Starting phenix.real_space_refine on Thu Mar 13 04:21:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vv3_32136/03_2025/7vv3_32136.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv3_32136/03_2025/7vv3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7vv3_32136/03_2025/7vv3_32136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv3_32136/03_2025/7vv3_32136.map" model { file = "/net/cci-nas-00/data/ceres_data/7vv3_32136/03_2025/7vv3_32136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv3_32136/03_2025/7vv3_32136.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.37, per 1000 atoms: 0.62 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.96 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: 2.54 Time building geometry restraints manager: 2.68 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: 4805 17.95 - 35.89: 364 35.89 - 53.84: 55 53.84 - 71.79: 9 71.79 - 89.73: 6 Dihedral angle restraints: 5239 sinusoidal: 2053 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 5236 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: 0.210 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.200 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 8823 Z= 0.550 Angle : 1.255 28.352 11961 Z= 0.682 Chirality : 0.073 0.478 1363 Planarity : 0.008 0.093 1498 Dihedral : 13.105 89.733 3173 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (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 TRP 0.013 0.002 TRP B 82 HIS 0.035 0.003 HIS B 142 PHE 0.022 0.003 PHE B 199 TYR 0.027 0.003 TYR B 105 ARG 0.023 0.001 ARG S 206 *********************** 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 : 1.033 Fit side-chains revert: symmetry clash REVERT: A 193 ASP cc_start: 0.7634 (t0) cc_final: 0.7096 (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: 1.4326 time to fit residues: 323.1947 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 : 1.011 ------------------------------------------------------------------------------- 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 91 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 294 ASN A 304 GLN B 17 GLN B 35 ASN B 266 HIS G 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.085975 restraints weight = 12830.850| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.32 r_work: 0.2890 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8823 Z= 0.241 Angle : 0.709 14.902 11961 Z= 0.348 Chirality : 0.044 0.298 1363 Planarity : 0.005 0.049 1498 Dihedral : 7.537 116.572 1257 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.77 % Allowed : 13.77 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.25), residues: 1089 helix: 0.92 (0.26), residues: 376 sheet: -0.28 (0.30), residues: 295 loop : -1.11 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.019 0.001 HIS B 142 PHE 0.021 0.001 PHE R 39 TYR 0.031 0.002 TYR R 222 ARG 0.009 0.001 ARG B 8 *********************** 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 196 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8128 (tt0) REVERT: A 21 ARG cc_start: 0.8625 (ttm-80) cc_final: 0.8405 (ttp-110) REVERT: A 193 ASP cc_start: 0.8532 (t0) cc_final: 0.8113 (t0) REVERT: B 156 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8826 (mm-40) REVERT: B 197 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8180 (tpm-80) REVERT: B 217 MET cc_start: 0.9012 (ptt) cc_final: 0.8798 (pp-130) REVERT: R 39 PHE cc_start: 0.8144 (t80) cc_final: 0.7922 (t80) outliers start: 26 outliers final: 10 residues processed: 190 average time/residue: 1.2504 time to fit residues: 251.8845 Evaluate side-chains 159 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 294 ASN 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 81 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 56 optimal weight: 0.3980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 255 ASN A 294 ASN A 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.123381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.085701 restraints weight = 13024.067| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.33 r_work: 0.2884 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8823 Z= 0.218 Angle : 0.641 13.737 11961 Z= 0.310 Chirality : 0.043 0.301 1363 Planarity : 0.004 0.043 1498 Dihedral : 6.459 81.443 1253 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.20 % Allowed : 18.25 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.25), residues: 1089 helix: 1.69 (0.27), residues: 377 sheet: -0.10 (0.30), residues: 291 loop : -0.93 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 154 HIS 0.018 0.001 HIS B 142 PHE 0.015 0.001 PHE R 39 TYR 0.026 0.002 TYR R 222 ARG 0.008 0.001 ARG S 206 *********************** 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 194 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.073 Fit side-chains REVERT: A 14 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: A 29 LYS cc_start: 0.8685 (tppp) cc_final: 0.8449 (ttmm) REVERT: A 193 ASP cc_start: 0.8576 (t0) cc_final: 0.8033 (t0) REVERT: B 10 GLU cc_start: 0.8574 (tt0) cc_final: 0.8087 (tp30) REVERT: B 197 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8154 (tpm-80) REVERT: B 217 MET cc_start: 0.9089 (ptt) cc_final: 0.8859 (ppp) REVERT: B 252 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8498 (tt) REVERT: R 39 PHE cc_start: 0.8135 (t80) cc_final: 0.7912 (t80) REVERT: R 75 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7232 (t0) outliers start: 30 outliers final: 10 residues processed: 184 average time/residue: 1.2949 time to fit residues: 252.7676 Evaluate side-chains 163 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 253 ILE 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 R residue 75 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 0.0670 chunk 24 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 100 optimal weight: 0.0970 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 255 ASN A 304 GLN B 88 ASN S 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.086158 restraints weight = 12937.702| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.29 r_work: 0.2888 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8823 Z= 0.199 Angle : 0.618 13.168 11961 Z= 0.298 Chirality : 0.043 0.298 1363 Planarity : 0.004 0.040 1498 Dihedral : 6.344 81.687 1253 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.63 % Allowed : 20.28 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.26), residues: 1089 helix: 2.06 (0.27), residues: 381 sheet: -0.07 (0.30), residues: 291 loop : -0.76 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 154 HIS 0.015 0.001 HIS B 142 PHE 0.012 0.001 PHE R 39 TYR 0.022 0.001 TYR R 222 ARG 0.010 0.001 ARG S 206 *********************** 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 206 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 172 time to evaluate : 1.064 Fit side-chains REVERT: A 14 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8132 (tt0) REVERT: A 21 ARG cc_start: 0.8660 (ttm-80) cc_final: 0.8392 (ttp-110) REVERT: A 29 LYS cc_start: 0.8691 (tppp) cc_final: 0.8435 (ttmm) REVERT: A 193 ASP cc_start: 0.8607 (t0) cc_final: 0.8186 (t0) REVERT: A 310 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8791 (mm) REVERT: B 197 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8083 (tpm-80) REVERT: B 217 MET cc_start: 0.9070 (ptt) cc_final: 0.8856 (ppp) REVERT: B 252 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8526 (tt) REVERT: B 258 ASP cc_start: 0.8671 (t0) cc_final: 0.7939 (t0) REVERT: R 122 THR cc_start: 0.8871 (t) cc_final: 0.8494 (t) outliers start: 34 outliers final: 18 residues processed: 193 average time/residue: 1.2005 time to fit residues: 246.6292 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 : 0.995 ------------------------------------------------------------------------------- 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 278 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER 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 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 258 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 6 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 49 optimal weight: 0.0670 chunk 97 optimal weight: 9.9990 overall best weight: 2.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3557 r_free = 0.3557 target = 0.120537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.082774 restraints weight = 13005.555| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.30 r_work: 0.2829 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8823 Z= 0.330 Angle : 0.680 14.876 11961 Z= 0.330 Chirality : 0.045 0.300 1363 Planarity : 0.004 0.044 1498 Dihedral : 6.506 83.056 1253 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.02 % Allowed : 21.13 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1089 helix: 2.16 (0.27), residues: 377 sheet: -0.14 (0.30), residues: 285 loop : -0.72 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 154 HIS 0.005 0.001 HIS B 142 PHE 0.011 0.001 PHE B 235 TYR 0.020 0.002 TYR R 222 ARG 0.010 0.001 ARG S 206 *********************** 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 198 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 151 time to evaluate : 1.206 Fit side-chains REVERT: A 21 ARG cc_start: 0.8697 (ttm-80) cc_final: 0.8430 (mtm-85) REVERT: A 29 LYS cc_start: 0.8752 (tppp) cc_final: 0.8470 (ttmm) REVERT: A 193 ASP cc_start: 0.8622 (t0) cc_final: 0.8187 (t0) REVERT: A 310 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8815 (mm) REVERT: B 23 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8460 (tmtm) REVERT: B 61 MET cc_start: 0.9309 (ppp) cc_final: 0.9034 (pp-130) REVERT: R 122 THR cc_start: 0.8819 (t) cc_final: 0.8441 (t) outliers start: 47 outliers final: 17 residues processed: 183 average time/residue: 1.2355 time to fit residues: 240.1660 Evaluate side-chains 167 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain B residue 23 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 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 19 LEU Chi-restraints excluded: chain G residue 54 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.120257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.082612 restraints weight = 12972.632| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.29 r_work: 0.2830 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8823 Z= 0.335 Angle : 0.705 15.545 11961 Z= 0.335 Chirality : 0.045 0.293 1363 Planarity : 0.004 0.050 1498 Dihedral : 6.606 84.127 1253 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.16 % Allowed : 23.48 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1089 helix: 2.15 (0.27), residues: 378 sheet: -0.14 (0.30), residues: 285 loop : -0.67 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 154 HIS 0.003 0.001 HIS A 213 PHE 0.027 0.001 PHE R 39 TYR 0.018 0.002 TYR R 222 ARG 0.009 0.001 ARG S 206 *********************** 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 199 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.923 Fit side-chains REVERT: A 21 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8374 (mtm-85) REVERT: A 29 LYS cc_start: 0.8698 (tppp) cc_final: 0.8410 (ttmm) REVERT: A 193 ASP cc_start: 0.8608 (t0) cc_final: 0.8154 (t0) REVERT: A 287 TYR cc_start: 0.7798 (m-80) cc_final: 0.7448 (m-80) REVERT: A 310 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8714 (mm) REVERT: B 61 MET cc_start: 0.9325 (ppp) cc_final: 0.9030 (pp-130) REVERT: B 197 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8129 (tpm-80) REVERT: R 122 THR cc_start: 0.8807 (t) cc_final: 0.8433 (t) REVERT: R 234 LEU cc_start: 0.8491 (mt) cc_final: 0.7624 (tm) REVERT: R 256 LEU cc_start: 0.8277 (pp) cc_final: 0.7661 (tp) outliers start: 39 outliers final: 21 residues processed: 186 average time/residue: 1.2028 time to fit residues: 238.4658 Evaluate side-chains 175 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 224 CYS 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 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 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 57 SER 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 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 15 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 76 optimal weight: 0.0000 chunk 104 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.4168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3582 r_free = 0.3582 target = 0.122517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.085304 restraints weight = 13090.413| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.30 r_work: 0.2873 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8823 Z= 0.207 Angle : 0.684 18.322 11961 Z= 0.323 Chirality : 0.043 0.276 1363 Planarity : 0.004 0.055 1498 Dihedral : 6.490 84.117 1253 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.77 % Allowed : 26.15 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.26), residues: 1089 helix: 2.23 (0.27), residues: 379 sheet: -0.09 (0.30), residues: 284 loop : -0.57 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 154 HIS 0.008 0.001 HIS B 142 PHE 0.009 0.001 PHE B 151 TYR 0.015 0.001 TYR R 222 ARG 0.012 0.001 ARG S 206 *********************** 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 184 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.823 Fit side-chains REVERT: A 21 ARG cc_start: 0.8693 (ttm-80) cc_final: 0.8399 (mtm-85) REVERT: A 29 LYS cc_start: 0.8694 (tppp) cc_final: 0.8424 (ttmm) REVERT: A 193 ASP cc_start: 0.8614 (t0) cc_final: 0.8159 (t0) REVERT: A 310 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8767 (mm) REVERT: B 61 MET cc_start: 0.9279 (ppp) cc_final: 0.9005 (pp-130) REVERT: B 197 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8146 (tpm-80) REVERT: B 226 GLU cc_start: 0.8543 (mp0) cc_final: 0.8294 (mm-30) REVERT: B 258 ASP cc_start: 0.8715 (t0) cc_final: 0.8034 (t0) REVERT: R 39 PHE cc_start: 0.8174 (t80) cc_final: 0.7930 (t80) REVERT: R 122 THR cc_start: 0.8787 (t) cc_final: 0.8431 (t) REVERT: R 234 LEU cc_start: 0.8493 (mt) cc_final: 0.7642 (tm) outliers start: 26 outliers final: 15 residues processed: 174 average time/residue: 1.1834 time to fit residues: 219.3602 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 : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 284 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 57 SER 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 245 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 89 optimal weight: 0.0270 chunk 69 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3594 r_free = 0.3594 target = 0.123436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.085851 restraints weight = 13254.254| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.39 r_work: 0.2886 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8823 Z= 0.170 Angle : 0.675 17.113 11961 Z= 0.315 Chirality : 0.042 0.253 1363 Planarity : 0.004 0.051 1498 Dihedral : 6.207 83.371 1253 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.09 % Allowed : 26.57 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1089 helix: 2.27 (0.27), residues: 380 sheet: 0.03 (0.31), residues: 268 loop : -0.49 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 154 HIS 0.003 0.000 HIS B 142 PHE 0.009 0.001 PHE R 104 TYR 0.013 0.001 TYR A 287 ARG 0.013 0.001 ARG S 206 *********************** 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 195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 1.014 Fit side-chains REVERT: A 21 ARG cc_start: 0.8669 (ttm-80) cc_final: 0.8377 (ttp-110) REVERT: A 29 LYS cc_start: 0.8603 (tppp) cc_final: 0.8368 (ttmm) REVERT: A 193 ASP cc_start: 0.8613 (t0) cc_final: 0.8155 (t0) REVERT: A 310 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8798 (mm) REVERT: A 324 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.7970 (t) REVERT: B 61 MET cc_start: 0.9177 (ppp) cc_final: 0.8959 (pp-130) REVERT: B 156 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8846 (mm-40) REVERT: B 197 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8249 (tpm-80) REVERT: B 258 ASP cc_start: 0.8575 (t0) cc_final: 0.7935 (t0) REVERT: S 73 ASP cc_start: 0.8519 (t0) cc_final: 0.8243 (t0) REVERT: R 39 PHE cc_start: 0.8166 (t80) cc_final: 0.7958 (t80) REVERT: R 122 THR cc_start: 0.8881 (t) cc_final: 0.8543 (t) REVERT: R 201 SER cc_start: 0.8383 (m) cc_final: 0.8041 (t) REVERT: R 234 LEU cc_start: 0.8484 (mt) cc_final: 0.7646 (tm) REVERT: R 242 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7681 (pp30) outliers start: 29 outliers final: 12 residues processed: 185 average time/residue: 1.1760 time to fit residues: 231.9628 Evaluate side-chains 169 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 LYS 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 254 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 35 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 258 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 101 optimal weight: 0.0020 chunk 55 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 23 optimal weight: 10.0000 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 304 GLN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.122936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.085434 restraints weight = 13274.666| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.38 r_work: 0.2882 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8823 Z= 0.193 Angle : 0.688 15.230 11961 Z= 0.325 Chirality : 0.043 0.237 1363 Planarity : 0.004 0.060 1498 Dihedral : 5.929 83.259 1253 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.56 % Allowed : 27.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1089 helix: 2.24 (0.27), residues: 381 sheet: 0.06 (0.32), residues: 268 loop : -0.49 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 154 HIS 0.003 0.001 HIS B 142 PHE 0.009 0.001 PHE B 253 TYR 0.012 0.001 TYR R 222 ARG 0.014 0.001 ARG S 206 *********************** 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 178 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.968 Fit side-chains REVERT: A 21 ARG cc_start: 0.8677 (ttm-80) cc_final: 0.8389 (ttp-110) REVERT: A 29 LYS cc_start: 0.8670 (tppp) cc_final: 0.8437 (ttmm) REVERT: A 193 ASP cc_start: 0.8613 (t0) cc_final: 0.8158 (t0) REVERT: A 287 TYR cc_start: 0.7111 (m-80) cc_final: 0.6621 (m-80) REVERT: A 310 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8761 (mm) REVERT: A 324 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7927 (t) REVERT: B 61 MET cc_start: 0.9203 (ppp) cc_final: 0.8968 (pp-130) REVERT: B 156 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8868 (mm-40) REVERT: B 197 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8193 (tpm-80) REVERT: B 258 ASP cc_start: 0.8577 (t0) cc_final: 0.7958 (t0) REVERT: S 73 ASP cc_start: 0.8592 (t0) cc_final: 0.8257 (t0) REVERT: R 122 THR cc_start: 0.8893 (t) cc_final: 0.8564 (t) REVERT: R 201 SER cc_start: 0.8389 (m) cc_final: 0.8030 (t) REVERT: R 234 LEU cc_start: 0.8498 (mt) cc_final: 0.7671 (tm) outliers start: 24 outliers final: 14 residues processed: 169 average time/residue: 1.3518 time to fit residues: 242.4539 Evaluate side-chains 165 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 137 ARG 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 254 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain G residue 54 VAL 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 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 107 optimal weight: 0.0020 chunk 106 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.124366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.087128 restraints weight = 13152.387| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.38 r_work: 0.2912 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8823 Z= 0.171 Angle : 0.678 15.153 11961 Z= 0.322 Chirality : 0.042 0.195 1363 Planarity : 0.004 0.056 1498 Dihedral : 5.453 82.934 1253 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.92 % Allowed : 28.28 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1089 helix: 2.24 (0.27), residues: 381 sheet: 0.11 (0.31), residues: 274 loop : -0.49 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 154 HIS 0.002 0.000 HIS A 322 PHE 0.008 0.001 PHE R 104 TYR 0.014 0.001 TYR A 320 ARG 0.013 0.001 ARG S 206 ********************** 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 180 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.023 Fit side-chains REVERT: A 21 ARG cc_start: 0.8668 (ttm-80) cc_final: 0.8384 (ttp-110) REVERT: A 29 LYS cc_start: 0.8607 (tppp) cc_final: 0.8362 (ttmm) REVERT: A 193 ASP cc_start: 0.8601 (t0) cc_final: 0.8143 (t0) REVERT: A 287 TYR cc_start: 0.7250 (m-80) cc_final: 0.6742 (m-80) REVERT: A 310 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8834 (mm) REVERT: A 324 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.7917 (t) REVERT: B 197 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8085 (tpm-80) REVERT: B 258 ASP cc_start: 0.8482 (t0) cc_final: 0.7899 (t0) REVERT: S 73 ASP cc_start: 0.8593 (t0) cc_final: 0.8259 (t0) REVERT: R 122 THR cc_start: 0.8872 (t) cc_final: 0.8534 (t) REVERT: R 201 SER cc_start: 0.8362 (m) cc_final: 0.8025 (t) REVERT: R 234 LEU cc_start: 0.8490 (mt) cc_final: 0.7667 (tm) REVERT: R 242 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7722 (pp30) outliers start: 18 outliers final: 13 residues processed: 175 average time/residue: 1.2381 time to fit residues: 230.4740 Evaluate side-chains 167 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 228 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 168 CYS Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 46 optimal weight: 0.0470 chunk 39 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.087172 restraints weight = 13144.971| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.37 r_work: 0.2915 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8823 Z= 0.177 Angle : 0.690 18.047 11961 Z= 0.328 Chirality : 0.043 0.333 1363 Planarity : 0.004 0.054 1498 Dihedral : 5.325 82.802 1253 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.03 % Allowed : 28.71 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1089 helix: 2.16 (0.27), residues: 381 sheet: 0.11 (0.31), residues: 276 loop : -0.45 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 154 HIS 0.003 0.000 HIS B 142 PHE 0.010 0.001 PHE R 81 TYR 0.012 0.001 TYR S 178 ARG 0.012 0.001 ARG S 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7809.22 seconds wall clock time: 135 minutes 18.47 seconds (8118.47 seconds total)