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 99 " -0.038 2.00e-02 2.50e+03 2.18e-02 1.18e+01 pdb=" CG TRP B 99 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 99 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 99 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 99 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 99 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP B 99 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 99 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 99 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 99 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 85 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.89e+00 pdb=" C LEU R 85 " -0.052 2.00e-02 2.50e+03 pdb=" O LEU R 85 " 0.020 2.00e-02 2.50e+03 pdb=" N PHE R 86 " 0.017 2.00e-02 2.50e+03 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 564 2.75 - 3.28: 8956 3.28 - 3.82: 14312 3.82 - 4.36: 18068 4.36 - 4.90: 30464 Nonbonded interactions: 72364 Sorted by model distance: nonbonded pdb=" O ASP R 112 " pdb=" OG1 THR R 115 " model vdw 2.207 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.247 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.294 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.338 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.348 3.040 ... (remaining 72359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.510 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 : 0.015 0.805 9127 Z= 0.842 Angle : 1.556 13.807 12379 Z= 1.034 Chirality : 0.093 0.478 1417 Planarity : 0.008 0.057 1560 Dihedral : 11.075 80.479 3230 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.04 % Allowed : 5.30 % Favored : 93.66 % Cbeta Deviations : 0.19 % 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 are not related in a simple way. whole: -0.20 (0.23), residues: 1132 helix: 0.97 (0.23), residues: 395 sheet: -0.19 (0.31), residues: 267 loop : -0.99 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.004 ARG D 18 TYR 0.020 0.005 TYR R 364 PHE 0.083 0.005 PHE R 174 TRP 0.043 0.007 TRP B 99 HIS 0.022 0.004 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00939 / 0.58 ( 9124) covalent geometry : angle 1.54668 / 1.03 (12373) SS BOND : bond 0.67302 / 30.24 ( 3) SS BOND : angle 7.68674 / 3.60 ( 6) hydrogen bonds : bond 0.19154 / 13.19 ( 466) hydrogen bonds : angle 7.55821 / 5.39 ( 1335) *********************** 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 396 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 386 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.9241 (m-40) cc_final: 0.8487 (m-40) REVERT: A 24 ARG cc_start: 0.8585 (mtt180) cc_final: 0.7932 (mtm180) REVERT: A 39 LEU cc_start: 0.8855 (mt) cc_final: 0.8604 (mt) REVERT: A 52 GLN cc_start: 0.9547 (tp40) cc_final: 0.8758 (tm-30) REVERT: A 255 ASN cc_start: 0.8464 (m-40) cc_final: 0.7939 (m110) REVERT: A 256 ASN cc_start: 0.8968 (t0) cc_final: 0.8690 (t0) REVERT: A 287 TYR cc_start: 0.9240 (m-10) cc_final: 0.9005 (m-80) REVERT: A 302 TYR cc_start: 0.8674 (t80) cc_final: 0.8439 (t80) REVERT: A 304 GLN cc_start: 0.9207 (tt0) cc_final: 0.8379 (tt0) REVERT: A 325 CYS cc_start: 0.7896 (m) cc_final: 0.7660 (t) REVERT: A 350 ASP cc_start: 0.9121 (m-30) cc_final: 0.8408 (m-30) REVERT: B 14 LEU cc_start: 0.9834 (mt) cc_final: 0.9255 (mt) REVERT: B 19 ARG cc_start: 0.9842 (ppp80) cc_final: 0.9640 (ttp80) REVERT: B 51 LEU cc_start: 0.8853 (mt) cc_final: 0.8486 (mp) REVERT: B 339 TRP cc_start: 0.8639 (m100) cc_final: 0.7623 (m100) REVERT: C 18 GLN cc_start: 0.9611 (tp-100) cc_final: 0.9135 (tp-100) REVERT: C 19 LEU cc_start: 0.9874 (mt) cc_final: 0.9450 (mp) REVERT: C 21 MET cc_start: 0.9585 (tmm) cc_final: 0.9372 (tmm) REVERT: C 25 ILE cc_start: 0.9249 (mm) cc_final: 0.9011 (mm) REVERT: D 12 VAL cc_start: 0.9001 (t) cc_final: 0.8633 (m) REVERT: D 113 GLN cc_start: 0.9274 (mt0) cc_final: 0.9031 (mp10) REVERT: D 117 LEU cc_start: 0.9320 (tt) cc_final: 0.8988 (mm) REVERT: D 137 VAL cc_start: 0.8697 (t) cc_final: 0.8456 (t) REVERT: D 221 LEU cc_start: 0.8900 (tp) cc_final: 0.8632 (tp) REVERT: D 232 LYS cc_start: 0.9293 (tttt) cc_final: 0.9085 (ttpp) REVERT: R 70 TYR cc_start: 0.9244 (m-10) cc_final: 0.8969 (m-80) REVERT: R 73 LEU cc_start: 0.9678 (mt) cc_final: 0.9361 (pp) REVERT: R 151 CYS cc_start: 0.9319 (m) cc_final: 0.8979 (p) REVERT: R 356 SER cc_start: 0.9510 (OUTLIER) cc_final: 0.9254 (p) REVERT: R 364 TYR cc_start: 0.7834 (m-80) cc_final: 0.7595 (m-80) outliers start: 10 outliers final: 3 residues processed: 391 average time/residue: 0.0979 time to fit residues: 49.9723 Evaluate side-chains 219 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 215 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain R residue 356 SER Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN A 244 HIS A 294 ASN A 331 ASN B 75 GLN B 91 HIS B 311 HIS D 130 GLN ** D 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN R 126 ASN ** R 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 240 ASN R 343 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.077268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.056697 restraints weight = 33595.549| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 4.57 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9127 Z= 0.170 Angle : 0.762 10.639 12379 Z= 0.394 Chirality : 0.046 0.178 1417 Planarity : 0.004 0.041 1560 Dihedral : 5.491 46.446 1252 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.74 % Allowed : 16.01 % Favored : 80.25 % 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 are not related in a simple way. whole: -0.04 (0.24), residues: 1132 helix: 1.17 (0.24), residues: 399 sheet: -0.22 (0.31), residues: 277 loop : -0.91 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 21 TYR 0.024 0.002 TYR R 339 PHE 0.033 0.002 PHE R 345 TRP 0.023 0.002 TRP R 134 HIS 0.009 0.001 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 ( 9124) covalent geometry : angle 0.76218 / 0.39 (12373) SS BOND : bond 0.00428 / 0.21 ( 3) SS BOND : angle 1.26333 / 0.66 ( 6) hydrogen bonds : bond 0.05446 / 3.71 ( 466) hydrogen bonds : angle 5.67826 / 4.04 ( 1335) *********************** 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 275 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.9113 (m110) cc_final: 0.8674 (m110) REVERT: A 24 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7528 (mtm180) REVERT: A 29 LYS cc_start: 0.9275 (tptm) cc_final: 0.8983 (tppt) REVERT: A 52 GLN cc_start: 0.9516 (tp40) cc_final: 0.8822 (tm-30) REVERT: A 205 ARG cc_start: 0.8898 (ptp-110) cc_final: 0.8614 (ptp-110) REVERT: A 242 ARG cc_start: 0.9339 (mtt180) cc_final: 0.8834 (ttm-80) REVERT: A 256 ASN cc_start: 0.9106 (t0) cc_final: 0.8695 (t0) REVERT: A 287 TYR cc_start: 0.8443 (m-10) cc_final: 0.7618 (m-80) REVERT: B 19 ARG cc_start: 0.9728 (ppp80) cc_final: 0.9348 (ttp80) REVERT: B 20 ASP cc_start: 0.9579 (OUTLIER) cc_final: 0.8967 (m-30) REVERT: B 45 MET cc_start: 0.8756 (mtm) cc_final: 0.8532 (mmt) REVERT: B 55 LEU cc_start: 0.8835 (mt) cc_final: 0.8338 (pp) REVERT: B 72 SER cc_start: 0.9487 (OUTLIER) cc_final: 0.9188 (p) REVERT: B 188 MET cc_start: 0.8831 (mmt) cc_final: 0.8501 (mmm) REVERT: B 226 GLU cc_start: 0.8949 (mp0) cc_final: 0.8728 (mp0) REVERT: B 262 MET cc_start: 0.9403 (tpt) cc_final: 0.9107 (tpp) REVERT: B 292 PHE cc_start: 0.9192 (m-10) cc_final: 0.8814 (m-10) REVERT: B 339 TRP cc_start: 0.8620 (m100) cc_final: 0.6897 (m100) REVERT: C 15 LEU cc_start: 0.9806 (mt) cc_final: 0.9537 (pp) REVERT: C 16 VAL cc_start: 0.9855 (p) cc_final: 0.9402 (m) REVERT: C 17 GLU cc_start: 0.9588 (tp30) cc_final: 0.9222 (mm-30) REVERT: C 18 GLN cc_start: 0.9532 (tp-100) cc_final: 0.9098 (tp-100) REVERT: C 20 LYS cc_start: 0.9503 (ptpt) cc_final: 0.9060 (pttm) REVERT: C 21 MET cc_start: 0.9253 (tmm) cc_final: 0.9051 (tmm) REVERT: C 29 LYS cc_start: 0.9383 (mmmt) cc_final: 0.8932 (tppt) REVERT: C 46 LYS cc_start: 0.9568 (tppt) cc_final: 0.9361 (tppp) REVERT: D 18 ARG cc_start: 0.8940 (tpp80) cc_final: 0.7662 (tpp80) REVERT: D 117 LEU cc_start: 0.9549 (tt) cc_final: 0.8751 (mm) REVERT: D 151 LYS cc_start: 0.8118 (tptp) cc_final: 0.7854 (tptp) REVERT: D 168 ARG cc_start: 0.9295 (mmt-90) cc_final: 0.8992 (mmp80) REVERT: D 219 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8229 (pp30) REVERT: L 12 ILE cc_start: 0.7659 (mp) cc_final: 0.7225 (mm) REVERT: R 73 LEU cc_start: 0.9728 (mt) cc_final: 0.9425 (pp) REVERT: R 149 ASP cc_start: 0.8828 (t0) cc_final: 0.7679 (t70) REVERT: R 151 CYS cc_start: 0.9410 (m) cc_final: 0.9025 (t) REVERT: R 180 MET cc_start: 0.8243 (mtp) cc_final: 0.7825 (mtp) REVERT: R 203 MET cc_start: 0.8463 (tpp) cc_final: 0.8039 (tpp) REVERT: R 207 MET cc_start: 0.8054 (tpt) cc_final: 0.7735 (tpt) REVERT: R 243 MET cc_start: 0.9215 (tpp) cc_final: 0.8869 (mmm) REVERT: R 249 MET cc_start: 0.9140 (tpp) cc_final: 0.8920 (mmt) REVERT: R 266 MET cc_start: 0.9311 (mmm) cc_final: 0.9064 (mmm) REVERT: R 359 ILE cc_start: 0.9299 (pt) cc_final: 0.9091 (pt) outliers start: 36 outliers final: 15 residues processed: 261 average time/residue: 0.0923 time to fit residues: 31.6862 Evaluate side-chains 209 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 234 LYS Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 363 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 90 optimal weight: 30.0000 chunk 109 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 60 optimal weight: 30.0000 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 343 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.071978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.052056 restraints weight = 34403.124| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 4.38 r_work: 0.2881 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 9127 Z= 0.335 Angle : 0.797 10.282 12379 Z= 0.416 Chirality : 0.048 0.164 1417 Planarity : 0.005 0.046 1560 Dihedral : 5.605 39.975 1249 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.09 % Allowed : 17.26 % Favored : 77.65 % 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 are not related in a simple way. whole: -0.22 (0.24), residues: 1132 helix: 0.89 (0.25), residues: 402 sheet: -0.14 (0.30), residues: 277 loop : -1.01 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 8 TYR 0.021 0.002 TYR A 287 PHE 0.043 0.003 PHE A 336 TRP 0.016 0.002 TRP R 193 HIS 0.007 0.002 HIS R 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00726 / 0.34 ( 9124) covalent geometry : angle 0.79697 / 0.42 (12373) SS BOND : bond 0.00762 / 0.38 ( 3) SS BOND : angle 1.43731 / 0.74 ( 6) hydrogen bonds : bond 0.05343 / 3.62 ( 466) hydrogen bonds : angle 5.76916 / 4.10 ( 1335) *********************** 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 227 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8828 (ttp) REVERT: A 22 ASN cc_start: 0.9206 (m110) cc_final: 0.8686 (m110) REVERT: A 24 ARG cc_start: 0.8490 (mtt180) cc_final: 0.8023 (mtm180) REVERT: A 29 LYS cc_start: 0.9313 (tptm) cc_final: 0.9035 (tppt) REVERT: A 37 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8396 (tp) REVERT: A 52 GLN cc_start: 0.9631 (tp40) cc_final: 0.8957 (tm-30) REVERT: A 205 ARG cc_start: 0.9380 (ptp-110) cc_final: 0.9071 (ptp-110) REVERT: A 242 ARG cc_start: 0.9465 (mtt180) cc_final: 0.8968 (ttm110) REVERT: A 256 ASN cc_start: 0.9213 (t0) cc_final: 0.8915 (t0) REVERT: B 12 GLU cc_start: 0.9722 (tp30) cc_final: 0.9493 (tm-30) REVERT: B 33 ILE cc_start: 0.9691 (OUTLIER) cc_final: 0.9113 (tt) REVERT: B 142 HIS cc_start: 0.7587 (OUTLIER) cc_final: 0.7365 (t-90) REVERT: B 226 GLU cc_start: 0.9003 (mp0) cc_final: 0.8692 (mp0) REVERT: B 252 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9300 (pp) REVERT: B 262 MET cc_start: 0.9431 (tpt) cc_final: 0.9065 (tpp) REVERT: B 292 PHE cc_start: 0.9199 (m-10) cc_final: 0.8765 (m-10) REVERT: B 339 TRP cc_start: 0.9004 (m100) cc_final: 0.7281 (m100) REVERT: C 16 VAL cc_start: 0.9889 (p) cc_final: 0.9457 (m) REVERT: C 18 GLN cc_start: 0.9615 (tp-100) cc_final: 0.9162 (tp-100) REVERT: C 21 MET cc_start: 0.9426 (tmm) cc_final: 0.9224 (tmm) REVERT: C 29 LYS cc_start: 0.9456 (mmmt) cc_final: 0.9106 (tppt) REVERT: C 41 CYS cc_start: 0.9486 (m) cc_final: 0.9280 (t) REVERT: D 18 ARG cc_start: 0.9174 (tpp80) cc_final: 0.8966 (tpp80) REVERT: D 151 LYS cc_start: 0.8050 (tptp) cc_final: 0.7752 (tptp) REVERT: D 168 ARG cc_start: 0.9334 (mmt-90) cc_final: 0.8999 (mmt-90) REVERT: L 12 ILE cc_start: 0.8127 (mp) cc_final: 0.7845 (mm) REVERT: R 131 HIS cc_start: 0.7516 (OUTLIER) cc_final: 0.6752 (m170) REVERT: R 203 MET cc_start: 0.8439 (tpp) cc_final: 0.7793 (tpp) REVERT: R 207 MET cc_start: 0.8240 (tpt) cc_final: 0.7583 (tpt) REVERT: R 266 MET cc_start: 0.9368 (mmm) cc_final: 0.9088 (mmm) outliers start: 49 outliers final: 32 residues processed: 213 average time/residue: 0.0964 time to fit residues: 27.0057 Evaluate side-chains 205 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 163 SER Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 324 LEU Chi-restraints excluded: chain R residue 363 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 0.4980 chunk 15 optimal weight: 40.0000 chunk 104 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS ** R 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.073845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.053904 restraints weight = 33686.955| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 4.43 r_work: 0.2942 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9127 Z= 0.172 Angle : 0.725 10.258 12379 Z= 0.367 Chirality : 0.045 0.248 1417 Planarity : 0.004 0.049 1560 Dihedral : 5.220 39.501 1249 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.16 % Allowed : 18.81 % Favored : 77.03 % 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 are not related in a simple way. whole: -0.06 (0.24), residues: 1132 helix: 0.95 (0.25), residues: 406 sheet: 0.19 (0.32), residues: 256 loop : -0.99 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 208 TYR 0.019 0.002 TYR D 94 PHE 0.030 0.001 PHE A 336 TRP 0.014 0.002 TRP B 339 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 9124) covalent geometry : angle 0.72446 / 0.37 (12373) SS BOND : bond 0.00502 / 0.25 ( 3) SS BOND : angle 0.94209 / 0.48 ( 6) hydrogen bonds : bond 0.04720 / 3.23 ( 466) hydrogen bonds : angle 5.43226 / 3.84 ( 1335) *********************** 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 229 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.9149 (ttp) cc_final: 0.8801 (ttp) REVERT: A 22 ASN cc_start: 0.9207 (m110) cc_final: 0.8536 (m110) REVERT: A 24 ARG cc_start: 0.8482 (mtt180) cc_final: 0.7909 (mtm180) REVERT: A 29 LYS cc_start: 0.9281 (tptm) cc_final: 0.8998 (tppt) REVERT: A 37 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8257 (tp) REVERT: A 52 GLN cc_start: 0.9636 (tp40) cc_final: 0.8884 (tm-30) REVERT: A 205 ARG cc_start: 0.9296 (ptp-110) cc_final: 0.9019 (ptp-110) REVERT: A 242 ARG cc_start: 0.9414 (mtt180) cc_final: 0.8968 (ttm-80) REVERT: A 256 ASN cc_start: 0.9192 (t0) cc_final: 0.8874 (t0) REVERT: A 302 TYR cc_start: 0.9119 (t80) cc_final: 0.8904 (t80) REVERT: B 12 GLU cc_start: 0.9739 (tp30) cc_final: 0.9517 (tm-30) REVERT: B 19 ARG cc_start: 0.9754 (ppp80) cc_final: 0.9536 (ttp80) REVERT: B 55 LEU cc_start: 0.8966 (mt) cc_final: 0.8484 (pp) REVERT: B 226 GLU cc_start: 0.9095 (mp0) cc_final: 0.8717 (mp0) REVERT: B 234 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8961 (m-80) REVERT: B 252 LEU cc_start: 0.9498 (OUTLIER) cc_final: 0.9283 (pp) REVERT: B 262 MET cc_start: 0.9493 (tpt) cc_final: 0.9059 (tpp) REVERT: B 292 PHE cc_start: 0.9157 (m-10) cc_final: 0.8693 (m-10) REVERT: B 339 TRP cc_start: 0.8895 (m100) cc_final: 0.7526 (m100) REVERT: C 15 LEU cc_start: 0.9824 (mt) cc_final: 0.9614 (pp) REVERT: C 18 GLN cc_start: 0.9576 (tp-100) cc_final: 0.9118 (tp-100) REVERT: C 21 MET cc_start: 0.9371 (tmm) cc_final: 0.9159 (tmm) REVERT: C 29 LYS cc_start: 0.9438 (mmmt) cc_final: 0.9214 (tppt) REVERT: C 41 CYS cc_start: 0.9530 (m) cc_final: 0.9277 (t) REVERT: D 12 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8673 (m) REVERT: D 18 ARG cc_start: 0.9134 (tpp80) cc_final: 0.8919 (tpp80) REVERT: D 93 MET cc_start: 0.9187 (tpp) cc_final: 0.8736 (tpp) REVERT: D 151 LYS cc_start: 0.8054 (tptp) cc_final: 0.7768 (tptp) REVERT: L 12 ILE cc_start: 0.7910 (mp) cc_final: 0.7576 (mm) REVERT: R 98 GLN cc_start: 0.9562 (mm-40) cc_final: 0.9340 (mm-40) REVERT: R 149 ASP cc_start: 0.9064 (t70) cc_final: 0.8000 (t70) REVERT: R 151 CYS cc_start: 0.9657 (m) cc_final: 0.8902 (t) REVERT: R 203 MET cc_start: 0.8326 (tpp) cc_final: 0.7884 (tpp) REVERT: R 207 MET cc_start: 0.8107 (tpt) cc_final: 0.7655 (tpt) REVERT: R 266 MET cc_start: 0.9384 (mmm) cc_final: 0.9066 (mmm) REVERT: R 347 MET cc_start: 0.9473 (ptp) cc_final: 0.9225 (ptp) REVERT: R 350 ASN cc_start: 0.8877 (m-40) cc_final: 0.8410 (m110) outliers start: 40 outliers final: 22 residues processed: 218 average time/residue: 0.0931 time to fit residues: 26.6045 Evaluate side-chains 202 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain R residue 362 ILE Chi-restraints excluded: chain R residue 363 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS ** R 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.074658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.054859 restraints weight = 33464.848| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 4.44 r_work: 0.2953 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.5551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9127 Z= 0.152 Angle : 0.700 12.702 12379 Z= 0.354 Chirality : 0.045 0.167 1417 Planarity : 0.004 0.051 1560 Dihedral : 5.025 38.039 1249 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.37 % Allowed : 19.13 % Favored : 76.51 % 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 are not related in a simple way. whole: -0.03 (0.25), residues: 1132 helix: 0.82 (0.25), residues: 411 sheet: 0.13 (0.31), residues: 272 loop : -0.82 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 208 TYR 0.016 0.002 TYR D 103 PHE 0.028 0.001 PHE R 345 TRP 0.024 0.002 TRP R 134 HIS 0.004 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 9124) covalent geometry : angle 0.70033 / 0.35 (12373) SS BOND : bond 0.00550 / 0.27 ( 3) SS BOND : angle 0.72848 / 0.38 ( 6) hydrogen bonds : bond 0.04397 / 3.01 ( 466) hydrogen bonds : angle 5.30588 / 3.72 ( 1335) *********************** 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 239 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.9139 (ttp) cc_final: 0.8623 (ttp) REVERT: A 22 ASN cc_start: 0.9116 (m110) cc_final: 0.8412 (m110) REVERT: A 24 ARG cc_start: 0.8463 (mtt180) cc_final: 0.7814 (mtm180) REVERT: A 29 LYS cc_start: 0.9273 (tptm) cc_final: 0.9059 (tppt) REVERT: A 52 GLN cc_start: 0.9638 (tp40) cc_final: 0.8966 (tm-30) REVERT: A 205 ARG cc_start: 0.9266 (ptp-110) cc_final: 0.9006 (ptp-110) REVERT: A 242 ARG cc_start: 0.9422 (mtt180) cc_final: 0.8851 (ttm-80) REVERT: A 256 ASN cc_start: 0.9201 (t0) cc_final: 0.8866 (t0) REVERT: A 302 TYR cc_start: 0.9115 (t80) cc_final: 0.8907 (t80) REVERT: B 12 GLU cc_start: 0.9747 (tp30) cc_final: 0.9525 (tm-30) REVERT: B 19 ARG cc_start: 0.9739 (ppp80) cc_final: 0.9510 (ttp80) REVERT: B 124 TYR cc_start: 0.8898 (m-80) cc_final: 0.8374 (m-10) REVERT: B 226 GLU cc_start: 0.9181 (mp0) cc_final: 0.8771 (mp0) REVERT: B 234 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8964 (m-80) REVERT: B 262 MET cc_start: 0.9478 (tpt) cc_final: 0.9045 (tpp) REVERT: B 292 PHE cc_start: 0.9142 (m-10) cc_final: 0.8630 (m-10) REVERT: B 339 TRP cc_start: 0.8876 (m100) cc_final: 0.7383 (m100) REVERT: C 17 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8655 (mm-30) REVERT: C 18 GLN cc_start: 0.9599 (tp-100) cc_final: 0.9073 (tp-100) REVERT: C 41 CYS cc_start: 0.9545 (m) cc_final: 0.9297 (m) REVERT: D 12 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8754 (m) REVERT: D 18 ARG cc_start: 0.8928 (tpp80) cc_final: 0.8630 (tpp80) REVERT: D 79 LEU cc_start: 0.9269 (tp) cc_final: 0.9017 (tp) REVERT: D 151 LYS cc_start: 0.8163 (tptp) cc_final: 0.7910 (tptp) REVERT: L 12 ILE cc_start: 0.7917 (mp) cc_final: 0.7673 (mm) REVERT: R 98 GLN cc_start: 0.9615 (mm-40) cc_final: 0.9371 (mm-40) REVERT: R 102 HIS cc_start: 0.9312 (m90) cc_final: 0.8987 (m90) REVERT: R 151 CYS cc_start: 0.9664 (m) cc_final: 0.8927 (t) REVERT: R 203 MET cc_start: 0.8346 (tpp) cc_final: 0.7939 (tpp) REVERT: R 266 MET cc_start: 0.9368 (mmm) cc_final: 0.9008 (mmm) REVERT: R 347 MET cc_start: 0.9459 (ptp) cc_final: 0.9034 (ppp) REVERT: R 350 ASN cc_start: 0.8925 (m-40) cc_final: 0.8459 (m110) outliers start: 42 outliers final: 22 residues processed: 226 average time/residue: 0.0989 time to fit residues: 29.3988 Evaluate side-chains 192 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 362 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 93 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 HIS A 294 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.074438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054502 restraints weight = 33817.238| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.50 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9127 Z= 0.149 Angle : 0.750 14.972 12379 Z= 0.367 Chirality : 0.044 0.168 1417 Planarity : 0.004 0.052 1560 Dihedral : 4.919 35.953 1249 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.33 % Allowed : 21.31 % Favored : 75.36 % 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 are not related in a simple way. whole: 0.08 (0.25), residues: 1132 helix: 0.97 (0.25), residues: 400 sheet: 0.27 (0.31), residues: 269 loop : -0.82 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 182 TYR 0.016 0.002 TYR D 103 PHE 0.028 0.001 PHE R 345 TRP 0.029 0.002 TRP R 134 HIS 0.003 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 9124) covalent geometry : angle 0.75019 / 0.37 (12373) SS BOND : bond 0.00412 / 0.21 ( 3) SS BOND : angle 0.78850 / 0.40 ( 6) hydrogen bonds : bond 0.04355 / 2.98 ( 466) hydrogen bonds : angle 5.19166 / 3.66 ( 1335) *********************** 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 219 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.8914 (ttp) cc_final: 0.8338 (ttp) REVERT: A 22 ASN cc_start: 0.8963 (m110) cc_final: 0.8255 (m110) REVERT: A 24 ARG cc_start: 0.8250 (mtt180) cc_final: 0.7497 (mtm180) REVERT: A 32 ARG cc_start: 0.8250 (ptp-110) cc_final: 0.8027 (mtm110) REVERT: A 52 GLN cc_start: 0.9593 (tp40) cc_final: 0.8932 (tm-30) REVERT: A 242 ARG cc_start: 0.9253 (mtt180) cc_final: 0.8704 (ttm-80) REVERT: A 256 ASN cc_start: 0.9109 (t0) cc_final: 0.8766 (t0) REVERT: B 10 GLU cc_start: 0.9590 (tp30) cc_final: 0.9267 (tp30) REVERT: B 12 GLU cc_start: 0.9712 (tp30) cc_final: 0.9489 (tm-30) REVERT: B 19 ARG cc_start: 0.9651 (ppp80) cc_final: 0.9379 (ttp80) REVERT: B 124 TYR cc_start: 0.8852 (m-80) cc_final: 0.8327 (m-10) REVERT: B 138 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8287 (mm-30) REVERT: B 172 GLU cc_start: 0.9197 (mp0) cc_final: 0.8979 (pm20) REVERT: B 226 GLU cc_start: 0.9083 (mp0) cc_final: 0.8637 (mp0) REVERT: B 234 PHE cc_start: 0.9171 (OUTLIER) cc_final: 0.8967 (m-80) REVERT: B 262 MET cc_start: 0.9325 (tpt) cc_final: 0.8846 (tpp) REVERT: B 280 LYS cc_start: 0.9382 (tttt) cc_final: 0.8968 (ttmt) REVERT: B 292 PHE cc_start: 0.9115 (m-10) cc_final: 0.8558 (m-10) REVERT: B 339 TRP cc_start: 0.8534 (m100) cc_final: 0.6947 (m100) REVERT: C 15 LEU cc_start: 0.9827 (mt) cc_final: 0.9612 (pp) REVERT: C 16 VAL cc_start: 0.9692 (m) cc_final: 0.9458 (p) REVERT: C 17 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8298 (mm-30) REVERT: C 20 LYS cc_start: 0.9173 (pttm) cc_final: 0.8697 (pttm) REVERT: C 21 MET cc_start: 0.8916 (tmm) cc_final: 0.8369 (tmm) REVERT: C 41 CYS cc_start: 0.9430 (m) cc_final: 0.9217 (m) REVERT: D 18 ARG cc_start: 0.8817 (tpp80) cc_final: 0.8615 (tpp80) REVERT: D 93 MET cc_start: 0.9102 (tpp) cc_final: 0.8592 (tpp) REVERT: D 151 LYS cc_start: 0.7902 (tptp) cc_final: 0.7684 (tptp) REVERT: L 12 ILE cc_start: 0.7998 (mp) cc_final: 0.7640 (mm) REVERT: R 98 GLN cc_start: 0.9520 (mm-40) cc_final: 0.9230 (mm-40) REVERT: R 102 HIS cc_start: 0.9087 (m90) cc_final: 0.8671 (m90) REVERT: R 131 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.6576 (m170) REVERT: R 151 CYS cc_start: 0.9595 (m) cc_final: 0.8859 (t) REVERT: R 180 MET cc_start: 0.8657 (mtp) cc_final: 0.8065 (mtp) REVERT: R 203 MET cc_start: 0.8339 (tpp) cc_final: 0.8046 (tpp) REVERT: R 207 MET cc_start: 0.8370 (tpt) cc_final: 0.6229 (tpt) REVERT: R 249 MET cc_start: 0.8704 (mmt) cc_final: 0.8377 (tpt) REVERT: R 266 MET cc_start: 0.9373 (mmm) cc_final: 0.8997 (mmm) REVERT: R 343 HIS cc_start: 0.8770 (m170) cc_final: 0.8569 (m170) REVERT: R 347 MET cc_start: 0.9437 (ptp) cc_final: 0.9078 (ppp) outliers start: 32 outliers final: 22 residues processed: 210 average time/residue: 0.0917 time to fit residues: 25.8137 Evaluate side-chains 195 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 113 LEU Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 362 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 50.0000 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.075273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.055513 restraints weight = 34033.176| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 4.56 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9127 Z= 0.139 Angle : 0.776 14.572 12379 Z= 0.376 Chirality : 0.045 0.276 1417 Planarity : 0.004 0.052 1560 Dihedral : 4.851 35.495 1249 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.81 % Allowed : 21.31 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.25), residues: 1132 helix: 1.02 (0.26), residues: 396 sheet: 0.20 (0.32), residues: 268 loop : -0.82 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 182 TYR 0.025 0.002 TYR A 302 PHE 0.027 0.001 PHE R 345 TRP 0.017 0.001 TRP R 134 HIS 0.004 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 9124) covalent geometry : angle 0.77581 / 0.38 (12373) SS BOND : bond 0.00414 / 0.21 ( 3) SS BOND : angle 0.73191 / 0.38 ( 6) hydrogen bonds : bond 0.04380 / 2.94 ( 466) hydrogen bonds : angle 5.09180 / 3.60 ( 1335) *********************** 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 217 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8286 (mtt180) cc_final: 0.7541 (mtm180) REVERT: A 52 GLN cc_start: 0.9603 (tp40) cc_final: 0.8881 (tm-30) REVERT: A 247 MET cc_start: 0.9313 (mtm) cc_final: 0.9097 (mtm) REVERT: A 256 ASN cc_start: 0.9166 (t0) cc_final: 0.8799 (t0) REVERT: A 294 ASN cc_start: 0.7362 (OUTLIER) cc_final: 0.6862 (t0) REVERT: B 10 GLU cc_start: 0.9657 (tp30) cc_final: 0.9303 (tp30) REVERT: B 12 GLU cc_start: 0.9713 (tp30) cc_final: 0.9488 (tm-30) REVERT: B 19 ARG cc_start: 0.9657 (ppp80) cc_final: 0.9376 (ttp80) REVERT: B 101 MET cc_start: 0.8952 (mtm) cc_final: 0.8631 (mtm) REVERT: B 124 TYR cc_start: 0.8752 (m-80) cc_final: 0.8249 (m-10) REVERT: B 138 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8255 (mm-30) REVERT: B 226 GLU cc_start: 0.9092 (mp0) cc_final: 0.8621 (mp0) REVERT: B 234 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8906 (m-80) REVERT: B 262 MET cc_start: 0.9341 (tpt) cc_final: 0.8820 (tpp) REVERT: B 280 LYS cc_start: 0.9396 (tttt) cc_final: 0.8950 (ttmt) REVERT: B 292 PHE cc_start: 0.9156 (m-10) cc_final: 0.8603 (m-10) REVERT: B 339 TRP cc_start: 0.8518 (m100) cc_final: 0.6968 (m100) REVERT: C 16 VAL cc_start: 0.9679 (m) cc_final: 0.9395 (p) REVERT: C 17 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8415 (mm-30) REVERT: C 18 GLN cc_start: 0.9541 (tp-100) cc_final: 0.9296 (tp-100) REVERT: C 20 LYS cc_start: 0.9172 (pttm) cc_final: 0.8681 (pttm) REVERT: C 21 MET cc_start: 0.8911 (tmm) cc_final: 0.8175 (tmm) REVERT: D 151 LYS cc_start: 0.7899 (tptp) cc_final: 0.7687 (tptp) REVERT: D 234 GLU cc_start: 0.7677 (mp0) cc_final: 0.7344 (mp0) REVERT: L 12 ILE cc_start: 0.7978 (mp) cc_final: 0.7669 (mm) REVERT: R 98 GLN cc_start: 0.9519 (mm-40) cc_final: 0.9212 (mm-40) REVERT: R 102 HIS cc_start: 0.9081 (m90) cc_final: 0.8534 (m90) REVERT: R 105 LEU cc_start: 0.9337 (mp) cc_final: 0.8772 (tt) REVERT: R 131 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.6509 (m170) REVERT: R 151 CYS cc_start: 0.9633 (m) cc_final: 0.8846 (t) REVERT: R 203 MET cc_start: 0.8359 (tpp) cc_final: 0.8015 (tpp) REVERT: R 207 MET cc_start: 0.8254 (tpt) cc_final: 0.6250 (tpt) REVERT: R 249 MET cc_start: 0.8734 (mmt) cc_final: 0.8394 (tpt) REVERT: R 266 MET cc_start: 0.9433 (mmm) cc_final: 0.9035 (mmm) REVERT: R 347 MET cc_start: 0.9413 (ptp) cc_final: 0.8937 (ppp) REVERT: R 350 ASN cc_start: 0.8832 (m-40) cc_final: 0.8316 (m110) outliers start: 27 outliers final: 20 residues processed: 210 average time/residue: 0.0895 time to fit residues: 24.8819 Evaluate side-chains 198 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 362 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 0.0000 chunk 83 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 76 optimal weight: 0.4980 overall best weight: 3.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.073930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.054219 restraints weight = 34160.138| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 4.48 r_work: 0.2958 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9127 Z= 0.179 Angle : 0.814 16.641 12379 Z= 0.394 Chirality : 0.046 0.184 1417 Planarity : 0.004 0.052 1560 Dihedral : 5.036 32.450 1249 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.22 % Allowed : 21.62 % Favored : 75.16 % 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 are not related in a simple way. whole: 0.11 (0.25), residues: 1132 helix: 1.13 (0.26), residues: 398 sheet: 0.04 (0.31), residues: 274 loop : -0.77 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 182 TYR 0.019 0.002 TYR A 302 PHE 0.026 0.002 PHE R 345 TRP 0.012 0.001 TRP R 134 HIS 0.004 0.001 HIS R 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 ( 9124) covalent geometry : angle 0.81352 / 0.39 (12373) SS BOND : bond 0.00456 / 0.23 ( 3) SS BOND : angle 0.85257 / 0.43 ( 6) hydrogen bonds : bond 0.04521 / 3.04 ( 466) hydrogen bonds : angle 5.15753 / 3.65 ( 1335) *********************** 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 211 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.9215 (m-40) cc_final: 0.8719 (m110) REVERT: A 24 ARG cc_start: 0.8528 (mtt180) cc_final: 0.7852 (mtm180) REVERT: A 32 ARG cc_start: 0.8069 (mtm110) cc_final: 0.7810 (mtm110) REVERT: A 52 GLN cc_start: 0.9667 (tp40) cc_final: 0.8916 (tm-30) REVERT: A 256 ASN cc_start: 0.9241 (t0) cc_final: 0.9005 (t0) REVERT: A 287 TYR cc_start: 0.8844 (m-80) cc_final: 0.8607 (m-80) REVERT: B 10 GLU cc_start: 0.9674 (tp30) cc_final: 0.9356 (tp30) REVERT: B 12 GLU cc_start: 0.9751 (tp30) cc_final: 0.9538 (tm-30) REVERT: B 19 ARG cc_start: 0.9720 (ppp80) cc_final: 0.9476 (ttp80) REVERT: B 226 GLU cc_start: 0.9247 (mp0) cc_final: 0.8790 (mp0) REVERT: B 262 MET cc_start: 0.9471 (tpt) cc_final: 0.9024 (tpp) REVERT: B 292 PHE cc_start: 0.9205 (m-10) cc_final: 0.8692 (m-10) REVERT: B 339 TRP cc_start: 0.8863 (m100) cc_final: 0.7385 (m100) REVERT: C 16 VAL cc_start: 0.9760 (m) cc_final: 0.9473 (p) REVERT: C 17 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8567 (mm-30) REVERT: C 18 GLN cc_start: 0.9573 (tp-100) cc_final: 0.9149 (tp-100) REVERT: C 20 LYS cc_start: 0.9319 (pttm) cc_final: 0.8966 (pttm) REVERT: C 21 MET cc_start: 0.9024 (tmm) cc_final: 0.8214 (tmm) REVERT: C 32 LYS cc_start: 0.9572 (ptmm) cc_final: 0.9244 (tmtt) REVERT: D 82 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8281 (mm-40) REVERT: D 93 MET cc_start: 0.9251 (tpp) cc_final: 0.8681 (tpp) REVERT: D 151 LYS cc_start: 0.8025 (tptp) cc_final: 0.7787 (tptp) REVERT: D 218 MET cc_start: 0.8421 (ttp) cc_final: 0.8109 (ttp) REVERT: L 12 ILE cc_start: 0.8122 (mp) cc_final: 0.7865 (mm) REVERT: R 98 GLN cc_start: 0.9614 (mm-40) cc_final: 0.9298 (mm-40) REVERT: R 102 HIS cc_start: 0.9196 (m90) cc_final: 0.8623 (m90) REVERT: R 131 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.6510 (m170) REVERT: R 151 CYS cc_start: 0.9699 (m) cc_final: 0.8979 (t) REVERT: R 180 MET cc_start: 0.8767 (mtp) cc_final: 0.8235 (mtp) REVERT: R 203 MET cc_start: 0.8386 (tpp) cc_final: 0.7925 (tpp) REVERT: R 207 MET cc_start: 0.8097 (tpt) cc_final: 0.6365 (tpt) REVERT: R 266 MET cc_start: 0.9460 (mmm) cc_final: 0.9076 (mmm) REVERT: R 347 MET cc_start: 0.9446 (ptp) cc_final: 0.8981 (ppp) REVERT: R 350 ASN cc_start: 0.8865 (m-40) cc_final: 0.8387 (m110) outliers start: 31 outliers final: 23 residues processed: 202 average time/residue: 0.0860 time to fit residues: 23.2230 Evaluate side-chains 193 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 362 ILE Chi-restraints excluded: chain R residue 363 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 95 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.071257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.051433 restraints weight = 34676.643| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 4.40 r_work: 0.2884 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.6304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 9127 Z= 0.282 Angle : 0.876 14.758 12379 Z= 0.437 Chirality : 0.048 0.258 1417 Planarity : 0.004 0.052 1560 Dihedral : 5.366 42.037 1247 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.43 % Allowed : 22.66 % Favored : 73.91 % 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 are not related in a simple way. whole: -0.19 (0.25), residues: 1132 helix: 0.77 (0.26), residues: 409 sheet: -0.22 (0.31), residues: 273 loop : -0.78 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 182 TYR 0.037 0.002 TYR A 302 PHE 0.028 0.002 PHE R 345 TRP 0.012 0.002 TRP A 258 HIS 0.009 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.28 ( 9124) covalent geometry : angle 0.87618 / 0.44 (12373) SS BOND : bond 0.00626 / 0.31 ( 3) SS BOND : angle 1.09882 / 0.57 ( 6) hydrogen bonds : bond 0.04980 / 3.30 ( 466) hydrogen bonds : angle 5.37245 / 3.81 ( 1335) *********************** 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 195 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.9211 (m-40) cc_final: 0.8608 (m110) REVERT: A 24 ARG cc_start: 0.8495 (mtt180) cc_final: 0.7917 (mtm180) REVERT: A 32 ARG cc_start: 0.8126 (mtm110) cc_final: 0.7838 (mtm110) REVERT: A 52 GLN cc_start: 0.9670 (tp40) cc_final: 0.8977 (tm-30) REVERT: A 242 ARG cc_start: 0.9384 (mtt180) cc_final: 0.8947 (ttm-80) REVERT: A 247 MET cc_start: 0.9421 (mtm) cc_final: 0.9145 (mpp) REVERT: A 256 ASN cc_start: 0.9310 (t0) cc_final: 0.9018 (t0) REVERT: B 10 GLU cc_start: 0.9728 (tp30) cc_final: 0.9519 (tp30) REVERT: B 12 GLU cc_start: 0.9747 (tp30) cc_final: 0.9439 (tm-30) REVERT: B 45 MET cc_start: 0.9068 (mmm) cc_final: 0.8786 (tpp) REVERT: B 55 LEU cc_start: 0.8942 (mt) cc_final: 0.8571 (pp) REVERT: B 217 MET cc_start: 0.8188 (pmm) cc_final: 0.7667 (pmm) REVERT: B 226 GLU cc_start: 0.9186 (mp0) cc_final: 0.8726 (mp0) REVERT: B 262 MET cc_start: 0.9455 (tpt) cc_final: 0.9144 (tpp) REVERT: B 292 PHE cc_start: 0.9211 (m-10) cc_final: 0.8723 (m-10) REVERT: C 16 VAL cc_start: 0.9714 (m) cc_final: 0.9464 (p) REVERT: C 17 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8617 (mm-30) REVERT: C 18 GLN cc_start: 0.9581 (tp-100) cc_final: 0.9166 (tp-100) REVERT: C 20 LYS cc_start: 0.9373 (pttm) cc_final: 0.8988 (pttm) REVERT: C 21 MET cc_start: 0.9072 (tmm) cc_final: 0.8364 (tmm) REVERT: C 32 LYS cc_start: 0.9591 (ptmm) cc_final: 0.9273 (tmtt) REVERT: C 41 CYS cc_start: 0.9546 (m) cc_final: 0.9163 (m) REVERT: D 218 MET cc_start: 0.8511 (ttp) cc_final: 0.7715 (ttp) REVERT: R 98 GLN cc_start: 0.9600 (mm-40) cc_final: 0.9265 (mm-40) REVERT: R 102 HIS cc_start: 0.9213 (m90) cc_final: 0.8621 (m90) REVERT: R 131 HIS cc_start: 0.7806 (OUTLIER) cc_final: 0.6804 (m170) REVERT: R 151 CYS cc_start: 0.9709 (m) cc_final: 0.9041 (t) REVERT: R 203 MET cc_start: 0.8350 (tpp) cc_final: 0.7858 (tpp) REVERT: R 207 MET cc_start: 0.8219 (tpt) cc_final: 0.6584 (tpt) REVERT: R 249 MET cc_start: 0.8990 (mmt) cc_final: 0.8044 (mmm) REVERT: R 266 MET cc_start: 0.9477 (mmm) cc_final: 0.9084 (mmm) REVERT: R 347 MET cc_start: 0.9484 (ptp) cc_final: 0.9165 (ppp) outliers start: 33 outliers final: 25 residues processed: 185 average time/residue: 0.0962 time to fit residues: 23.3605 Evaluate side-chains 177 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 362 ILE Chi-restraints excluded: chain R residue 363 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 99 optimal weight: 40.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 13 GLN B 110 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 172 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.071832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.052301 restraints weight = 34769.642| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 4.31 r_work: 0.2887 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9127 Z= 0.276 Angle : 0.900 17.017 12379 Z= 0.445 Chirality : 0.048 0.260 1417 Planarity : 0.005 0.054 1560 Dihedral : 5.445 40.105 1247 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.01 % Allowed : 23.70 % Favored : 73.28 % 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 are not related in a simple way. whole: -0.39 (0.25), residues: 1132 helix: 0.57 (0.25), residues: 408 sheet: -0.23 (0.31), residues: 275 loop : -0.94 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 182 TYR 0.020 0.002 TYR D 94 PHE 0.026 0.002 PHE R 345 TRP 0.013 0.002 TRP B 339 HIS 0.008 0.001 HIS D 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.28 ( 9124) covalent geometry : angle 0.90028 / 0.44 (12373) SS BOND : bond 0.00584 / 0.29 ( 3) SS BOND : angle 1.12789 / 0.61 ( 6) hydrogen bonds : bond 0.05002 / 3.32 ( 466) hydrogen bonds : angle 5.38529 / 3.81 ( 1335) ********************** 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 189 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 ASN cc_start: 0.9096 (m-40) cc_final: 0.8530 (m110) REVERT: A 24 ARG cc_start: 0.8479 (mtt180) cc_final: 0.7878 (mtm180) REVERT: A 52 GLN cc_start: 0.9652 (tp40) cc_final: 0.8959 (tm-30) REVERT: A 242 ARG cc_start: 0.9373 (mtt180) cc_final: 0.8885 (ttm-80) REVERT: A 247 MET cc_start: 0.9440 (mtm) cc_final: 0.9060 (mpp) REVERT: A 256 ASN cc_start: 0.9325 (t0) cc_final: 0.8957 (t0) REVERT: A 287 TYR cc_start: 0.9078 (m-80) cc_final: 0.8815 (m-80) REVERT: B 45 MET cc_start: 0.9146 (mmm) cc_final: 0.8745 (tpp) REVERT: B 55 LEU cc_start: 0.8959 (mt) cc_final: 0.8491 (pp) REVERT: B 217 MET cc_start: 0.8216 (pmm) cc_final: 0.7639 (pmm) REVERT: B 226 GLU cc_start: 0.9172 (mp0) cc_final: 0.8698 (mp0) REVERT: B 262 MET cc_start: 0.9474 (tpt) cc_final: 0.9142 (tpp) REVERT: B 292 PHE cc_start: 0.9285 (m-10) cc_final: 0.8758 (m-10) REVERT: C 14 LYS cc_start: 0.9483 (mtmm) cc_final: 0.9239 (ptpp) REVERT: C 18 GLN cc_start: 0.9580 (tp-100) cc_final: 0.9147 (tp-100) REVERT: C 20 LYS cc_start: 0.9397 (pttm) cc_final: 0.9075 (pttm) REVERT: C 21 MET cc_start: 0.9131 (tmm) cc_final: 0.8454 (tmm) REVERT: C 32 LYS cc_start: 0.9582 (ptmm) cc_final: 0.9284 (tmtt) REVERT: D 90 ASP cc_start: 0.8576 (m-30) cc_final: 0.8331 (m-30) REVERT: D 98 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7575 (ppt-90) REVERT: D 151 LYS cc_start: 0.7943 (tptp) cc_final: 0.7731 (tptp) REVERT: R 70 TYR cc_start: 0.9021 (m-80) cc_final: 0.8123 (m-80) REVERT: R 102 HIS cc_start: 0.9255 (m90) cc_final: 0.8812 (m90) REVERT: R 131 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7221 (m170) REVERT: R 151 CYS cc_start: 0.9661 (m) cc_final: 0.8920 (t) REVERT: R 180 MET cc_start: 0.9021 (mtp) cc_final: 0.8685 (mtp) REVERT: R 203 MET cc_start: 0.8234 (tpp) cc_final: 0.7766 (tpp) REVERT: R 207 MET cc_start: 0.8378 (tpt) cc_final: 0.6747 (tpt) REVERT: R 266 MET cc_start: 0.9485 (mmm) cc_final: 0.9083 (mmm) REVERT: R 315 CYS cc_start: 0.8896 (m) cc_final: 0.8645 (p) REVERT: R 347 MET cc_start: 0.9520 (ptp) cc_final: 0.9066 (ppp) outliers start: 29 outliers final: 24 residues processed: 181 average time/residue: 0.0844 time to fit residues: 20.2986 Evaluate side-chains 184 residues out of total 987 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 131 HIS Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 201 VAL Chi-restraints excluded: chain R residue 218 HIS Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 362 ILE Chi-restraints excluded: chain R residue 363 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.072563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052201 restraints weight = 34355.894| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 4.58 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.6538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9127 Z= 0.234 Angle : 0.899 16.117 12379 Z= 0.440 Chirality : 0.048 0.173 1417 Planarity : 0.005 0.053 1560 Dihedral : 5.420 39.175 1247 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.22 % Allowed : 24.12 % Favored : 72.66 % 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 are not related in a simple way. whole: -0.37 (0.25), residues: 1132 helix: 0.59 (0.25), residues: 410 sheet: -0.27 (0.31), residues: 276 loop : -0.90 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 32 TYR 0.039 0.002 TYR A 302 PHE 0.025 0.002 PHE R 345 TRP 0.013 0.002 TRP B 339 HIS 0.009 0.001 HIS A 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 ( 9124) covalent geometry : angle 0.89912 / 0.44 (12373) SS BOND : bond 0.00515 / 0.26 ( 3) SS BOND : angle 0.98102 / 0.52 ( 6) hydrogen bonds : bond 0.04815 / 3.21 ( 466) hydrogen bonds : angle 5.34413 / 3.77 ( 1335) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1919.62 seconds wall clock time: 33 minutes 41.54 seconds (2021.54 seconds total)