Starting phenix.real_space_refine on Thu Jul 2 11:55:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vv3_32136/07_2026/7vv3_32136.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv3_32136/07_2026/7vv3_32136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7vv3_32136/07_2026/7vv3_32136.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vv3_32136/07_2026/7vv3_32136.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vv3_32136/07_2026/7vv3_32136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv3_32136/07_2026/7vv3_32136.map" model { file = "/net/cci-nas-00/data/ceres_data/7vv3_32136/07_2026/7vv3_32136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv3_32136/07_2026/7vv3_32136.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 63 5.16 5 C 5531 2.51 5 N 1449 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 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: 8633 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1751 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2590 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 333} 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: "G" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 415 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1762 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 2087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2087 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 8, 'TRANS': 253} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.81, per 1000 atoms: 0.21 Number of scatterers: 8633 At special positions: 0 Unit cell: (118.876, 112.564, 104.148, 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 63 16.00 O 1590 8.00 N 1449 7.00 C 5531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.06 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " distance=2.02 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: 0.63 Conformation dependent library (CDL) restraints added in 420.7 milliseconds 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2054 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 38.6% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.901A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.426A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.085A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 308 removed outlier: 3.711A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.950A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.924A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.701A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.116A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.690A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 57 removed outlier: 3.691A pdb=" N ILE R 32 " --> pdb=" O LYS R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix removed outlier: 3.657A pdb=" N LEU R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 95 removed outlier: 3.618A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU R 77 " --> pdb=" O GLY R 73 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR R 89 " --> pdb=" O ASN R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 133 removed outlier: 3.650A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 168 removed outlier: 3.508A pdb=" N GLU R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS R 168 " --> pdb=" O GLU R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 213 removed outlier: 3.898A pdb=" N THR R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE R 183 " --> pdb=" O TRP R 179 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR R 187 " --> pdb=" O PHE R 183 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER R 213 " --> pdb=" O ILE R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 235 Processing helix chain 'R' and resid 236 through 244 removed outlier: 4.300A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 251 removed outlier: 3.799A pdb=" N TRP R 248 " --> pdb=" O PHE R 244 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE R 249 " --> pdb=" O LEU R 245 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 259 removed outlier: 4.020A pdb=" N CYS R 258 " --> pdb=" O ASP R 254 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 280 removed outlier: 3.947A pdb=" N VAL R 263 " --> pdb=" O HIS R 259 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 280 through 285 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.637A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.618A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.732A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.531A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 151 removed outlier: 6.123A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.654A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.672A 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: 3.810A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.603A 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: 6.136A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.794A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.146A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.895A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.515A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1242 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: 1.28 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2625 1.34 - 1.47: 2386 1.47 - 1.60: 3724 1.60 - 1.73: 1 1.73 - 1.86: 87 Bond restraints: 8823 Sorted by residual: bond pdb=" C17 CLR R 401 " pdb=" C20 CLR R 401 " ideal model delta sigma weight residual 1.535 1.621 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CG LEU B 146 " pdb=" CD1 LEU B 146 " ideal model delta sigma weight residual 1.521 1.399 0.122 3.30e-02 9.18e+02 1.36e+01 bond pdb=" C HIS R 261 " pdb=" O HIS R 261 " ideal model delta sigma weight residual 1.244 1.217 0.027 9.80e-03 1.04e+04 7.64e+00 bond pdb=" C ARG S 168 " pdb=" N PRO S 169 " ideal model delta sigma weight residual 1.333 1.360 -0.027 1.01e-02 9.80e+03 6.99e+00 bond pdb=" C ASN R 271 " pdb=" O ASN R 271 " ideal model delta sigma weight residual 1.237 1.206 0.031 1.17e-02 7.31e+03 6.89e+00 ... (remaining 8818 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.67: 11885 5.67 - 11.34: 69 11.34 - 17.01: 5 17.01 - 22.68: 1 22.68 - 28.35: 1 Bond angle restraints: 11961 Sorted by residual: angle pdb=" N LEU R 256 " pdb=" CA LEU R 256 " pdb=" C LEU R 256 " ideal model delta sigma weight residual 111.14 120.33 -9.19 1.08e+00 8.57e-01 7.24e+01 angle pdb=" CA LEU B 4 " pdb=" CB LEU B 4 " pdb=" CG LEU B 4 " ideal model delta sigma weight residual 116.30 144.65 -28.35 3.50e+00 8.16e-02 6.56e+01 angle pdb=" N SER R 253 " pdb=" CA SER R 253 " pdb=" C SER R 253 " ideal model delta sigma weight residual 111.28 119.10 -7.82 1.09e+00 8.42e-01 5.14e+01 angle pdb=" N ILE R 260 " pdb=" CA ILE R 260 " pdb=" C ILE R 260 " ideal model delta sigma weight residual 110.72 117.16 -6.44 1.01e+00 9.80e-01 4.07e+01 angle pdb=" N ILE R 249 " pdb=" CA ILE R 249 " pdb=" C ILE R 249 " ideal model delta sigma weight residual 110.72 116.86 -6.14 1.01e+00 9.80e-01 3.70e+01 ... (remaining 11956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4760 17.95 - 35.89: 356 35.89 - 53.84: 54 53.84 - 71.79: 7 71.79 - 89.73: 6 Dihedral angle restraints: 5183 sinusoidal: 1997 harmonic: 3186 Sorted by residual: 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 93.00 163.36 -70.36 1 1.00e+01 1.00e-02 6.37e+01 dihedral pdb=" CA ASP B 290 " pdb=" C ASP B 290 " pdb=" N ASP B 291 " pdb=" CA ASP B 291 " ideal model delta harmonic sigma weight residual 180.00 145.57 34.43 0 5.00e+00 4.00e-02 4.74e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 140.91 -47.91 1 1.00e+01 1.00e-02 3.17e+01 ... (remaining 5180 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1181 0.096 - 0.191: 148 0.191 - 0.287: 22 0.287 - 0.382: 7 0.382 - 0.478: 5 Chirality restraints: 1363 Sorted by residual: chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CA HIS R 261 " pdb=" N HIS R 261 " pdb=" C HIS R 261 " pdb=" CB HIS R 261 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.52e+00 chirality pdb=" CA ARG R 140 " pdb=" N ARG R 140 " pdb=" C ARG R 140 " pdb=" CB ARG R 140 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.40 2.00e-01 2.50e+01 3.90e+00 ... (remaining 1360 not shown) Planarity restraints: 1498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 142 " 0.038 2.00e-02 2.50e+03 3.64e-02 1.99e+01 pdb=" CG HIS B 142 " -0.075 2.00e-02 2.50e+03 pdb=" ND1 HIS B 142 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS B 142 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 HIS B 142 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS B 142 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " 0.062 5.00e-02 4.00e+02 9.30e-02 1.38e+01 pdb=" N PRO G 53 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.73e+00 pdb=" N PRO G 55 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.041 5.00e-02 4.00e+02 ... (remaining 1495 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 3 2.26 - 2.92: 3479 2.92 - 3.58: 11854 3.58 - 4.24: 20370 4.24 - 4.90: 34831 Nonbonded interactions: 70537 Sorted by model distance: nonbonded pdb=" OD1 ASP R 75 " pdb=" OG SER R 272 " model vdw 1.600 3.040 nonbonded pdb=" O THR R 107 " pdb=" OG SER R 161 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP R 75 " pdb=" CB SER R 272 " model vdw 2.247 3.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.284 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.287 3.040 ... (remaining 70532 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: 0.250 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.670 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 : 0.009 0.122 8827 Z= 0.396 Angle : 1.257 28.352 11969 Z= 0.682 Chirality : 0.073 0.478 1363 Planarity : 0.008 0.093 1498 Dihedral : 13.028 89.733 3117 Min Nonbonded Distance : 1.600 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.75 % Allowed : 1.39 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.23), residues: 1089 helix: -0.86 (0.24), residues: 374 sheet: -0.71 (0.29), residues: 283 loop : -1.52 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG S 206 TYR 0.027 0.003 TYR B 105 PHE 0.022 0.003 PHE B 199 TRP 0.013 0.002 TRP B 82 HIS 0.035 0.003 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00865 / 0.40 ( 8823) covalent geometry : angle 1.25528 / 0.68 (11961) SS BOND : bond 0.01491 / 0.75 ( 4) SS BOND : angle 2.66725 / 1.54 ( 8) hydrogen bonds : bond 0.18313 / 12.35 ( 434) hydrogen bonds : angle 7.27885 / 5.07 ( 1242) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 210 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7634 (t0) cc_final: 0.7095 (t0) REVERT: S 65 LYS cc_start: 0.8674 (tptp) cc_final: 0.8340 (tppp) REVERT: R 77 LEU cc_start: 0.8265 (mt) cc_final: 0.7942 (mt) REVERT: R 242 GLN cc_start: 0.8159 (pp30) cc_final: 0.7682 (pp30) outliers start: 7 outliers final: 2 residues processed: 214 average time/residue: 0.5574 time to fit residues: 125.8593 Evaluate side-chains 142 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 140 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain S residue 189 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.1980 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN A 294 ASN A 304 GLN B 35 ASN G 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.088618 restraints weight = 12944.142| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.34 r_work: 0.2938 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8827 Z= 0.130 Angle : 0.676 13.717 11969 Z= 0.332 Chirality : 0.043 0.302 1363 Planarity : 0.004 0.049 1498 Dihedral : 6.906 128.457 1201 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.67 % Allowed : 13.13 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.33 (0.25), residues: 1089 helix: 0.88 (0.26), residues: 377 sheet: -0.25 (0.30), residues: 286 loop : -1.12 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 8 TYR 0.031 0.001 TYR R 222 PHE 0.024 0.001 PHE R 39 TRP 0.018 0.001 TRP B 169 HIS 0.016 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 8823) covalent geometry : angle 0.67538 / 0.33 (11961) SS BOND : bond 0.00453 / 0.21 ( 4) SS BOND : angle 1.36213 / 0.78 ( 8) hydrogen bonds : bond 0.04309 / 2.85 ( 434) hydrogen bonds : angle 4.64298 / 3.19 ( 1242) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: A 193 ASP cc_start: 0.8525 (t0) cc_final: 0.8118 (t0) REVERT: B 10 GLU cc_start: 0.8522 (tt0) cc_final: 0.7968 (tp30) REVERT: B 156 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8790 (mm-40) REVERT: B 197 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8192 (tpm-80) REVERT: S 73 ASP cc_start: 0.8656 (t0) cc_final: 0.8347 (t0) REVERT: R 39 PHE cc_start: 0.8207 (t80) cc_final: 0.7967 (t80) outliers start: 25 outliers final: 9 residues processed: 188 average time/residue: 0.4810 time to fit residues: 96.1536 Evaluate side-chains 156 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 216 LEU Chi-restraints excluded: chain R residue 258 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 0.0970 chunk 102 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 255 ASN A 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.085079 restraints weight = 12907.862| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.31 r_work: 0.2875 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8827 Z= 0.182 Angle : 0.666 14.276 11969 Z= 0.321 Chirality : 0.044 0.296 1363 Planarity : 0.004 0.042 1498 Dihedral : 5.594 81.211 1197 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.74 % Allowed : 17.50 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.23 (0.25), residues: 1089 helix: 1.60 (0.27), residues: 377 sheet: -0.10 (0.30), residues: 286 loop : -0.94 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 206 TYR 0.026 0.002 TYR R 222 PHE 0.014 0.001 PHE R 39 TRP 0.013 0.001 TRP R 154 HIS 0.017 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 8823) covalent geometry : angle 0.66535 / 0.32 (11961) SS BOND : bond 0.00721 / 0.35 ( 4) SS BOND : angle 1.52687 / 0.86 ( 8) hydrogen bonds : bond 0.04091 / 2.68 ( 434) hydrogen bonds : angle 4.39639 / 2.98 ( 1242) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.380 Fit side-chains REVERT: A 14 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: A 29 LYS cc_start: 0.8693 (tppp) cc_final: 0.8450 (ttmm) REVERT: A 193 ASP cc_start: 0.8559 (t0) cc_final: 0.8120 (t0) REVERT: B 10 GLU cc_start: 0.8523 (tt0) cc_final: 0.7966 (tp30) REVERT: S 73 ASP cc_start: 0.8658 (t0) cc_final: 0.8330 (t0) REVERT: R 39 PHE cc_start: 0.8158 (t80) cc_final: 0.7939 (t80) outliers start: 35 outliers final: 15 residues processed: 178 average time/residue: 0.5389 time to fit residues: 101.5383 Evaluate side-chains 165 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 258 CYS Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 103 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.080186 restraints weight = 13536.763| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.39 r_work: 0.2796 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8827 Z= 0.220 Angle : 0.673 14.920 11969 Z= 0.327 Chirality : 0.044 0.286 1363 Planarity : 0.004 0.040 1498 Dihedral : 5.604 82.486 1197 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.48 % Allowed : 19.85 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.51 (0.26), residues: 1089 helix: 1.96 (0.27), residues: 378 sheet: -0.08 (0.30), residues: 293 loop : -0.83 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 206 TYR 0.023 0.002 TYR R 222 PHE 0.012 0.001 PHE R 39 TRP 0.013 0.001 TRP R 154 HIS 0.018 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 ( 8823) covalent geometry : angle 0.67233 / 0.33 (11961) SS BOND : bond 0.00875 / 0.41 ( 4) SS BOND : angle 1.66441 / 0.94 ( 8) hydrogen bonds : bond 0.04104 / 2.67 ( 434) hydrogen bonds : angle 4.31657 / 2.92 ( 1242) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.206 Fit side-chains REVERT: A 14 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: A 29 LYS cc_start: 0.8722 (tppp) cc_final: 0.8433 (ttmm) REVERT: A 193 ASP cc_start: 0.8569 (t0) cc_final: 0.7993 (t0) REVERT: A 310 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8798 (mm) REVERT: B 8 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7433 (mtm180) REVERT: B 156 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8881 (mm-40) REVERT: S 73 ASP cc_start: 0.8607 (t0) cc_final: 0.8224 (t0) outliers start: 42 outliers final: 18 residues processed: 181 average time/residue: 0.4871 time to fit residues: 93.5870 Evaluate side-chains 169 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 258 CYS Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN B 88 ASN S 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.081948 restraints weight = 13309.544| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.34 r_work: 0.2821 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8827 Z= 0.153 Angle : 0.632 14.303 11969 Z= 0.307 Chirality : 0.043 0.271 1363 Planarity : 0.003 0.046 1498 Dihedral : 5.380 82.724 1197 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.84 % Allowed : 21.77 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.68 (0.26), residues: 1089 helix: 2.16 (0.27), residues: 379 sheet: -0.12 (0.30), residues: 286 loop : -0.68 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG S 206 TYR 0.020 0.001 TYR R 222 PHE 0.010 0.001 PHE S 27 TRP 0.016 0.001 TRP R 154 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 ( 8823) covalent geometry : angle 0.63127 / 0.31 (11961) SS BOND : bond 0.00693 / 0.32 ( 4) SS BOND : angle 1.24022 / 0.69 ( 8) hydrogen bonds : bond 0.03744 / 2.44 ( 434) hydrogen bonds : angle 4.16510 / 2.82 ( 1242) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.322 Fit side-chains REVERT: A 14 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: A 29 LYS cc_start: 0.8700 (tppp) cc_final: 0.8422 (ttmm) REVERT: A 193 ASP cc_start: 0.8614 (t0) cc_final: 0.8137 (t0) REVERT: A 280 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8541 (mptp) REVERT: A 287 TYR cc_start: 0.7940 (m-80) cc_final: 0.7521 (m-80) REVERT: A 310 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8801 (mm) REVERT: B 61 MET cc_start: 0.9247 (ppp) cc_final: 0.8990 (pp-130) REVERT: B 197 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8135 (tpm-80) REVERT: S 73 ASP cc_start: 0.8614 (t0) cc_final: 0.8207 (t0) outliers start: 36 outliers final: 14 residues processed: 192 average time/residue: 0.4711 time to fit residues: 96.0902 Evaluate side-chains 166 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 280 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 77 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.118913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.081193 restraints weight = 13308.217| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.37 r_work: 0.2809 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8827 Z= 0.175 Angle : 0.681 15.537 11969 Z= 0.324 Chirality : 0.043 0.260 1363 Planarity : 0.004 0.050 1498 Dihedral : 5.370 83.178 1197 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.52 % Allowed : 24.01 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.73 (0.26), residues: 1089 helix: 2.17 (0.27), residues: 378 sheet: -0.12 (0.30), residues: 287 loop : -0.57 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 206 TYR 0.018 0.002 TYR R 222 PHE 0.029 0.001 PHE R 39 TRP 0.018 0.001 TRP R 154 HIS 0.002 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 8823) covalent geometry : angle 0.68049 / 0.32 (11961) SS BOND : bond 0.00772 / 0.36 ( 4) SS BOND : angle 1.47752 / 0.81 ( 8) hydrogen bonds : bond 0.03853 / 2.50 ( 434) hydrogen bonds : angle 4.15051 / 2.80 ( 1242) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.278 Fit side-chains REVERT: A 14 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8206 (tt0) REVERT: A 29 LYS cc_start: 0.8708 (tppp) cc_final: 0.8439 (ttmm) REVERT: A 193 ASP cc_start: 0.8602 (t0) cc_final: 0.8150 (t0) REVERT: A 310 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8811 (mm) REVERT: B 61 MET cc_start: 0.9288 (ppp) cc_final: 0.8987 (pp-130) REVERT: B 197 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8144 (tpm-80) REVERT: S 73 ASP cc_start: 0.8634 (t0) cc_final: 0.8234 (t0) REVERT: R 256 LEU cc_start: 0.8293 (pp) cc_final: 0.7667 (tp) outliers start: 33 outliers final: 17 residues processed: 177 average time/residue: 0.4693 time to fit residues: 88.1816 Evaluate side-chains 167 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 258 CYS Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.116248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.078272 restraints weight = 13454.905| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.36 r_work: 0.2755 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 8827 Z= 0.299 Angle : 0.770 17.487 11969 Z= 0.369 Chirality : 0.047 0.254 1363 Planarity : 0.004 0.055 1498 Dihedral : 5.629 85.002 1197 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.27 % Allowed : 24.44 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.62 (0.26), residues: 1089 helix: 2.06 (0.27), residues: 377 sheet: -0.15 (0.30), residues: 284 loop : -0.63 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 206 TYR 0.018 0.002 TYR R 222 PHE 0.012 0.002 PHE B 234 TRP 0.020 0.002 TRP R 154 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.30 ( 8823) covalent geometry : angle 0.76590 / 0.37 (11961) SS BOND : bond 0.01106 / 0.52 ( 4) SS BOND : angle 3.27216 / 1.84 ( 8) hydrogen bonds : bond 0.04369 / 2.83 ( 434) hydrogen bonds : angle 4.32518 / 2.91 ( 1242) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 164 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8347 (tt0) REVERT: A 29 LYS cc_start: 0.8798 (tppp) cc_final: 0.8526 (ttmm) REVERT: A 193 ASP cc_start: 0.8594 (t0) cc_final: 0.8127 (t0) REVERT: A 310 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8768 (mm) REVERT: B 156 GLN cc_start: 0.9157 (OUTLIER) cc_final: 0.8925 (mm-40) REVERT: S 73 ASP cc_start: 0.8699 (t0) cc_final: 0.8304 (t0) REVERT: R 39 PHE cc_start: 0.8184 (t80) cc_final: 0.7940 (t80) REVERT: R 234 LEU cc_start: 0.8545 (mt) cc_final: 0.7714 (tm) outliers start: 40 outliers final: 23 residues processed: 188 average time/residue: 0.4468 time to fit residues: 89.3565 Evaluate side-chains 180 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 213 SER Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 258 CYS Chi-restraints excluded: chain R residue 263 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 107 optimal weight: 0.0170 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.121893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.084594 restraints weight = 13214.938| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.37 r_work: 0.2869 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8827 Z= 0.117 Angle : 0.685 21.630 11969 Z= 0.320 Chirality : 0.042 0.220 1363 Planarity : 0.004 0.054 1498 Dihedral : 5.210 84.597 1197 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.03 % Allowed : 28.28 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.84 (0.26), residues: 1089 helix: 2.20 (0.27), residues: 380 sheet: -0.03 (0.31), residues: 284 loop : -0.47 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 206 TYR 0.015 0.001 TYR S 178 PHE 0.009 0.001 PHE R 104 TRP 0.023 0.001 TRP R 154 HIS 0.002 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 ( 8823) covalent geometry : angle 0.68452 / 0.32 (11961) SS BOND : bond 0.00592 / 0.25 ( 4) SS BOND : angle 1.15713 / 0.61 ( 8) hydrogen bonds : bond 0.03564 / 2.33 ( 434) hydrogen bonds : angle 4.12777 / 2.80 ( 1242) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.270 Fit side-chains REVERT: A 14 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8158 (tt0) REVERT: A 29 LYS cc_start: 0.8589 (tppp) cc_final: 0.8334 (ttmm) REVERT: A 193 ASP cc_start: 0.8594 (t0) cc_final: 0.8144 (t0) REVERT: A 287 TYR cc_start: 0.7549 (m-80) cc_final: 0.7106 (m-80) REVERT: A 310 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8803 (mm) REVERT: B 215 GLU cc_start: 0.8577 (pt0) cc_final: 0.7850 (pp20) REVERT: B 258 ASP cc_start: 0.8619 (t0) cc_final: 0.8010 (t0) REVERT: S 73 ASP cc_start: 0.8644 (t0) cc_final: 0.8203 (t0) REVERT: R 39 PHE cc_start: 0.8139 (t80) cc_final: 0.7930 (t80) REVERT: R 234 LEU cc_start: 0.8523 (mt) cc_final: 0.7688 (tm) outliers start: 19 outliers final: 11 residues processed: 173 average time/residue: 0.4699 time to fit residues: 86.4302 Evaluate side-chains 164 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 258 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 17 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.119532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.081929 restraints weight = 13272.624| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.37 r_work: 0.2822 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8827 Z= 0.168 Angle : 0.743 25.899 11969 Z= 0.342 Chirality : 0.044 0.220 1363 Planarity : 0.004 0.062 1498 Dihedral : 5.257 84.595 1197 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.67 % Allowed : 27.43 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.85 (0.26), residues: 1089 helix: 2.19 (0.27), residues: 380 sheet: 0.04 (0.31), residues: 284 loop : -0.50 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 206 TYR 0.013 0.002 TYR R 222 PHE 0.009 0.001 PHE S 27 TRP 0.024 0.001 TRP R 154 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 8823) covalent geometry : angle 0.74305 / 0.34 (11961) SS BOND : bond 0.00656 / 0.30 ( 4) SS BOND : angle 1.23808 / 0.69 ( 8) hydrogen bonds : bond 0.03900 / 2.52 ( 434) hydrogen bonds : angle 4.15314 / 2.82 ( 1242) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.262 Fit side-chains REVERT: A 14 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: A 29 LYS cc_start: 0.8670 (tppp) cc_final: 0.8415 (ttmm) REVERT: A 193 ASP cc_start: 0.8547 (t0) cc_final: 0.8092 (t0) REVERT: A 287 TYR cc_start: 0.7709 (m-80) cc_final: 0.7466 (m-80) REVERT: A 310 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8736 (mm) REVERT: B 19 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7914 (ttp80) REVERT: B 215 GLU cc_start: 0.8383 (pt0) cc_final: 0.8049 (pp20) REVERT: B 258 ASP cc_start: 0.8700 (t0) cc_final: 0.7990 (t0) REVERT: S 73 ASP cc_start: 0.8658 (t0) cc_final: 0.8238 (t0) REVERT: R 39 PHE cc_start: 0.8180 (t80) cc_final: 0.7956 (t80) REVERT: R 201 SER cc_start: 0.8319 (m) cc_final: 0.7936 (t) REVERT: R 234 LEU cc_start: 0.8523 (mt) cc_final: 0.7681 (tm) outliers start: 25 outliers final: 15 residues processed: 171 average time/residue: 0.4830 time to fit residues: 87.8714 Evaluate side-chains 168 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 258 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.121237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.083015 restraints weight = 13266.372| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.41 r_work: 0.2832 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8827 Z= 0.133 Angle : 0.719 25.396 11969 Z= 0.331 Chirality : 0.043 0.205 1363 Planarity : 0.004 0.057 1498 Dihedral : 5.166 84.465 1197 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.03 % Allowed : 28.60 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.86 (0.26), residues: 1089 helix: 2.15 (0.27), residues: 381 sheet: 0.02 (0.30), residues: 290 loop : -0.43 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 206 TYR 0.012 0.001 TYR S 178 PHE 0.009 0.001 PHE B 151 TRP 0.027 0.001 TRP R 154 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 8823) covalent geometry : angle 0.71855 / 0.33 (11961) SS BOND : bond 0.00573 / 0.25 ( 4) SS BOND : angle 1.14835 / 0.62 ( 8) hydrogen bonds : bond 0.03726 / 2.40 ( 434) hydrogen bonds : angle 4.15431 / 2.83 ( 1242) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2178 Ramachandran restraints generated. 1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.217 Fit side-chains REVERT: A 29 LYS cc_start: 0.8625 (tppp) cc_final: 0.8395 (ttmm) REVERT: A 193 ASP cc_start: 0.8553 (t0) cc_final: 0.8100 (t0) REVERT: A 287 TYR cc_start: 0.7826 (m-80) cc_final: 0.7495 (m-80) REVERT: A 310 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8694 (mm) REVERT: B 215 GLU cc_start: 0.8424 (pt0) cc_final: 0.8201 (pp20) REVERT: B 258 ASP cc_start: 0.8581 (t0) cc_final: 0.7918 (t0) REVERT: S 73 ASP cc_start: 0.8628 (t0) cc_final: 0.8162 (t0) REVERT: R 201 SER cc_start: 0.8340 (m) cc_final: 0.7909 (t) REVERT: R 234 LEU cc_start: 0.8519 (mt) cc_final: 0.7697 (tm) outliers start: 19 outliers final: 14 residues processed: 166 average time/residue: 0.4585 time to fit residues: 80.7219 Evaluate side-chains 162 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain R residue 50 PHE Chi-restraints excluded: chain R residue 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 209 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 258 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.0970 chunk 72 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 15 optimal weight: 0.0870 chunk 101 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.085008 restraints weight = 13169.022| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.39 r_work: 0.2865 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8827 Z= 0.117 Angle : 0.690 21.333 11969 Z= 0.320 Chirality : 0.042 0.197 1363 Planarity : 0.004 0.054 1498 Dihedral : 5.025 83.836 1197 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.92 % Allowed : 28.50 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.91 (0.26), residues: 1089 helix: 2.15 (0.28), residues: 381 sheet: 0.13 (0.30), residues: 285 loop : -0.44 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG S 206 TYR 0.014 0.001 TYR A 320 PHE 0.008 0.001 PHE B 151 TRP 0.025 0.001 TRP R 154 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8823) covalent geometry : angle 0.69035 / 0.32 (11961) SS BOND : bond 0.00500 / 0.21 ( 4) SS BOND : angle 0.80309 / 0.40 ( 8) hydrogen bonds : bond 0.03596 / 2.35 ( 434) hydrogen bonds : angle 4.11721 / 2.81 ( 1242) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3035.63 seconds wall clock time: 52 minutes 25.11 seconds (3145.11 seconds total)