Starting phenix.real_space_refine on Thu Feb 13 02:18:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk3_34843/02_2025/8hk3_34843.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk3_34843/02_2025/8hk3_34843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hk3_34843/02_2025/8hk3_34843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk3_34843/02_2025/8hk3_34843.map" model { file = "/net/cci-nas-00/data/ceres_data/8hk3_34843/02_2025/8hk3_34843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk3_34843/02_2025/8hk3_34843.cif" } resolution = 3.2 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= 0.002 sd= 0.033 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 69 5.16 5 C 5585 2.51 5 N 1488 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8746 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1801 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "C" Number of atoms: 2244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2244 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 15, 'TRANS': 268} Chain breaks: 1 Chain: "G" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Time building chain proxies: 4.86, per 1000 atoms: 0.56 Number of scatterers: 8746 At special positions: 0 Unit cell: (105.04, 115.44, 131.04, 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 69 16.00 O 1604 8.00 N 1488 7.00 C 5585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " distance=2.03 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: 2.60 Conformation dependent library (CDL) restraints added in 1.2 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 39.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 8 through 31 removed outlier: 4.111A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 54 removed outlier: 3.976A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.661A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.020A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.855A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.597A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.552A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.876A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 51 removed outlier: 4.223A pdb=" N LEU C 38 " --> pdb=" O PHE C 34 " (cutoff:3.500A) Proline residue: C 39 - end of helix Processing helix chain 'C' and resid 55 through 84 Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 91 through 126 removed outlier: 4.043A pdb=" N CYS C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 96 " --> pdb=" O ARG C 92 " (cutoff:3.500A) Proline residue: C 99 - end of helix removed outlier: 3.772A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 134 removed outlier: 3.602A pdb=" N ASN C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 161 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 331 through 365 removed outlier: 5.709A pdb=" N LEU C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 372 through 403 removed outlier: 3.855A pdb=" N PHE C 376 " --> pdb=" O GLN C 372 " (cutoff:3.500A) Proline residue: C 392 - end of helix removed outlier: 3.552A pdb=" N LEU C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU C 402 " --> pdb=" O VAL C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 431 removed outlier: 3.623A pdb=" N LYS C 411 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS C 420 " --> pdb=" O TRP C 416 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 421 " --> pdb=" O ASP C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 439 through 454 removed outlier: 3.516A pdb=" N ARG C 443 " --> pdb=" O GLY C 439 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS C 444 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.704A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.510A pdb=" N ASP A 200 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 187 " --> pdb=" O MET A 198 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.192A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.672A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.648A 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: 6.856A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.849A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.830A 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: 3.554A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.470A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.548A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 162 through 165 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.643A pdb=" N VAL H 5 " --> pdb=" O SER H 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.107A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.587A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE H 189 " --> pdb=" O TRP H 176 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN H 194 " --> pdb=" O TYR H 190 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1194 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: 2.71 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1408 1.31 - 1.43: 2456 1.43 - 1.56: 4973 1.56 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 8935 Sorted by residual: bond pdb=" C LEU C 32 " pdb=" O LEU C 32 " ideal model delta sigma weight residual 1.236 1.183 0.054 1.26e-02 6.30e+03 1.82e+01 bond pdb=" C PHE C 345 " pdb=" O PHE C 345 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.36e-02 5.41e+03 1.46e+01 bond pdb=" C LEU C 38 " pdb=" O LEU C 38 " ideal model delta sigma weight residual 1.241 1.206 0.036 9.80e-03 1.04e+04 1.33e+01 bond pdb=" CA GLN C 372 " pdb=" C GLN C 372 " ideal model delta sigma weight residual 1.527 1.497 0.030 1.30e-02 5.92e+03 5.32e+00 bond pdb=" C THR C 33 " pdb=" O THR C 33 " ideal model delta sigma weight residual 1.237 1.211 0.025 1.16e-02 7.43e+03 4.76e+00 ... (remaining 8930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 12061 2.45 - 4.90: 55 4.90 - 7.34: 4 7.34 - 9.79: 0 9.79 - 12.24: 1 Bond angle restraints: 12121 Sorted by residual: angle pdb=" N GLY C 91 " pdb=" CA GLY C 91 " pdb=" C GLY C 91 " ideal model delta sigma weight residual 112.83 119.62 -6.79 1.70e+00 3.46e-01 1.60e+01 angle pdb=" CA LEU C 35 " pdb=" CB LEU C 35 " pdb=" CG LEU C 35 " ideal model delta sigma weight residual 116.30 128.54 -12.24 3.50e+00 8.16e-02 1.22e+01 angle pdb=" CA GLN C 372 " pdb=" CB GLN C 372 " pdb=" CG GLN C 372 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N ARG C 92 " pdb=" CA ARG C 92 " pdb=" C ARG C 92 " ideal model delta sigma weight residual 111.69 115.66 -3.97 1.23e+00 6.61e-01 1.04e+01 angle pdb=" C LEU C 38 " pdb=" N PRO C 39 " pdb=" CA PRO C 39 " ideal model delta sigma weight residual 118.97 115.99 2.98 1.04e+00 9.25e-01 8.22e+00 ... (remaining 12116 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 5192 15.97 - 31.94: 67 31.94 - 47.92: 15 47.92 - 63.89: 2 63.89 - 79.86: 2 Dihedral angle restraints: 5278 sinusoidal: 1996 harmonic: 3282 Sorted by residual: dihedral pdb=" N GLN C 372 " pdb=" C GLN C 372 " pdb=" CA GLN C 372 " pdb=" CB GLN C 372 " ideal model delta harmonic sigma weight residual 122.80 131.22 -8.42 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" N LEU C 38 " pdb=" C LEU C 38 " pdb=" CA LEU C 38 " pdb=" CB LEU C 38 " ideal model delta harmonic sigma weight residual 122.80 130.89 -8.09 0 2.50e+00 1.60e-01 1.05e+01 dihedral pdb=" C GLN C 372 " pdb=" N GLN C 372 " pdb=" CA GLN C 372 " pdb=" CB GLN C 372 " ideal model delta harmonic sigma weight residual -122.60 -130.23 7.63 0 2.50e+00 1.60e-01 9.32e+00 ... (remaining 5275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1278 0.073 - 0.147: 107 0.147 - 0.220: 0 0.220 - 0.293: 2 0.293 - 0.367: 3 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CA LEU C 38 " pdb=" N LEU C 38 " pdb=" C LEU C 38 " pdb=" CB LEU C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA GLN C 372 " pdb=" N GLN C 372 " pdb=" C GLN C 372 " pdb=" CB GLN C 372 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CG LEU C 38 " pdb=" CB LEU C 38 " pdb=" CD1 LEU C 38 " pdb=" CD2 LEU C 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 1387 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 90 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C TYR C 90 " -0.059 2.00e-02 2.50e+03 pdb=" O TYR C 90 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY C 91 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 31 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C SER C 31 " 0.045 2.00e-02 2.50e+03 pdb=" O SER C 31 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU C 32 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 345 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C PHE C 345 " 0.029 2.00e-02 2.50e+03 pdb=" O PHE C 345 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU C 346 " -0.010 2.00e-02 2.50e+03 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 82 2.63 - 3.20: 8136 3.20 - 3.77: 12881 3.77 - 4.33: 18184 4.33 - 4.90: 30718 Nonbonded interactions: 70001 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.069 3.040 nonbonded pdb=" OG1 THR C 55 " pdb=" OG1 THR C 58 " model vdw 2.149 3.040 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.160 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.181 3.120 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.197 3.040 ... (remaining 69996 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: 0.340 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.830 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 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 : 0.002 0.054 8935 Z= 0.150 Angle : 0.421 12.240 12121 Z= 0.233 Chirality : 0.042 0.367 1390 Planarity : 0.002 0.034 1528 Dihedral : 6.311 79.860 3155 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.11 % Allowed : 1.81 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.24), residues: 1119 helix: 0.65 (0.26), residues: 397 sheet: -1.05 (0.28), residues: 287 loop : -1.56 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 99 HIS 0.001 0.000 HIS C 394 PHE 0.008 0.001 PHE C 34 TYR 0.003 0.000 TYR H 190 ARG 0.002 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 280 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 36 LEU cc_start: 0.7685 (mt) cc_final: 0.7460 (mp) REVERT: A 191 PHE cc_start: 0.8168 (t80) cc_final: 0.7968 (t80) REVERT: A 197 LYS cc_start: 0.7625 (mtpp) cc_final: 0.7081 (mtpp) REVERT: B 61 MET cc_start: 0.6755 (ppp) cc_final: 0.6376 (ppp) REVERT: B 102 THR cc_start: 0.7984 (t) cc_final: 0.7769 (t) REVERT: B 170 ASP cc_start: 0.6201 (t70) cc_final: 0.5998 (t0) REVERT: B 246 ASP cc_start: 0.7459 (m-30) cc_final: 0.7216 (m-30) REVERT: B 277 SER cc_start: 0.8547 (t) cc_final: 0.8103 (m) REVERT: C 138 MET cc_start: 0.6859 (ttp) cc_final: 0.6429 (ttp) REVERT: C 141 SER cc_start: 0.7926 (t) cc_final: 0.7724 (p) REVERT: C 156 PRO cc_start: 0.7669 (Cg_exo) cc_final: 0.7437 (Cg_endo) REVERT: C 399 LEU cc_start: 0.7811 (mp) cc_final: 0.7580 (mt) REVERT: H 161 SER cc_start: 0.8318 (t) cc_final: 0.8117 (p) outliers start: 1 outliers final: 1 residues processed: 281 average time/residue: 0.2359 time to fit residues: 89.9904 Evaluate side-chains 229 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 75 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 220 GLN B 268 ASN B 295 ASN ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 HIS H 179 GLN H 194 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110474 restraints weight = 12088.427| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.95 r_work: 0.3223 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 8935 Z= 0.399 Angle : 0.627 9.906 12121 Z= 0.323 Chirality : 0.046 0.170 1390 Planarity : 0.005 0.044 1528 Dihedral : 4.405 57.750 1218 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.70 % Allowed : 8.73 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.24), residues: 1119 helix: 1.47 (0.26), residues: 402 sheet: -0.54 (0.29), residues: 284 loop : -1.51 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.010 0.002 HIS B 91 PHE 0.032 0.003 PHE B 199 TYR 0.025 0.003 TYR H 102 ARG 0.005 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 219 time to evaluate : 0.953 Fit side-chains REVERT: A 14 GLU cc_start: 0.7876 (tp30) cc_final: 0.7575 (tp30) REVERT: A 197 LYS cc_start: 0.8207 (mtpp) cc_final: 0.8007 (mtpt) REVERT: A 198 MET cc_start: 0.8347 (mtp) cc_final: 0.8139 (ttm) REVERT: B 14 LEU cc_start: 0.7990 (mm) cc_final: 0.7755 (mt) REVERT: B 46 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7564 (mtp-110) REVERT: B 50 THR cc_start: 0.8465 (m) cc_final: 0.8252 (t) REVERT: B 155 ASN cc_start: 0.7918 (t0) cc_final: 0.7519 (t0) REVERT: B 170 ASP cc_start: 0.7376 (t70) cc_final: 0.6983 (t0) REVERT: B 220 GLN cc_start: 0.8361 (mt0) cc_final: 0.8131 (mt0) REVERT: B 295 ASN cc_start: 0.8500 (m-40) cc_final: 0.8259 (m-40) REVERT: C 391 THR cc_start: 0.8465 (m) cc_final: 0.8249 (m) REVERT: C 399 LEU cc_start: 0.8099 (mp) cc_final: 0.7864 (mt) REVERT: H 80 PHE cc_start: 0.7559 (m-80) cc_final: 0.7343 (m-10) REVERT: H 119 VAL cc_start: 0.7784 (t) cc_final: 0.7424 (p) REVERT: H 161 SER cc_start: 0.8430 (t) cc_final: 0.8199 (p) outliers start: 16 outliers final: 13 residues processed: 225 average time/residue: 0.2164 time to fit residues: 67.4295 Evaluate side-chains 210 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 32 GLN B 75 GLN B 110 ASN B 156 GLN B 237 ASN ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.128068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109662 restraints weight = 12319.596| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.97 r_work: 0.3239 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8935 Z= 0.215 Angle : 0.521 7.292 12121 Z= 0.268 Chirality : 0.042 0.163 1390 Planarity : 0.004 0.047 1528 Dihedral : 4.152 58.062 1218 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.02 % Allowed : 10.44 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1119 helix: 1.83 (0.27), residues: 403 sheet: -0.23 (0.29), residues: 286 loop : -1.19 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.005 0.001 HIS B 91 PHE 0.020 0.002 PHE B 199 TYR 0.015 0.002 TYR H 95 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 1.034 Fit side-chains REVERT: A 29 LYS cc_start: 0.8286 (ttpt) cc_final: 0.8086 (ttpt) REVERT: A 225 VAL cc_start: 0.8664 (p) cc_final: 0.8345 (m) REVERT: B 46 ARG cc_start: 0.7894 (mtp-110) cc_final: 0.7567 (mtp-110) REVERT: B 61 MET cc_start: 0.7914 (ppp) cc_final: 0.7605 (ppp) REVERT: B 155 ASN cc_start: 0.8001 (t0) cc_final: 0.7596 (t0) REVERT: B 170 ASP cc_start: 0.7385 (t70) cc_final: 0.6974 (t0) REVERT: B 295 ASN cc_start: 0.8528 (m-40) cc_final: 0.8311 (m-40) REVERT: C 340 ARG cc_start: 0.7868 (ttp-170) cc_final: 0.7461 (ttp-170) REVERT: C 391 THR cc_start: 0.8448 (m) cc_final: 0.8203 (m) REVERT: C 399 LEU cc_start: 0.8172 (mp) cc_final: 0.7917 (mt) REVERT: C 414 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7465 (mpp) REVERT: G 27 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8089 (mtt-85) REVERT: H 103 TYR cc_start: 0.8230 (t80) cc_final: 0.7909 (t80) REVERT: H 119 VAL cc_start: 0.7847 (t) cc_final: 0.7434 (p) REVERT: H 161 SER cc_start: 0.8404 (t) cc_final: 0.8187 (p) outliers start: 19 outliers final: 12 residues processed: 203 average time/residue: 0.2393 time to fit residues: 64.4994 Evaluate side-chains 208 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 35 optimal weight: 3.9990 chunk 89 optimal weight: 0.0060 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 70 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 63 HIS C 169 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107530 restraints weight = 12240.326| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.99 r_work: 0.3198 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8935 Z= 0.302 Angle : 0.549 9.168 12121 Z= 0.286 Chirality : 0.043 0.173 1390 Planarity : 0.004 0.046 1528 Dihedral : 4.405 59.522 1218 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.24 % Allowed : 12.25 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1119 helix: 1.92 (0.26), residues: 405 sheet: -0.21 (0.29), residues: 289 loop : -1.00 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 339 HIS 0.005 0.001 HIS B 91 PHE 0.024 0.002 PHE B 199 TYR 0.018 0.002 TYR H 95 ARG 0.005 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.998 Fit side-chains REVERT: A 14 GLU cc_start: 0.7941 (tp30) cc_final: 0.7658 (tp30) REVERT: A 29 LYS cc_start: 0.8286 (ttpt) cc_final: 0.8074 (ttpt) REVERT: A 32 ARG cc_start: 0.8125 (ttm-80) cc_final: 0.7851 (ttm-80) REVERT: A 53 MET cc_start: 0.6890 (mpp) cc_final: 0.6229 (mpp) REVERT: A 225 VAL cc_start: 0.8703 (p) cc_final: 0.8368 (m) REVERT: B 46 ARG cc_start: 0.7913 (mtp-110) cc_final: 0.7599 (mtp-110) REVERT: B 155 ASN cc_start: 0.8069 (t0) cc_final: 0.7662 (t0) REVERT: B 170 ASP cc_start: 0.7539 (t70) cc_final: 0.7185 (t0) REVERT: B 237 ASN cc_start: 0.8390 (t0) cc_final: 0.8179 (t0) REVERT: C 340 ARG cc_start: 0.7861 (ttp-170) cc_final: 0.7469 (ttp-170) REVERT: C 352 MET cc_start: 0.8339 (mtt) cc_final: 0.7983 (mtp) REVERT: C 357 SER cc_start: 0.8289 (m) cc_final: 0.8074 (m) REVERT: C 391 THR cc_start: 0.8531 (m) cc_final: 0.8313 (m) REVERT: C 399 LEU cc_start: 0.8211 (mp) cc_final: 0.8011 (mt) REVERT: C 414 MET cc_start: 0.7990 (mtp) cc_final: 0.7509 (mpp) REVERT: G 27 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.8185 (mtt-85) REVERT: H 67 ARG cc_start: 0.8391 (ttp80) cc_final: 0.8019 (ttm170) REVERT: H 119 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7476 (p) REVERT: H 161 SER cc_start: 0.8378 (t) cc_final: 0.8168 (p) outliers start: 21 outliers final: 16 residues processed: 213 average time/residue: 0.2436 time to fit residues: 69.1146 Evaluate side-chains 216 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.0370 chunk 38 optimal weight: 0.6980 chunk 32 optimal weight: 0.0050 overall best weight: 0.4872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.127884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.109975 restraints weight = 12197.259| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.96 r_work: 0.3238 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8935 Z= 0.149 Angle : 0.471 6.792 12121 Z= 0.246 Chirality : 0.040 0.151 1390 Planarity : 0.004 0.046 1528 Dihedral : 4.108 58.973 1218 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.60 % Allowed : 12.89 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.25), residues: 1119 helix: 2.14 (0.26), residues: 406 sheet: -0.17 (0.29), residues: 290 loop : -0.82 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.005 0.001 HIS A 188 PHE 0.017 0.001 PHE B 199 TYR 0.009 0.001 TYR H 190 ARG 0.003 0.000 ARG C 443 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8680 (p) cc_final: 0.8347 (m) REVERT: B 46 ARG cc_start: 0.7849 (mtp-110) cc_final: 0.7552 (mtp-110) REVERT: B 61 MET cc_start: 0.7715 (ppp) cc_final: 0.7491 (ppp) REVERT: B 155 ASN cc_start: 0.8107 (t0) cc_final: 0.7779 (t0) REVERT: B 170 ASP cc_start: 0.7446 (t70) cc_final: 0.7088 (t0) REVERT: B 237 ASN cc_start: 0.8299 (t0) cc_final: 0.8069 (t0) REVERT: B 290 ASP cc_start: 0.7790 (m-30) cc_final: 0.7491 (m-30) REVERT: C 340 ARG cc_start: 0.7829 (ttp-170) cc_final: 0.7424 (ttp-170) REVERT: C 391 THR cc_start: 0.8518 (m) cc_final: 0.8291 (m) REVERT: C 414 MET cc_start: 0.7966 (mtp) cc_final: 0.7497 (mpp) REVERT: G 27 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.8242 (mtt-85) REVERT: H 67 ARG cc_start: 0.8353 (ttp80) cc_final: 0.7975 (ttm170) REVERT: H 68 PHE cc_start: 0.7230 (m-10) cc_final: 0.7013 (m-10) REVERT: H 110 PHE cc_start: 0.8559 (t80) cc_final: 0.8347 (t80) REVERT: H 119 VAL cc_start: 0.7912 (t) cc_final: 0.7487 (p) REVERT: H 192 MET cc_start: 0.7356 (ptt) cc_final: 0.7153 (ptt) outliers start: 15 outliers final: 12 residues processed: 210 average time/residue: 0.2474 time to fit residues: 68.9501 Evaluate side-chains 207 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 9 optimal weight: 0.3980 chunk 48 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.128640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110766 restraints weight = 12164.285| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.95 r_work: 0.3235 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8935 Z= 0.162 Angle : 0.477 7.067 12121 Z= 0.247 Chirality : 0.040 0.143 1390 Planarity : 0.004 0.047 1528 Dihedral : 4.051 58.627 1218 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.13 % Allowed : 13.95 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.25), residues: 1119 helix: 2.18 (0.26), residues: 407 sheet: -0.10 (0.29), residues: 289 loop : -0.73 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.018 0.001 PHE B 199 TYR 0.012 0.001 TYR H 95 ARG 0.005 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8315 (ttpt) cc_final: 0.8088 (ttpt) REVERT: A 32 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7802 (ttm-80) REVERT: A 198 MET cc_start: 0.8352 (mtp) cc_final: 0.8137 (ttm) REVERT: A 225 VAL cc_start: 0.8688 (p) cc_final: 0.8341 (m) REVERT: A 341 ASP cc_start: 0.7717 (t70) cc_final: 0.7186 (t0) REVERT: B 46 ARG cc_start: 0.7788 (mtp-110) cc_final: 0.7463 (mtp-110) REVERT: B 61 MET cc_start: 0.7634 (ppp) cc_final: 0.7421 (ppp) REVERT: B 137 ARG cc_start: 0.8167 (ttm170) cc_final: 0.7939 (ttm170) REVERT: B 155 ASN cc_start: 0.8134 (t0) cc_final: 0.7800 (t0) REVERT: B 170 ASP cc_start: 0.7458 (t70) cc_final: 0.7051 (t0) REVERT: B 237 ASN cc_start: 0.8310 (t0) cc_final: 0.8062 (t0) REVERT: B 290 ASP cc_start: 0.7773 (m-30) cc_final: 0.7463 (m-30) REVERT: C 340 ARG cc_start: 0.7825 (ttp-170) cc_final: 0.7396 (ttp-170) REVERT: C 377 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7378 (ttt180) REVERT: C 391 THR cc_start: 0.8490 (m) cc_final: 0.8259 (m) REVERT: C 414 MET cc_start: 0.7924 (mtp) cc_final: 0.7446 (mpp) REVERT: C 437 LEU cc_start: 0.8495 (mp) cc_final: 0.8273 (mt) REVERT: G 27 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8134 (mtt-85) REVERT: H 67 ARG cc_start: 0.8328 (ttp80) cc_final: 0.7874 (ttm170) REVERT: H 68 PHE cc_start: 0.7168 (m-10) cc_final: 0.6905 (m-10) REVERT: H 110 PHE cc_start: 0.8556 (t80) cc_final: 0.8347 (t80) REVERT: H 119 VAL cc_start: 0.7837 (t) cc_final: 0.7412 (p) outliers start: 20 outliers final: 14 residues processed: 206 average time/residue: 0.2503 time to fit residues: 67.6578 Evaluate side-chains 214 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 377 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 0.0000 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.127930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109973 restraints weight = 12227.515| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.95 r_work: 0.3222 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8935 Z= 0.193 Angle : 0.484 7.325 12121 Z= 0.251 Chirality : 0.041 0.152 1390 Planarity : 0.004 0.047 1528 Dihedral : 4.113 58.583 1218 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.34 % Allowed : 14.06 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1119 helix: 2.23 (0.26), residues: 408 sheet: -0.08 (0.29), residues: 289 loop : -0.68 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS H 35 PHE 0.019 0.001 PHE B 199 TYR 0.013 0.001 TYR H 95 ARG 0.003 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8093 (ttm-80) cc_final: 0.7856 (ttm-80) REVERT: A 225 VAL cc_start: 0.8725 (p) cc_final: 0.8401 (m) REVERT: A 240 MET cc_start: 0.4722 (mmm) cc_final: 0.4516 (mmm) REVERT: A 245 GLU cc_start: 0.7339 (tp30) cc_final: 0.6583 (tp30) REVERT: B 50 THR cc_start: 0.8533 (m) cc_final: 0.8190 (t) REVERT: B 61 MET cc_start: 0.7621 (ppp) cc_final: 0.7421 (ppp) REVERT: B 136 SER cc_start: 0.8522 (t) cc_final: 0.8297 (p) REVERT: B 155 ASN cc_start: 0.8194 (t0) cc_final: 0.7879 (t0) REVERT: B 170 ASP cc_start: 0.7566 (t70) cc_final: 0.7206 (t0) REVERT: B 237 ASN cc_start: 0.8315 (t0) cc_final: 0.8066 (t0) REVERT: B 290 ASP cc_start: 0.7776 (m-30) cc_final: 0.7522 (m-30) REVERT: C 340 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.7440 (ttp-170) REVERT: C 357 SER cc_start: 0.8300 (m) cc_final: 0.8088 (m) REVERT: C 377 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7434 (ttt180) REVERT: C 391 THR cc_start: 0.8488 (m) cc_final: 0.8259 (m) REVERT: C 414 MET cc_start: 0.7917 (mtp) cc_final: 0.7453 (mpp) REVERT: C 430 PHE cc_start: 0.7164 (m-10) cc_final: 0.6836 (m-80) REVERT: C 437 LEU cc_start: 0.8551 (mp) cc_final: 0.8317 (mt) REVERT: G 27 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8160 (mtt-85) REVERT: H 67 ARG cc_start: 0.8355 (ttp80) cc_final: 0.7875 (ttm170) REVERT: H 68 PHE cc_start: 0.7167 (m-10) cc_final: 0.6911 (m-10) REVERT: H 119 VAL cc_start: 0.7955 (t) cc_final: 0.7529 (p) outliers start: 22 outliers final: 18 residues processed: 218 average time/residue: 0.2427 time to fit residues: 70.0888 Evaluate side-chains 221 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 377 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 0.1980 chunk 79 optimal weight: 4.9990 chunk 106 optimal weight: 0.0670 chunk 99 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN C 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.128809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110883 restraints weight = 12321.584| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.96 r_work: 0.3240 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8935 Z= 0.155 Angle : 0.479 7.624 12121 Z= 0.246 Chirality : 0.040 0.145 1390 Planarity : 0.004 0.047 1528 Dihedral : 4.029 58.065 1218 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.13 % Allowed : 14.59 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1119 helix: 2.29 (0.26), residues: 410 sheet: -0.02 (0.29), residues: 289 loop : -0.64 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.002 0.001 HIS H 35 PHE 0.017 0.001 PHE B 199 TYR 0.010 0.001 TYR H 95 ARG 0.004 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 225 VAL cc_start: 0.8719 (p) cc_final: 0.8404 (m) REVERT: A 240 MET cc_start: 0.4717 (mmm) cc_final: 0.4412 (mmm) REVERT: A 245 GLU cc_start: 0.7308 (tp30) cc_final: 0.6550 (tp30) REVERT: A 341 ASP cc_start: 0.7725 (t70) cc_final: 0.7218 (t0) REVERT: B 46 ARG cc_start: 0.7791 (mtp-110) cc_final: 0.7475 (mtp-110) REVERT: B 50 THR cc_start: 0.8508 (m) cc_final: 0.8184 (t) REVERT: B 61 MET cc_start: 0.7605 (ppp) cc_final: 0.7404 (ppp) REVERT: B 136 SER cc_start: 0.8455 (t) cc_final: 0.8225 (p) REVERT: B 155 ASN cc_start: 0.8182 (t0) cc_final: 0.7852 (t0) REVERT: B 170 ASP cc_start: 0.7554 (t70) cc_final: 0.7221 (t0) REVERT: B 237 ASN cc_start: 0.8306 (t0) cc_final: 0.8063 (t0) REVERT: B 246 ASP cc_start: 0.8009 (m-30) cc_final: 0.7798 (m-30) REVERT: B 290 ASP cc_start: 0.7757 (m-30) cc_final: 0.7503 (m-30) REVERT: C 340 ARG cc_start: 0.7859 (ttp-170) cc_final: 0.7420 (ttp-170) REVERT: C 357 SER cc_start: 0.8301 (m) cc_final: 0.8084 (m) REVERT: C 377 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7415 (ttt180) REVERT: C 391 THR cc_start: 0.8488 (m) cc_final: 0.8261 (m) REVERT: C 414 MET cc_start: 0.7918 (mtp) cc_final: 0.7463 (mpp) REVERT: C 430 PHE cc_start: 0.7115 (m-10) cc_final: 0.6812 (m-80) REVERT: C 437 LEU cc_start: 0.8538 (mp) cc_final: 0.8294 (mt) REVERT: G 27 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8120 (mtt-85) REVERT: H 67 ARG cc_start: 0.8362 (ttp80) cc_final: 0.7885 (ttm170) REVERT: H 68 PHE cc_start: 0.7163 (m-10) cc_final: 0.6892 (m-10) REVERT: H 119 VAL cc_start: 0.7952 (t) cc_final: 0.7520 (p) outliers start: 20 outliers final: 18 residues processed: 218 average time/residue: 0.2314 time to fit residues: 66.5917 Evaluate side-chains 230 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 211 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 377 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 0.0170 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 156 GLN B 259 GLN C 131 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106649 restraints weight = 12365.268| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.94 r_work: 0.3185 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8935 Z= 0.345 Angle : 0.564 8.734 12121 Z= 0.291 Chirality : 0.044 0.193 1390 Planarity : 0.004 0.048 1528 Dihedral : 4.442 59.610 1218 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.34 % Allowed : 14.91 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.25), residues: 1119 helix: 2.11 (0.26), residues: 406 sheet: -0.11 (0.29), residues: 295 loop : -0.71 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.002 HIS H 35 PHE 0.025 0.002 PHE B 199 TYR 0.017 0.002 TYR A 320 ARG 0.006 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: B 14 LEU cc_start: 0.8007 (mm) cc_final: 0.7758 (mt) REVERT: B 46 ARG cc_start: 0.7889 (mtp-110) cc_final: 0.7554 (mtp-110) REVERT: B 136 SER cc_start: 0.8512 (t) cc_final: 0.8279 (p) REVERT: B 137 ARG cc_start: 0.8078 (ttm170) cc_final: 0.7857 (ttm170) REVERT: B 155 ASN cc_start: 0.8203 (t0) cc_final: 0.7946 (t0) REVERT: B 171 ILE cc_start: 0.7929 (mm) cc_final: 0.7481 (mt) REVERT: B 237 ASN cc_start: 0.8411 (t0) cc_final: 0.8155 (t0) REVERT: B 246 ASP cc_start: 0.7969 (m-30) cc_final: 0.7650 (m-30) REVERT: B 290 ASP cc_start: 0.7725 (m-30) cc_final: 0.7475 (m-30) REVERT: C 340 ARG cc_start: 0.7902 (ttp-170) cc_final: 0.7489 (ttp-170) REVERT: C 357 SER cc_start: 0.8341 (m) cc_final: 0.8121 (m) REVERT: C 377 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7497 (ttt180) REVERT: C 391 THR cc_start: 0.8523 (m) cc_final: 0.8292 (m) REVERT: C 414 MET cc_start: 0.7980 (mtp) cc_final: 0.7464 (mpp) REVERT: C 430 PHE cc_start: 0.7279 (m-10) cc_final: 0.6907 (m-80) REVERT: G 27 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.8078 (mtt-85) REVERT: H 67 ARG cc_start: 0.8380 (ttp80) cc_final: 0.7858 (ttm170) REVERT: H 68 PHE cc_start: 0.7339 (m-10) cc_final: 0.7075 (m-10) REVERT: H 119 VAL cc_start: 0.7992 (t) cc_final: 0.7585 (p) outliers start: 22 outliers final: 20 residues processed: 218 average time/residue: 0.2453 time to fit residues: 70.6963 Evaluate side-chains 223 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 377 ARG Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN C 131 GLN C 170 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109904 restraints weight = 12224.102| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.93 r_work: 0.3226 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8935 Z= 0.187 Angle : 0.499 7.679 12121 Z= 0.258 Chirality : 0.041 0.166 1390 Planarity : 0.004 0.045 1528 Dihedral : 4.214 58.718 1218 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.92 % Allowed : 15.12 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1119 helix: 2.23 (0.26), residues: 405 sheet: -0.09 (0.29), residues: 296 loop : -0.62 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS A 188 PHE 0.017 0.001 PHE B 199 TYR 0.010 0.001 TYR A 320 ARG 0.003 0.000 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: B 46 ARG cc_start: 0.7783 (mtp-110) cc_final: 0.7451 (mtp-110) REVERT: B 136 SER cc_start: 0.8417 (t) cc_final: 0.8188 (p) REVERT: B 155 ASN cc_start: 0.8211 (t0) cc_final: 0.7905 (t0) REVERT: B 170 ASP cc_start: 0.7611 (t70) cc_final: 0.7256 (t0) REVERT: B 237 ASN cc_start: 0.8317 (t0) cc_final: 0.8073 (t0) REVERT: B 246 ASP cc_start: 0.7990 (m-30) cc_final: 0.7763 (m-30) REVERT: B 290 ASP cc_start: 0.7777 (m-30) cc_final: 0.7527 (m-30) REVERT: C 340 ARG cc_start: 0.7868 (ttp-170) cc_final: 0.7437 (ttp-170) REVERT: C 357 SER cc_start: 0.8293 (m) cc_final: 0.8085 (m) REVERT: C 391 THR cc_start: 0.8488 (m) cc_final: 0.8263 (m) REVERT: C 414 MET cc_start: 0.7951 (mtp) cc_final: 0.7464 (mpp) REVERT: C 430 PHE cc_start: 0.7179 (m-10) cc_final: 0.6844 (m-80) REVERT: G 27 ARG cc_start: 0.8440 (ttm-80) cc_final: 0.8230 (mtt-85) REVERT: H 67 ARG cc_start: 0.8387 (ttp80) cc_final: 0.7895 (ttm170) REVERT: H 68 PHE cc_start: 0.7191 (m-10) cc_final: 0.6941 (m-10) REVERT: H 119 VAL cc_start: 0.7988 (t) cc_final: 0.7572 (p) outliers start: 18 outliers final: 16 residues processed: 209 average time/residue: 0.2450 time to fit residues: 67.7656 Evaluate side-chains 219 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 131 GLN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN C 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.109013 restraints weight = 12222.163| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.93 r_work: 0.3208 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8935 Z= 0.257 Angle : 0.528 7.657 12121 Z= 0.272 Chirality : 0.042 0.179 1390 Planarity : 0.004 0.048 1528 Dihedral : 4.305 59.106 1218 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.02 % Allowed : 15.55 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1119 helix: 2.13 (0.26), residues: 406 sheet: -0.13 (0.29), residues: 301 loop : -0.67 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS A 188 PHE 0.021 0.002 PHE B 199 TYR 0.013 0.001 TYR A 320 ARG 0.004 0.000 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4735.88 seconds wall clock time: 84 minutes 37.76 seconds (5077.76 seconds total)