Starting phenix.real_space_refine on Sat Dec 28 13:57:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vv3_32136/12_2024/7vv3_32136.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vv3_32136/12_2024/7vv3_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_32136/12_2024/7vv3_32136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vv3_32136/12_2024/7vv3_32136.map" model { file = "/net/cci-nas-00/data/ceres_data/7vv3_32136/12_2024/7vv3_32136.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vv3_32136/12_2024/7vv3_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-5532/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: 5.56, per 1000 atoms: 0.64 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: 2.91 Conformation dependent library (CDL) restraints added in 1.0 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: 1.03 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: 2.48 Time building geometry restraints manager: 2.49 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: 0.230 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 21.870 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: 0.000 Load rotamer database and sin/cos tables:11.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.510 ------------------------------------------------------------------------------- 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 : 1.066 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: 1.5102 time to fit residues: 340.9458 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 : 1.092 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 14.904 11961 Z= 0.348 Chirality : 0.044 0.298 1363 Planarity : 0.005 0.049 1498 Dihedral : 7.538 116.588 1257 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.22 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 : 1.034 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7957 (ttp-110) REVERT: A 193 ASP cc_start: 0.7693 (t0) cc_final: 0.7352 (t0) REVERT: B 15 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8816 (ttpp) REVERT: B 156 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8552 (mm-40) REVERT: B 197 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7346 (tpm-80) REVERT: B 215 GLU cc_start: 0.7465 (pt0) cc_final: 0.7254 (pt0) REVERT: R 39 PHE cc_start: 0.7889 (t80) cc_final: 0.7627 (t80) outliers start: 26 outliers final: 10 residues processed: 190 average time/residue: 1.2713 time to fit residues: 256.4573 Evaluate side-chains 159 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 54 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 294 ASN A 304 GLN B 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8823 Z= 0.300 Angle : 0.679 15.120 11961 Z= 0.329 Chirality : 0.044 0.304 1363 Planarity : 0.004 0.042 1498 Dihedral : 6.624 82.054 1253 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.95 % Allowed : 18.04 % Favored : 78.01 % 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: 0.23 (0.25), residues: 1089 helix: 1.63 (0.27), residues: 377 sheet: -0.13 (0.30), residues: 293 loop : -0.94 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 154 HIS 0.019 0.001 HIS B 142 PHE 0.015 0.001 PHE R 39 TYR 0.027 0.002 TYR R 222 ARG 0.007 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 197 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 1.001 Fit side-chains REVERT: A 29 LYS cc_start: 0.8451 (tppp) cc_final: 0.8185 (ttmm) REVERT: A 193 ASP cc_start: 0.7707 (t0) cc_final: 0.7363 (t0) REVERT: B 10 GLU cc_start: 0.8454 (tt0) cc_final: 0.8140 (tp30) REVERT: R 39 PHE cc_start: 0.7878 (t80) cc_final: 0.7600 (t80) outliers start: 37 outliers final: 13 residues processed: 184 average time/residue: 1.2711 time to fit residues: 248.3842 Evaluate side-chains 167 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 253 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 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 258 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2428 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= 0.203 Angle : 0.626 14.666 11961 Z= 0.303 Chirality : 0.042 0.295 1363 Planarity : 0.004 0.040 1498 Dihedral : 6.464 82.162 1253 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.99 % Allowed : 21.02 % Favored : 75.99 % 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: 0.57 (0.26), residues: 1089 helix: 2.05 (0.27), residues: 378 sheet: -0.07 (0.30), residues: 291 loop : -0.82 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.014 0.001 HIS B 142 PHE 0.012 0.001 PHE R 39 TYR 0.023 0.002 TYR R 222 ARG 0.009 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 192 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.987 Fit side-chains REVERT: A 21 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7915 (ttp-110) REVERT: A 29 LYS cc_start: 0.8450 (tppp) cc_final: 0.8178 (ttmm) REVERT: A 193 ASP cc_start: 0.7723 (t0) cc_final: 0.7278 (t0) REVERT: A 287 TYR cc_start: 0.7780 (m-80) cc_final: 0.7536 (m-80) REVERT: A 310 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8767 (mm) REVERT: B 197 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7333 (tpm-80) REVERT: G 29 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8390 (mmtm) REVERT: R 39 PHE cc_start: 0.7847 (t80) cc_final: 0.7629 (t80) outliers start: 28 outliers final: 14 residues processed: 180 average time/residue: 1.1679 time to fit residues: 224.5384 Evaluate side-chains 165 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 197 ARG 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 29 LYS 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 0.0370 chunk 43 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 8823 Z= 0.386 Angle : 0.696 14.816 11961 Z= 0.339 Chirality : 0.046 0.298 1363 Planarity : 0.004 0.038 1498 Dihedral : 6.688 83.732 1253 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.59 % Allowed : 22.31 % Favored : 73.11 % 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: 0.56 (0.26), residues: 1089 helix: 2.08 (0.27), residues: 377 sheet: -0.22 (0.30), residues: 289 loop : -0.72 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 154 HIS 0.004 0.001 HIS B 142 PHE 0.011 0.001 PHE B 235 TYR 0.020 0.002 TYR R 222 ARG 0.006 0.001 ARG B 8 *********************** 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 205 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.054 Fit side-chains REVERT: A 21 ARG cc_start: 0.8264 (ttm-80) cc_final: 0.7974 (mtm-85) REVERT: A 29 LYS cc_start: 0.8514 (tppp) cc_final: 0.8224 (ttmm) REVERT: A 193 ASP cc_start: 0.7738 (t0) cc_final: 0.7384 (t0) REVERT: A 287 TYR cc_start: 0.7994 (m-80) cc_final: 0.7719 (m-80) REVERT: A 310 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8745 (mm) REVERT: B 197 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7327 (tpm-80) REVERT: R 234 LEU cc_start: 0.8433 (mt) cc_final: 0.7557 (tm) REVERT: R 242 GLN cc_start: 0.8044 (pp30) cc_final: 0.7541 (pp30) outliers start: 43 outliers final: 18 residues processed: 190 average time/residue: 1.2512 time to fit residues: 252.8252 Evaluate side-chains 170 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 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 47 GLU 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 35 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 ** R 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2759 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= 0.173 Angle : 0.659 15.602 11961 Z= 0.311 Chirality : 0.042 0.279 1363 Planarity : 0.004 0.050 1498 Dihedral : 6.510 83.331 1253 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.31 % Allowed : 24.65 % Favored : 72.04 % 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: 0.72 (0.26), residues: 1089 helix: 2.24 (0.27), residues: 379 sheet: -0.18 (0.30), residues: 286 loop : -0.63 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 154 HIS 0.004 0.001 HIS B 142 PHE 0.010 0.001 PHE R 81 TYR 0.018 0.001 TYR R 222 ARG 0.010 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 195 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7949 (mtm-85) REVERT: A 29 LYS cc_start: 0.8432 (tppp) cc_final: 0.8150 (ttmm) REVERT: A 193 ASP cc_start: 0.7769 (t0) cc_final: 0.7424 (t0) REVERT: A 310 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8774 (mm) REVERT: B 61 MET cc_start: 0.8352 (ppp) cc_final: 0.8135 (pp-130) REVERT: B 258 ASP cc_start: 0.8268 (t0) cc_final: 0.7629 (t0) REVERT: R 39 PHE cc_start: 0.7887 (t80) cc_final: 0.7644 (t80) REVERT: R 75 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6843 (t0) REVERT: R 234 LEU cc_start: 0.8362 (mt) cc_final: 0.7487 (tm) REVERT: R 256 LEU cc_start: 0.8318 (pp) cc_final: 0.7652 (tp) outliers start: 31 outliers final: 16 residues processed: 184 average time/residue: 1.2070 time to fit residues: 237.2255 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 : 1.003 ------------------------------------------------------------------------------- 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 349 LYS Chi-restraints excluded: chain B residue 8 ARG Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER 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 R residue 35 PHE Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 50 PHE 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 213 SER Chi-restraints excluded: chain R residue 258 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8823 Z= 0.259 Angle : 0.701 20.728 11961 Z= 0.329 Chirality : 0.044 0.277 1363 Planarity : 0.003 0.033 1498 Dihedral : 6.564 83.643 1253 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.42 % Allowed : 25.61 % Favored : 70.97 % 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: 0.79 (0.26), residues: 1089 helix: 2.28 (0.27), residues: 379 sheet: -0.15 (0.30), residues: 287 loop : -0.55 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 154 HIS 0.002 0.001 HIS A 322 PHE 0.011 0.001 PHE R 183 TYR 0.015 0.002 TYR R 222 ARG 0.007 0.000 ARG S 148 *********************** 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 191 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 1.002 Fit side-chains REVERT: A 21 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7951 (mtm-85) REVERT: A 29 LYS cc_start: 0.8458 (tppp) cc_final: 0.8159 (ttmm) REVERT: A 193 ASP cc_start: 0.7765 (t0) cc_final: 0.7405 (t0) REVERT: A 310 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8787 (mm) REVERT: B 23 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8414 (tmtm) REVERT: B 61 MET cc_start: 0.8455 (ppp) cc_final: 0.8152 (pp-130) REVERT: B 258 ASP cc_start: 0.8336 (t0) cc_final: 0.7692 (t0) REVERT: R 39 PHE cc_start: 0.7895 (t80) cc_final: 0.7672 (t80) REVERT: R 234 LEU cc_start: 0.8444 (mt) cc_final: 0.7584 (tm) REVERT: R 242 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7410 (pp30) outliers start: 32 outliers final: 19 residues processed: 177 average time/residue: 1.2503 time to fit residues: 235.2482 Evaluate side-chains 171 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 349 LYS Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 58 ILE 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 47 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 35 PHE 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 210 LEU Chi-restraints excluded: chain R residue 258 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8823 Z= 0.194 Angle : 0.702 24.119 11961 Z= 0.323 Chirality : 0.043 0.252 1363 Planarity : 0.004 0.051 1498 Dihedral : 6.297 83.639 1253 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.99 % Allowed : 26.36 % Favored : 70.65 % 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: 0.82 (0.26), residues: 1089 helix: 2.29 (0.27), residues: 379 sheet: -0.14 (0.30), residues: 286 loop : -0.52 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 154 HIS 0.007 0.001 HIS B 142 PHE 0.009 0.001 PHE B 151 TYR 0.013 0.001 TYR R 222 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 191 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 1.032 Fit side-chains REVERT: A 21 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7932 (ttp-110) REVERT: A 29 LYS cc_start: 0.8449 (tppp) cc_final: 0.8179 (ttmm) REVERT: A 193 ASP cc_start: 0.7797 (t0) cc_final: 0.7446 (t0) REVERT: A 310 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8823 (mm) REVERT: B 61 MET cc_start: 0.8353 (ppp) cc_final: 0.8090 (pp-130) REVERT: B 226 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7850 (mp0) REVERT: B 258 ASP cc_start: 0.8267 (t0) cc_final: 0.7675 (t0) REVERT: R 39 PHE cc_start: 0.7945 (t80) cc_final: 0.7678 (t80) REVERT: R 201 SER cc_start: 0.8290 (m) cc_final: 0.7847 (t) REVERT: R 234 LEU cc_start: 0.8431 (mt) cc_final: 0.7590 (tm) outliers start: 28 outliers final: 17 residues processed: 181 average time/residue: 1.2367 time to fit residues: 238.5271 Evaluate side-chains 168 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 349 LYS Chi-restraints excluded: chain B residue 161 SER 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 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 35 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2976 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= 0.220 Angle : 0.730 23.560 11961 Z= 0.338 Chirality : 0.043 0.235 1363 Planarity : 0.004 0.061 1498 Dihedral : 6.002 83.671 1253 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.56 % Allowed : 27.64 % 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: 0.87 (0.26), residues: 1089 helix: 2.28 (0.27), residues: 379 sheet: -0.06 (0.30), residues: 284 loop : -0.48 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 154 HIS 0.004 0.001 HIS B 142 PHE 0.009 0.001 PHE B 151 TYR 0.019 0.001 TYR A 287 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 177 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.995 Fit side-chains REVERT: A 21 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.7934 (ttp-110) REVERT: A 29 LYS cc_start: 0.8448 (tppp) cc_final: 0.8177 (ttmm) REVERT: A 193 ASP cc_start: 0.7803 (t0) cc_final: 0.7444 (t0) REVERT: A 310 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8821 (mm) REVERT: B 61 MET cc_start: 0.8376 (ppp) cc_final: 0.8110 (pp-130) REVERT: B 258 ASP cc_start: 0.8252 (t0) cc_final: 0.7664 (t0) REVERT: R 39 PHE cc_start: 0.7950 (t80) cc_final: 0.7687 (t80) REVERT: R 201 SER cc_start: 0.8321 (m) cc_final: 0.7864 (t) REVERT: R 234 LEU cc_start: 0.8478 (mt) cc_final: 0.7652 (tm) REVERT: R 242 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7698 (pp30) outliers start: 24 outliers final: 20 residues processed: 168 average time/residue: 1.2732 time to fit residues: 227.4284 Evaluate side-chains 168 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 349 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 161 SER 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 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 S residue 222 GLU Chi-restraints excluded: chain R residue 35 PHE 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 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 102 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3061 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= 0.190 Angle : 0.718 22.899 11961 Z= 0.333 Chirality : 0.043 0.200 1363 Planarity : 0.004 0.057 1498 Dihedral : 5.604 83.606 1253 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.35 % Allowed : 28.07 % 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 (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: 0.91 (0.26), residues: 1089 helix: 2.28 (0.27), residues: 380 sheet: 0.04 (0.31), residues: 273 loop : -0.48 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 154 HIS 0.002 0.000 HIS B 142 PHE 0.009 0.001 PHE B 253 TYR 0.013 0.001 TYR A 287 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 181 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 0.972 Fit side-chains REVERT: A 21 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.7934 (ttp-110) REVERT: A 29 LYS cc_start: 0.8420 (tppp) cc_final: 0.8190 (ttmm) REVERT: A 193 ASP cc_start: 0.7784 (t0) cc_final: 0.7442 (t0) REVERT: A 310 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8790 (mm) REVERT: B 61 MET cc_start: 0.8331 (ppp) cc_final: 0.8089 (pp-130) REVERT: B 258 ASP cc_start: 0.8222 (t0) cc_final: 0.7655 (t0) REVERT: B 262 MET cc_start: 0.8477 (tpp) cc_final: 0.8215 (ttm) REVERT: R 201 SER cc_start: 0.8293 (m) cc_final: 0.7844 (t) REVERT: R 234 LEU cc_start: 0.8481 (mt) cc_final: 0.7659 (tm) REVERT: R 242 GLN cc_start: 0.8018 (tm-30) cc_final: 0.7665 (pp30) outliers start: 22 outliers final: 18 residues processed: 175 average time/residue: 1.2484 time to fit residues: 232.3494 Evaluate side-chains 169 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 349 LYS Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 254 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 S residue 222 GLU Chi-restraints excluded: chain R residue 35 PHE 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 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 91 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 0.0980 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.123405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.086121 restraints weight = 12940.989| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.35 r_work: 0.2894 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3152 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= 0.179 Angle : 0.711 21.263 11961 Z= 0.335 Chirality : 0.043 0.249 1363 Planarity : 0.004 0.054 1498 Dihedral : 5.265 83.310 1253 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.45 % Allowed : 28.50 % Favored : 69.05 % 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: 2.26 (0.27), residues: 381 sheet: 0.04 (0.31), residues: 270 loop : -0.45 (0.30), residues: 438 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 0.033 0.001 PHE R 39 TYR 0.013 0.001 TYR A 320 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: 4043.49 seconds wall clock time: 73 minutes 0.95 seconds (4380.95 seconds total)