Starting phenix.real_space_refine on Sat Jun 7 07:58:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hk3_34843/06_2025/8hk3_34843.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hk3_34843/06_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_34843/06_2025/8hk3_34843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hk3_34843/06_2025/8hk3_34843.map" model { file = "/net/cci-nas-00/data/ceres_data/8hk3_34843/06_2025/8hk3_34843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hk3_34843/06_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-5710/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: 5.15, per 1000 atoms: 0.59 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: 2.12 Conformation dependent library (CDL) restraints added in 1.0 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: 1.07 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: 3.02 Time building geometry restraints manager: 2.55 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: 0.950 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.110 Find NCS groups from input model: 0.110 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:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.950 ------------------------------------------------------------------------------- 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 8936 Z= 0.150 Angle : 0.421 12.240 12123 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 Details of bonding type rmsd hydrogen bonds : bond 0.19944 ( 427) hydrogen bonds : angle 6.49706 ( 1194) SS BOND : bond 0.00047 ( 1) SS BOND : angle 0.84684 ( 2) covalent geometry : bond 0.00231 ( 8935) covalent geometry : angle 0.42085 (12121) *********************** 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 : 0.987 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: 0.2246 time to fit residues: 85.2620 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 : 0.902 ------------------------------------------------------------------------------- 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 = 0.110460 restraints weight = 12088.427| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.96 r_work: 0.3223 rms_B_bonded: 2.34 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 8936 Z= 0.253 Angle : 0.627 9.906 12123 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 Details of bonding type rmsd hydrogen bonds : bond 0.04723 ( 427) hydrogen bonds : angle 4.72746 ( 1194) SS BOND : bond 0.00610 ( 1) SS BOND : angle 0.94679 ( 2) covalent geometry : bond 0.00600 ( 8935) covalent geometry : angle 0.62658 (12121) *********************** 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 : 0.898 Fit side-chains REVERT: A 14 GLU cc_start: 0.7876 (tp30) cc_final: 0.7575 (tp30) REVERT: A 197 LYS cc_start: 0.8208 (mtpp) cc_final: 0.8008 (mtpt) REVERT: A 198 MET cc_start: 0.8347 (mtp) cc_final: 0.8139 (ttm) REVERT: B 14 LEU cc_start: 0.7989 (mm) cc_final: 0.7755 (mt) REVERT: B 46 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7563 (mtp-110) REVERT: B 50 THR cc_start: 0.8464 (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: 0.7375 (t70) cc_final: 0.6982 (t0) REVERT: B 220 GLN cc_start: 0.8362 (mt0) cc_final: 0.8132 (mt0) REVERT: B 295 ASN cc_start: 0.8499 (m-40) cc_final: 0.8259 (m-40) REVERT: C 391 THR cc_start: 0.8464 (m) cc_final: 0.8249 (m) REVERT: C 399 LEU cc_start: 0.8100 (mp) cc_final: 0.7863 (mt) REVERT: H 80 PHE cc_start: 0.7561 (m-80) cc_final: 0.7343 (m-10) REVERT: H 119 VAL cc_start: 0.7785 (t) cc_final: 0.7425 (p) REVERT: H 161 SER cc_start: 0.8431 (t) cc_final: 0.8201 (p) outliers start: 16 outliers final: 13 residues processed: 225 average time/residue: 0.2061 time to fit residues: 64.4283 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 : 0.874 ------------------------------------------------------------------------------- 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: 0.0870 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 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: 0.6960 ------------------------------------------------------------------------------- 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 ** C 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.129767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.111270 restraints weight = 12306.300| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.01 r_work: 0.3228 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8936 Z= 0.124 Angle : 0.507 6.918 12123 Z= 0.261 Chirality : 0.041 0.160 1390 Planarity : 0.004 0.046 1528 Dihedral : 4.074 57.784 1218 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.60 % Allowed : 10.86 % 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: 0.26 (0.25), residues: 1119 helix: 1.87 (0.27), residues: 404 sheet: -0.22 (0.29), residues: 287 loop : -1.18 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS B 91 PHE 0.019 0.001 PHE B 199 TYR 0.014 0.001 TYR H 95 ARG 0.004 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03595 ( 427) hydrogen bonds : angle 4.33191 ( 1194) SS BOND : bond 0.00286 ( 1) SS BOND : angle 0.52184 ( 2) covalent geometry : bond 0.00283 ( 8935) covalent geometry : angle 0.50719 (12121) *********************** 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 208 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.907 Fit side-chains REVERT: A 225 VAL cc_start: 0.8661 (p) cc_final: 0.8347 (m) REVERT: B 46 ARG cc_start: 0.7879 (mtp-110) cc_final: 0.7556 (mtp-110) REVERT: B 61 MET cc_start: 0.7904 (ppp) cc_final: 0.7596 (ppp) REVERT: B 155 ASN cc_start: 0.7945 (t0) cc_final: 0.7535 (t0) REVERT: B 170 ASP cc_start: 0.7347 (t70) cc_final: 0.6955 (t0) REVERT: B 295 ASN cc_start: 0.8527 (m-40) cc_final: 0.8315 (m-40) REVERT: C 340 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7460 (ttp-170) REVERT: C 391 THR cc_start: 0.8446 (m) cc_final: 0.8219 (m) REVERT: C 399 LEU cc_start: 0.8167 (mp) cc_final: 0.7916 (mt) REVERT: C 414 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7448 (mpp) REVERT: G 27 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.8065 (mtt-85) REVERT: H 103 TYR cc_start: 0.8215 (t80) cc_final: 0.7868 (t80) REVERT: H 119 VAL cc_start: 0.7837 (t) cc_final: 0.7424 (p) REVERT: H 161 SER cc_start: 0.8401 (t) cc_final: 0.8184 (p) outliers start: 15 outliers final: 9 residues processed: 201 average time/residue: 0.2251 time to fit residues: 60.6907 Evaluate side-chains 205 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 26 SER Chi-restraints excluded: chain C residue 34 PHE 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: 0.0030 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 70 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.8996 ------------------------------------------------------------------------------- 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 C 63 HIS C 169 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.124419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106271 restraints weight = 12250.122| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.97 r_work: 0.3173 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8936 Z= 0.263 Angle : 0.604 10.281 12123 Z= 0.315 Chirality : 0.046 0.198 1390 Planarity : 0.005 0.047 1528 Dihedral : 4.662 59.705 1218 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.34 % Allowed : 12.46 % Favored : 85.20 % 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: 0.20 (0.25), residues: 1119 helix: 1.71 (0.26), residues: 406 sheet: -0.31 (0.29), residues: 296 loop : -1.07 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.007 0.002 HIS B 91 PHE 0.028 0.002 PHE B 199 TYR 0.020 0.002 TYR A 320 ARG 0.007 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04678 ( 427) hydrogen bonds : angle 4.60068 ( 1194) SS BOND : bond 0.00547 ( 1) SS BOND : angle 0.59361 ( 2) covalent geometry : bond 0.00620 ( 8935) covalent geometry : angle 0.60439 (12121) *********************** 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 223 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.888 Fit side-chains REVERT: A 14 GLU cc_start: 0.8008 (tp30) cc_final: 0.7719 (tp30) REVERT: A 32 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7849 (ttm-80) REVERT: B 14 LEU cc_start: 0.8012 (mm) cc_final: 0.7764 (mt) REVERT: B 46 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7623 (mtp-110) REVERT: B 137 ARG cc_start: 0.8225 (ttm170) cc_final: 0.8016 (ttm170) REVERT: B 155 ASN cc_start: 0.8107 (t0) cc_final: 0.7716 (t0) REVERT: B 170 ASP cc_start: 0.7585 (t70) cc_final: 0.7178 (t0) REVERT: C 340 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.7464 (ttp-170) REVERT: C 357 SER cc_start: 0.8309 (m) cc_final: 0.8092 (m) REVERT: C 391 THR cc_start: 0.8539 (m) cc_final: 0.8327 (m) REVERT: C 399 LEU cc_start: 0.8213 (mp) cc_final: 0.7992 (mt) REVERT: C 414 MET cc_start: 0.7982 (mtp) cc_final: 0.7485 (mpp) REVERT: G 27 ARG cc_start: 0.8588 (ttm-80) cc_final: 0.8192 (mtm-85) REVERT: H 103 TYR cc_start: 0.8431 (t80) cc_final: 0.8076 (t80) REVERT: H 119 VAL cc_start: 0.7907 (OUTLIER) cc_final: 0.7525 (p) REVERT: H 161 SER cc_start: 0.8409 (t) cc_final: 0.8179 (p) outliers start: 22 outliers final: 17 residues processed: 212 average time/residue: 0.2314 time to fit residues: 65.6637 Evaluate side-chains 211 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 2.9990 chunk 11 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108383 restraints weight = 12187.506| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.00 r_work: 0.3212 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8936 Z= 0.131 Angle : 0.494 7.603 12123 Z= 0.259 Chirality : 0.041 0.163 1390 Planarity : 0.004 0.045 1528 Dihedral : 4.302 59.616 1218 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.34 % Allowed : 13.53 % Favored : 84.13 % 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: 0.42 (0.25), residues: 1119 helix: 1.90 (0.26), residues: 411 sheet: -0.21 (0.29), residues: 289 loop : -0.95 (0.29), residues: 419 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 0.019 0.001 PHE B 199 TYR 0.011 0.001 TYR A 320 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 427) hydrogen bonds : angle 4.27354 ( 1194) SS BOND : bond 0.00254 ( 1) SS BOND : angle 0.37217 ( 2) covalent geometry : bond 0.00299 ( 8935) covalent geometry : angle 0.49451 (12121) *********************** 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 231 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 1.504 Fit side-chains REVERT: A 14 GLU cc_start: 0.7942 (tp30) cc_final: 0.7657 (tp30) REVERT: B 46 ARG cc_start: 0.7881 (mtp-110) cc_final: 0.7581 (mtp-110) REVERT: B 101 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7832 (ptm) REVERT: B 155 ASN cc_start: 0.8168 (t0) cc_final: 0.7846 (t0) REVERT: B 170 ASP cc_start: 0.7487 (t70) cc_final: 0.7111 (t0) REVERT: C 340 ARG cc_start: 0.7859 (ttp-170) cc_final: 0.7465 (ttp-170) REVERT: C 357 SER cc_start: 0.8290 (m) cc_final: 0.8081 (m) REVERT: C 391 THR cc_start: 0.8518 (m) cc_final: 0.8317 (m) REVERT: C 414 MET cc_start: 0.7959 (mtp) cc_final: 0.7446 (mpp) REVERT: G 27 ARG cc_start: 0.8524 (ttm-80) cc_final: 0.8224 (mtt-85) REVERT: H 67 ARG cc_start: 0.8399 (ttp80) cc_final: 0.7687 (ttm170) REVERT: H 68 PHE cc_start: 0.7390 (m-10) cc_final: 0.7190 (m-10) REVERT: H 95 TYR cc_start: 0.8273 (m-80) cc_final: 0.8062 (m-80) REVERT: H 103 TYR cc_start: 0.8391 (t80) cc_final: 0.8019 (t80) REVERT: H 119 VAL cc_start: 0.7883 (t) cc_final: 0.7487 (p) outliers start: 22 outliers final: 17 residues processed: 219 average time/residue: 0.2274 time to fit residues: 67.9277 Evaluate side-chains 212 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 101 MET Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 346 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 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.1980 chunk 95 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.126908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109216 restraints weight = 12131.041| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.92 r_work: 0.3228 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8936 Z= 0.113 Angle : 0.486 6.927 12123 Z= 0.253 Chirality : 0.040 0.149 1390 Planarity : 0.004 0.048 1528 Dihedral : 4.167 59.593 1218 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.45 % Allowed : 14.38 % Favored : 83.17 % 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: 0.56 (0.25), residues: 1119 helix: 2.01 (0.26), residues: 412 sheet: -0.13 (0.29), residues: 289 loop : -0.88 (0.29), 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 0.018 0.001 PHE B 199 TYR 0.009 0.001 TYR H 190 ARG 0.004 0.000 ARG C 443 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 427) hydrogen bonds : angle 4.15657 ( 1194) SS BOND : bond 0.00257 ( 1) SS BOND : angle 0.33352 ( 2) covalent geometry : bond 0.00253 ( 8935) covalent geometry : angle 0.48636 (12121) *********************** 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 222 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7839 (tp30) cc_final: 0.7544 (tp30) REVERT: A 240 MET cc_start: 0.4707 (mmm) cc_final: 0.4500 (mmm) REVERT: B 46 ARG cc_start: 0.7870 (mtp-110) cc_final: 0.7542 (mtp-110) REVERT: B 137 ARG cc_start: 0.8258 (ttm170) cc_final: 0.8022 (ttm170) REVERT: B 155 ASN cc_start: 0.8161 (t0) cc_final: 0.7853 (t0) REVERT: B 170 ASP cc_start: 0.7460 (t70) cc_final: 0.7098 (t0) REVERT: B 290 ASP cc_start: 0.7805 (m-30) cc_final: 0.7511 (m-30) REVERT: C 340 ARG cc_start: 0.7830 (ttp-170) cc_final: 0.7409 (ttp-170) REVERT: C 391 THR cc_start: 0.8502 (m) cc_final: 0.8281 (m) REVERT: C 414 MET cc_start: 0.7895 (mtp) cc_final: 0.7394 (mpp) REVERT: G 27 ARG cc_start: 0.8474 (ttm-80) cc_final: 0.8202 (mtt-85) REVERT: H 67 ARG cc_start: 0.8362 (ttp80) cc_final: 0.7821 (ttm170) REVERT: H 103 TYR cc_start: 0.8378 (t80) cc_final: 0.7981 (t80) REVERT: H 119 VAL cc_start: 0.7926 (t) cc_final: 0.7512 (p) outliers start: 23 outliers final: 18 residues processed: 208 average time/residue: 0.2471 time to fit residues: 68.6363 Evaluate side-chains 215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 225 VAL 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 341 LEU Chi-restraints excluded: chain C residue 346 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 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN C 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.125160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107306 restraints weight = 12246.715| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.93 r_work: 0.3201 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8936 Z= 0.172 Angle : 0.526 7.859 12123 Z= 0.272 Chirality : 0.042 0.175 1390 Planarity : 0.004 0.048 1528 Dihedral : 4.326 59.897 1218 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.56 % Allowed : 14.91 % Favored : 82.53 % 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: 0.66 (0.25), residues: 1119 helix: 2.11 (0.26), residues: 405 sheet: -0.16 (0.29), residues: 294 loop : -0.73 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.021 0.001 PHE B 199 TYR 0.013 0.002 TYR A 320 ARG 0.004 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 427) hydrogen bonds : angle 4.24036 ( 1194) SS BOND : bond 0.00357 ( 1) SS BOND : angle 0.35387 ( 2) covalent geometry : bond 0.00403 ( 8935) covalent geometry : angle 0.52576 (12121) *********************** 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 225 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7951 (tp30) cc_final: 0.7642 (tp30) REVERT: B 46 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.7579 (mtp-110) REVERT: B 136 SER cc_start: 0.8573 (t) cc_final: 0.8347 (p) REVERT: B 155 ASN cc_start: 0.8210 (t0) cc_final: 0.7915 (t0) REVERT: B 170 ASP cc_start: 0.7553 (t70) cc_final: 0.7209 (t0) REVERT: C 340 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.7446 (ttp-170) REVERT: C 357 SER cc_start: 0.8310 (m) cc_final: 0.8091 (m) REVERT: C 391 THR cc_start: 0.8518 (m) cc_final: 0.8293 (m) REVERT: C 414 MET cc_start: 0.7912 (mtp) cc_final: 0.7431 (mpp) REVERT: G 27 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.8215 (mtt-85) REVERT: H 103 TYR cc_start: 0.8420 (t80) cc_final: 0.8011 (t80) REVERT: H 119 VAL cc_start: 0.7973 (t) cc_final: 0.7568 (p) REVERT: H 192 MET cc_start: 0.7702 (ptt) cc_final: 0.7370 (ptm) outliers start: 24 outliers final: 23 residues processed: 211 average time/residue: 0.2380 time to fit residues: 66.8743 Evaluate side-chains 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 225 VAL 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 237 ASN 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 339 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 346 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 189 ILE 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: 1.9990 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.126077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108360 restraints weight = 12337.278| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.92 r_work: 0.3132 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8936 Z= 0.139 Angle : 0.511 7.283 12123 Z= 0.264 Chirality : 0.041 0.167 1390 Planarity : 0.004 0.047 1528 Dihedral : 4.264 59.688 1218 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.24 % Allowed : 14.80 % 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: 0.73 (0.25), residues: 1119 helix: 2.15 (0.26), residues: 405 sheet: -0.07 (0.29), residues: 288 loop : -0.71 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.019 0.001 PHE B 199 TYR 0.011 0.001 TYR A 320 ARG 0.004 0.000 ARG C 443 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 427) hydrogen bonds : angle 4.17902 ( 1194) SS BOND : bond 0.00311 ( 1) SS BOND : angle 0.35977 ( 2) covalent geometry : bond 0.00320 ( 8935) covalent geometry : angle 0.51066 (12121) *********************** 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 226 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7822 (tp30) cc_final: 0.7508 (tp30) REVERT: A 240 MET cc_start: 0.4710 (mmm) cc_final: 0.4459 (mmm) REVERT: B 14 LEU cc_start: 0.7787 (mm) cc_final: 0.7564 (mt) REVERT: B 46 ARG cc_start: 0.7869 (mtp-110) cc_final: 0.7511 (mtp-110) REVERT: B 136 SER cc_start: 0.8554 (t) cc_final: 0.8310 (p) REVERT: B 137 ARG cc_start: 0.8332 (ttm170) cc_final: 0.8082 (ttm170) REVERT: B 155 ASN cc_start: 0.8187 (t0) cc_final: 0.7867 (t0) REVERT: B 170 ASP cc_start: 0.7468 (t70) cc_final: 0.7075 (t0) REVERT: B 246 ASP cc_start: 0.7972 (m-30) cc_final: 0.7755 (m-30) REVERT: C 340 ARG cc_start: 0.7810 (ttp-170) cc_final: 0.7365 (ttp-170) REVERT: C 357 SER cc_start: 0.8237 (m) cc_final: 0.8015 (m) REVERT: C 391 THR cc_start: 0.8453 (m) cc_final: 0.8229 (m) REVERT: C 414 MET cc_start: 0.7864 (mtp) cc_final: 0.7363 (mpp) REVERT: G 27 ARG cc_start: 0.8475 (ttm-80) cc_final: 0.8192 (mtt-85) REVERT: H 103 TYR cc_start: 0.8402 (t80) cc_final: 0.7966 (t80) REVERT: H 119 VAL cc_start: 0.7880 (t) cc_final: 0.7459 (p) outliers start: 21 outliers final: 19 residues processed: 213 average time/residue: 0.2332 time to fit residues: 66.5578 Evaluate side-chains 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 225 VAL 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 341 LEU Chi-restraints excluded: chain C residue 346 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 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: 1.9990 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.125456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107496 restraints weight = 12326.623| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.97 r_work: 0.3201 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8936 Z= 0.162 Angle : 0.525 7.387 12123 Z= 0.271 Chirality : 0.042 0.179 1390 Planarity : 0.004 0.048 1528 Dihedral : 4.338 59.727 1218 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.34 % Allowed : 14.80 % Favored : 82.85 % 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: 0.71 (0.25), residues: 1119 helix: 2.17 (0.26), residues: 404 sheet: -0.16 (0.29), residues: 295 loop : -0.69 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS H 35 PHE 0.020 0.001 PHE B 199 TYR 0.012 0.001 TYR H 102 ARG 0.004 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03761 ( 427) hydrogen bonds : angle 4.20955 ( 1194) SS BOND : bond 0.00325 ( 1) SS BOND : angle 0.33445 ( 2) covalent geometry : bond 0.00380 ( 8935) covalent geometry : angle 0.52499 (12121) *********************** 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 224 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7956 (tp30) cc_final: 0.7655 (tp30) REVERT: A 240 MET cc_start: 0.4854 (mmm) cc_final: 0.4615 (mmm) REVERT: B 14 LEU cc_start: 0.7958 (mm) cc_final: 0.7720 (mt) REVERT: B 46 ARG cc_start: 0.7890 (mtp-110) cc_final: 0.7578 (mtp-110) REVERT: B 137 ARG cc_start: 0.8323 (ttm170) cc_final: 0.8074 (ttm170) REVERT: B 155 ASN cc_start: 0.8246 (t0) cc_final: 0.7956 (t0) REVERT: B 170 ASP cc_start: 0.7631 (t70) cc_final: 0.7290 (t0) REVERT: B 246 ASP cc_start: 0.7986 (m-30) cc_final: 0.7759 (m-30) REVERT: C 340 ARG cc_start: 0.7897 (ttp-170) cc_final: 0.7459 (ttp-170) REVERT: C 357 SER cc_start: 0.8314 (m) cc_final: 0.8095 (m) REVERT: C 391 THR cc_start: 0.8523 (m) cc_final: 0.8306 (m) REVERT: C 414 MET cc_start: 0.7951 (mtp) cc_final: 0.7479 (mpp) REVERT: C 430 PHE cc_start: 0.7218 (m-10) cc_final: 0.6893 (m-80) REVERT: G 27 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8201 (mtt-85) REVERT: H 103 TYR cc_start: 0.8431 (t80) cc_final: 0.8020 (t80) REVERT: H 119 VAL cc_start: 0.7983 (t) cc_final: 0.7576 (p) outliers start: 22 outliers final: 22 residues processed: 208 average time/residue: 0.2285 time to fit residues: 63.3978 Evaluate side-chains 221 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 225 VAL 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 339 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 346 LEU 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 G residue 21 MET Chi-restraints excluded: chain H residue 189 ILE 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: 1.9990 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.127520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109630 restraints weight = 12244.749| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.93 r_work: 0.3214 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8936 Z= 0.134 Angle : 0.502 7.506 12123 Z= 0.260 Chirality : 0.041 0.169 1390 Planarity : 0.004 0.047 1528 Dihedral : 4.235 59.494 1218 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.13 % Allowed : 15.34 % Favored : 82.53 % 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: 2.17 (0.26), residues: 405 sheet: 0.00 (0.29), residues: 288 loop : -0.68 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.005 0.001 HIS B 62 PHE 0.018 0.001 PHE B 199 TYR 0.010 0.001 TYR A 320 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 427) hydrogen bonds : angle 4.15587 ( 1194) SS BOND : bond 0.00268 ( 1) SS BOND : angle 0.28336 ( 2) covalent geometry : bond 0.00310 ( 8935) covalent geometry : angle 0.50185 (12121) ********************** 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 222 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7927 (tp30) cc_final: 0.7630 (tp30) REVERT: A 240 MET cc_start: 0.4830 (mmm) cc_final: 0.4591 (mmm) REVERT: B 14 LEU cc_start: 0.7964 (mm) cc_final: 0.7720 (mt) REVERT: B 137 ARG cc_start: 0.8300 (ttm170) cc_final: 0.8058 (ttm170) REVERT: B 155 ASN cc_start: 0.8243 (t0) cc_final: 0.7956 (t0) REVERT: B 170 ASP cc_start: 0.7601 (t70) cc_final: 0.7263 (t0) REVERT: B 246 ASP cc_start: 0.7994 (m-30) cc_final: 0.7765 (m-30) REVERT: C 340 ARG cc_start: 0.7879 (ttp-170) cc_final: 0.7436 (ttp-170) REVERT: C 357 SER cc_start: 0.8293 (m) cc_final: 0.8081 (m) REVERT: C 391 THR cc_start: 0.8490 (m) cc_final: 0.8269 (m) REVERT: C 414 MET cc_start: 0.8029 (mtp) cc_final: 0.7519 (mpp) REVERT: C 430 PHE cc_start: 0.7213 (m-10) cc_final: 0.6893 (m-80) REVERT: G 27 ARG cc_start: 0.8465 (ttm-80) cc_final: 0.8200 (mtt-85) REVERT: H 34 MET cc_start: 0.8434 (mmm) cc_final: 0.8171 (mmt) REVERT: H 103 TYR cc_start: 0.8433 (t80) cc_final: 0.8008 (t80) REVERT: H 119 VAL cc_start: 0.8000 (t) cc_final: 0.7586 (p) outliers start: 20 outliers final: 18 residues processed: 207 average time/residue: 0.2328 time to fit residues: 64.4581 Evaluate side-chains 219 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL 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 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 341 LEU Chi-restraints excluded: chain C residue 346 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 189 ILE 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: 0.8980 chunk 20 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 89 optimal weight: 0.0070 chunk 0 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.127149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.109363 restraints weight = 12238.188| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.93 r_work: 0.3231 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8936 Z= 0.112 Angle : 0.488 8.296 12123 Z= 0.251 Chirality : 0.041 0.155 1390 Planarity : 0.004 0.048 1528 Dihedral : 4.134 59.200 1218 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.24 % Allowed : 15.76 % Favored : 82.00 % 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: 0.83 (0.25), residues: 1119 helix: 2.16 (0.26), residues: 407 sheet: 0.05 (0.29), residues: 288 loop : -0.65 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS B 62 PHE 0.016 0.001 PHE B 199 TYR 0.010 0.001 TYR H 228 ARG 0.002 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 427) hydrogen bonds : angle 4.09735 ( 1194) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.26670 ( 2) covalent geometry : bond 0.00253 ( 8935) covalent geometry : angle 0.48846 (12121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4933.29 seconds wall clock time: 85 minutes 44.66 seconds (5144.66 seconds total)