Starting phenix.real_space_refine on Tue Apr 29 07:41:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z65_39792/04_2025/8z65_39792.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z65_39792/04_2025/8z65_39792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z65_39792/04_2025/8z65_39792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z65_39792/04_2025/8z65_39792.map" model { file = "/net/cci-nas-00/data/ceres_data/8z65_39792/04_2025/8z65_39792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z65_39792/04_2025/8z65_39792.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 52 5.16 5 C 5415 2.51 5 N 1481 2.21 5 O 1546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8494 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1860 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 135 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 5, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "B" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2447 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "G" Number of atoms: 321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 321 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "S" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1695 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "R" Number of atoms: 2171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2171 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 282} Chain breaks: 2 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 282 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 149 Time building chain proxies: 6.04, per 1000 atoms: 0.71 Number of scatterers: 8494 At special positions: 0 Unit cell: (87.74, 121.36, 126.28, 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 52 16.00 O 1546 8.00 N 1481 7.00 C 5415 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 37.5% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 6 through 39 removed outlier: 3.506A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 243 through 249 removed outlier: 3.561A pdb=" N ASN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.554A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.542A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 14 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 62 through 65 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.891A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.091A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 18 through 48 removed outlier: 3.832A pdb=" N PHE R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 52 through 78 removed outlier: 3.565A pdb=" N ASN R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 120 removed outlier: 4.550A pdb=" N ILE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 129 Processing helix chain 'R' and resid 130 through 149 Processing helix chain 'R' and resid 151 through 155 Processing helix chain 'R' and resid 177 through 190 removed outlier: 3.616A pdb=" N PHE R 190 " --> pdb=" O VAL R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 210 removed outlier: 4.299A pdb=" N GLY R 210 " --> pdb=" O ARG R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 252 Proline residue: R 239 - end of helix removed outlier: 3.672A pdb=" N ILE R 250 " --> pdb=" O SER R 246 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR R 251 " --> pdb=" O ARG R 247 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU R 252 " --> pdb=" O SER R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 263 Processing helix chain 'R' and resid 264 through 276 Processing helix chain 'R' and resid 277 through 287 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 290 through 304 removed outlier: 3.647A pdb=" N ASN R 303 " --> pdb=" O LYS R 299 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 217 through 223 removed outlier: 4.634A pdb=" N VAL A 234 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N GLY A 47 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A 253 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.320A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.752A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.657A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.534A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 6.906A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.513A 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: 6.434A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.852A 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: 6.259A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.439A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.439A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 147 through 148 removed outlier: 6.152A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1299 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: 2.56 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1355 1.30 - 1.43: 2433 1.43 - 1.56: 4831 1.56 - 1.69: 0 1.69 - 1.82: 72 Bond restraints: 8691 Sorted by residual: bond pdb=" C GLU A 27 " pdb=" O GLU A 27 " ideal model delta sigma weight residual 1.237 1.167 0.069 1.17e-02 7.31e+03 3.52e+01 bond pdb=" CZ ARG A 15 " pdb=" NH2 ARG A 15 " ideal model delta sigma weight residual 1.330 1.256 0.074 1.30e-02 5.92e+03 3.22e+01 bond pdb=" CA ASP A 9 " pdb=" CB ASP A 9 " ideal model delta sigma weight residual 1.528 1.442 0.087 1.56e-02 4.11e+03 3.08e+01 bond pdb=" CA ASP A 9 " pdb=" C ASP A 9 " ideal model delta sigma weight residual 1.523 1.458 0.066 1.30e-02 5.92e+03 2.54e+01 bond pdb=" CA HIS R 269 " pdb=" C HIS R 269 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.29e-02 6.01e+03 2.01e+01 ... (remaining 8686 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 11602 2.39 - 4.78: 215 4.78 - 7.17: 28 7.17 - 9.55: 7 9.55 - 11.94: 3 Bond angle restraints: 11855 Sorted by residual: angle pdb=" N ARG R 162 " pdb=" CA ARG R 162 " pdb=" C ARG R 162 " ideal model delta sigma weight residual 112.54 123.31 -10.77 1.22e+00 6.72e-01 7.79e+01 angle pdb=" C HIS R 165 " pdb=" CA HIS R 165 " pdb=" CB HIS R 165 " ideal model delta sigma weight residual 110.62 99.99 10.63 1.51e+00 4.39e-01 4.96e+01 angle pdb=" N ASP R 161 " pdb=" CA ASP R 161 " pdb=" C ASP R 161 " ideal model delta sigma weight residual 109.24 118.49 -9.25 1.51e+00 4.39e-01 3.76e+01 angle pdb=" N TRP R 256 " pdb=" CA TRP R 256 " pdb=" C TRP R 256 " ideal model delta sigma weight residual 111.07 104.69 6.38 1.07e+00 8.73e-01 3.55e+01 angle pdb=" N VAL R 186 " pdb=" CA VAL R 186 " pdb=" C VAL R 186 " ideal model delta sigma weight residual 110.62 117.01 -6.39 1.14e+00 7.69e-01 3.15e+01 ... (remaining 11850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.72: 4564 16.72 - 33.44: 393 33.44 - 50.16: 75 50.16 - 66.88: 13 66.88 - 83.59: 8 Dihedral angle restraints: 5053 sinusoidal: 1717 harmonic: 3336 Sorted by residual: dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 152.16 27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" C GLN A 29 " pdb=" N GLN A 29 " pdb=" CA GLN A 29 " pdb=" CB GLN A 29 " ideal model delta harmonic sigma weight residual -122.60 -135.48 12.88 0 2.50e+00 1.60e-01 2.65e+01 dihedral pdb=" C LYS A 17 " pdb=" N LYS A 17 " pdb=" CA LYS A 17 " pdb=" CB LYS A 17 " ideal model delta harmonic sigma weight residual -122.60 -135.10 12.50 0 2.50e+00 1.60e-01 2.50e+01 ... (remaining 5050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1325 0.116 - 0.232: 32 0.232 - 0.348: 5 0.348 - 0.465: 1 0.465 - 0.581: 3 Chirality restraints: 1366 Sorted by residual: chirality pdb=" CA HIS R 269 " pdb=" N HIS R 269 " pdb=" C HIS R 269 " pdb=" CB HIS R 269 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" CA GLN A 29 " pdb=" N GLN A 29 " pdb=" C GLN A 29 " pdb=" CB GLN A 29 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" CA LYS A 17 " pdb=" N LYS A 17 " pdb=" C LYS A 17 " pdb=" CB LYS A 17 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.70e+00 ... (remaining 1363 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.022 2.00e-02 2.50e+03 1.67e-02 5.57e+00 pdb=" CG TYR B 59 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO S 75 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 260 " -0.011 2.00e-02 2.50e+03 1.40e-02 3.44e+00 pdb=" CG PHE R 260 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE R 260 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE R 260 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE R 260 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 260 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE R 260 " -0.000 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 75 2.60 - 3.17: 7267 3.17 - 3.75: 13156 3.75 - 4.32: 18392 4.32 - 4.90: 30999 Nonbonded interactions: 69889 Sorted by model distance: nonbonded pdb=" OG SER R 112 " pdb=" OG SER R 200 " model vdw 2.023 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.063 3.040 nonbonded pdb=" NZ LYS A 243 " pdb=" OD2 ASP B 228 " model vdw 2.159 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.189 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.202 3.040 ... (remaining 69884 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: 2.650 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.810 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.008 0.087 8693 Z= 0.429 Angle : 0.818 11.942 11859 Z= 0.482 Chirality : 0.060 0.581 1366 Planarity : 0.005 0.049 1513 Dihedral : 13.564 83.594 2895 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.24 % Allowed : 0.73 % Favored : 99.03 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 5.41 % 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: -0.38 (0.25), residues: 1131 helix: 0.69 (0.27), residues: 381 sheet: -0.07 (0.30), residues: 289 loop : -1.11 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 244 HIS 0.018 0.002 HIS A 357 PHE 0.032 0.002 PHE R 260 TYR 0.040 0.003 TYR B 59 ARG 0.011 0.001 ARG S 180 Details of bonding type rmsd hydrogen bonds : bond 0.18118 ( 449) hydrogen bonds : angle 7.34065 ( 1299) SS BOND : bond 0.00084 ( 2) SS BOND : angle 1.35901 ( 4) covalent geometry : bond 0.00800 ( 8691) covalent geometry : angle 0.81764 (11855) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 229 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: A 221 LYS cc_start: 0.7680 (mppt) cc_final: 0.7444 (mppt) REVERT: A 258 VAL cc_start: 0.8657 (p) cc_final: 0.8311 (t) REVERT: A 347 ARG cc_start: 0.7860 (ttm-80) cc_final: 0.7653 (ttm-80) REVERT: B 258 ASP cc_start: 0.6702 (t70) cc_final: 0.6419 (t0) REVERT: S 116 THR cc_start: 0.8119 (t) cc_final: 0.7831 (p) REVERT: R 104 SER cc_start: 0.7867 (m) cc_final: 0.7663 (m) REVERT: R 141 VAL cc_start: 0.8343 (p) cc_final: 0.8008 (t) REVERT: R 174 MET cc_start: 0.7142 (tpp) cc_final: 0.6686 (mmm) REVERT: R 190 PHE cc_start: 0.7758 (t80) cc_final: 0.7494 (t80) outliers start: 2 outliers final: 2 residues processed: 230 average time/residue: 1.0491 time to fit residues: 259.9998 Evaluate side-chains 207 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 205 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain R residue 105 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 53 optimal weight: 0.1980 chunk 65 optimal weight: 0.4980 chunk 102 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 88 ASN B 230 ASN S 39 GLN S 82 GLN R 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.105663 restraints weight = 12699.876| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.81 r_work: 0.3226 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8693 Z= 0.168 Angle : 0.615 11.380 11859 Z= 0.325 Chirality : 0.044 0.137 1366 Planarity : 0.005 0.046 1513 Dihedral : 4.817 38.160 1241 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.91 % Allowed : 10.91 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 1131 helix: 1.46 (0.27), residues: 377 sheet: 0.09 (0.31), residues: 277 loop : -0.89 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 339 HIS 0.009 0.001 HIS A 357 PHE 0.016 0.002 PHE A 222 TYR 0.025 0.002 TYR B 59 ARG 0.005 0.000 ARG R 202 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 449) hydrogen bonds : angle 5.15906 ( 1299) SS BOND : bond 0.00175 ( 2) SS BOND : angle 0.99597 ( 4) covalent geometry : bond 0.00383 ( 8691) covalent geometry : angle 0.61501 (11855) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8459 (t) cc_final: 0.8121 (t) REVERT: A 56 ILE cc_start: 0.7756 (mt) cc_final: 0.7452 (tp) REVERT: A 221 LYS cc_start: 0.8200 (mppt) cc_final: 0.7781 (mppt) REVERT: A 299 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7120 (mt-10) REVERT: A 347 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.8064 (ttp-110) REVERT: A 368 ASP cc_start: 0.6978 (m-30) cc_final: 0.6586 (m-30) REVERT: B 136 SER cc_start: 0.8417 (t) cc_final: 0.8182 (m) REVERT: B 170 ASP cc_start: 0.7948 (t0) cc_final: 0.7665 (t70) REVERT: B 225 HIS cc_start: 0.8091 (OUTLIER) cc_final: 0.7806 (m-70) REVERT: B 230 ASN cc_start: 0.8404 (m110) cc_final: 0.8198 (m-40) REVERT: B 258 ASP cc_start: 0.7330 (t70) cc_final: 0.6794 (t0) REVERT: B 304 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7725 (mmm-85) REVERT: B 323 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7586 (p0) REVERT: B 329 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.8137 (m) REVERT: S 116 THR cc_start: 0.8235 (t) cc_final: 0.7958 (p) REVERT: R 95 PHE cc_start: 0.7203 (t80) cc_final: 0.6785 (t80) REVERT: R 174 MET cc_start: 0.7039 (tpp) cc_final: 0.6759 (mmm) REVERT: R 190 PHE cc_start: 0.8239 (t80) cc_final: 0.8038 (t80) REVERT: R 280 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8264 (m) outliers start: 24 outliers final: 11 residues processed: 217 average time/residue: 1.1817 time to fit residues: 277.6351 Evaluate side-chains 219 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 276 SER Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 87 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 106 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.104698 restraints weight = 12872.791| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.84 r_work: 0.3211 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8693 Z= 0.180 Angle : 0.591 9.343 11859 Z= 0.312 Chirality : 0.043 0.140 1366 Planarity : 0.005 0.050 1513 Dihedral : 4.673 41.416 1239 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.00 % Allowed : 15.52 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.33 (0.25), residues: 1131 helix: 1.68 (0.27), residues: 374 sheet: -0.00 (0.31), residues: 274 loop : -0.78 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 339 HIS 0.011 0.001 HIS A 357 PHE 0.016 0.002 PHE A 222 TYR 0.018 0.002 TYR B 59 ARG 0.006 0.000 ARG R 124 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 449) hydrogen bonds : angle 4.82637 ( 1299) SS BOND : bond 0.00224 ( 2) SS BOND : angle 0.98793 ( 4) covalent geometry : bond 0.00413 ( 8691) covalent geometry : angle 0.59125 (11855) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 1.074 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8501 (t) cc_final: 0.8161 (t) REVERT: A 56 ILE cc_start: 0.7703 (mt) cc_final: 0.7455 (tp) REVERT: A 219 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6949 (tp30) REVERT: A 221 LYS cc_start: 0.8165 (mppt) cc_final: 0.7742 (mppt) REVERT: A 299 GLU cc_start: 0.7399 (mt-10) cc_final: 0.7178 (mt-10) REVERT: A 347 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.8081 (ttp-110) REVERT: A 368 ASP cc_start: 0.7001 (m-30) cc_final: 0.6596 (m-30) REVERT: A 380 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7288 (ttp80) REVERT: B 158 VAL cc_start: 0.8505 (t) cc_final: 0.8269 (p) REVERT: B 228 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7920 (OUTLIER) REVERT: B 258 ASP cc_start: 0.7346 (t70) cc_final: 0.6832 (t0) REVERT: B 323 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7587 (p0) REVERT: S 7 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7888 (m) REVERT: S 116 THR cc_start: 0.8224 (t) cc_final: 0.7967 (p) REVERT: S 227 TYR cc_start: 0.8298 (m-80) cc_final: 0.7980 (m-80) REVERT: R 174 MET cc_start: 0.7234 (tpp) cc_final: 0.7024 (mmm) REVERT: R 280 VAL cc_start: 0.8505 (p) cc_final: 0.8210 (m) outliers start: 33 outliers final: 18 residues processed: 220 average time/residue: 0.8560 time to fit residues: 204.9210 Evaluate side-chains 228 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 178 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 84 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 108 optimal weight: 0.0000 chunk 107 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.1980 chunk 45 optimal weight: 0.5980 chunk 59 optimal weight: 0.4980 chunk 101 optimal weight: 0.8980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107534 restraints weight = 12751.232| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.76 r_work: 0.3243 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8693 Z= 0.130 Angle : 0.546 11.161 11859 Z= 0.286 Chirality : 0.042 0.135 1366 Planarity : 0.004 0.052 1513 Dihedral : 4.439 45.148 1239 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.64 % Allowed : 17.09 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.46 (0.26), residues: 1131 helix: 1.84 (0.27), residues: 377 sheet: 0.07 (0.31), residues: 273 loop : -0.75 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 PHE 0.020 0.002 PHE R 93 TYR 0.013 0.001 TYR A 37 ARG 0.009 0.000 ARG R 124 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 449) hydrogen bonds : angle 4.54381 ( 1299) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.70258 ( 4) covalent geometry : bond 0.00297 ( 8691) covalent geometry : angle 0.54638 (11855) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8405 (t) cc_final: 0.8071 (t) REVERT: A 56 ILE cc_start: 0.7675 (mt) cc_final: 0.7459 (tp) REVERT: A 219 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6916 (tp30) REVERT: A 221 LYS cc_start: 0.8044 (mppt) cc_final: 0.7582 (mppt) REVERT: A 299 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7143 (mt-10) REVERT: A 347 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.8016 (ttp-110) REVERT: A 368 ASP cc_start: 0.6973 (m-30) cc_final: 0.6554 (m-30) REVERT: A 380 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7283 (ttp80) REVERT: B 158 VAL cc_start: 0.8451 (t) cc_final: 0.8232 (p) REVERT: B 170 ASP cc_start: 0.7900 (t0) cc_final: 0.7604 (t70) REVERT: B 258 ASP cc_start: 0.7387 (t70) cc_final: 0.6928 (OUTLIER) REVERT: B 323 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7638 (p0) REVERT: S 7 SER cc_start: 0.8358 (OUTLIER) cc_final: 0.8022 (m) REVERT: S 227 TYR cc_start: 0.8285 (m-80) cc_final: 0.7999 (m-80) REVERT: R 174 MET cc_start: 0.7261 (tpp) cc_final: 0.6991 (mmm) outliers start: 30 outliers final: 17 residues processed: 220 average time/residue: 0.9074 time to fit residues: 217.4471 Evaluate side-chains 225 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 276 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 105 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.121761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.105347 restraints weight = 12709.886| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.84 r_work: 0.3215 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8693 Z= 0.168 Angle : 0.578 10.124 11859 Z= 0.302 Chirality : 0.043 0.161 1366 Planarity : 0.004 0.051 1513 Dihedral : 4.557 46.985 1239 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.00 % Allowed : 17.94 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.47 (0.26), residues: 1131 helix: 1.82 (0.27), residues: 377 sheet: 0.01 (0.30), residues: 285 loop : -0.70 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.009 0.001 HIS A 357 PHE 0.016 0.002 PHE R 93 TYR 0.020 0.002 TYR B 59 ARG 0.009 0.000 ARG R 124 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 449) hydrogen bonds : angle 4.62879 ( 1299) SS BOND : bond 0.00239 ( 2) SS BOND : angle 0.88373 ( 4) covalent geometry : bond 0.00391 ( 8691) covalent geometry : angle 0.57809 (11855) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 214 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8492 (t) cc_final: 0.8182 (t) REVERT: A 56 ILE cc_start: 0.7715 (mt) cc_final: 0.7456 (tp) REVERT: A 258 VAL cc_start: 0.8684 (p) cc_final: 0.8435 (t) REVERT: A 299 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7156 (mt-10) REVERT: A 347 ARG cc_start: 0.8250 (ttm-80) cc_final: 0.8034 (ttp-110) REVERT: A 368 ASP cc_start: 0.7010 (m-30) cc_final: 0.6595 (m-30) REVERT: A 380 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7312 (ttp80) REVERT: B 155 ASN cc_start: 0.8048 (t0) cc_final: 0.7647 (t0) REVERT: B 158 VAL cc_start: 0.8486 (t) cc_final: 0.8245 (p) REVERT: B 175 GLN cc_start: 0.7729 (mm110) cc_final: 0.7504 (mm110) REVERT: B 190 LEU cc_start: 0.8366 (tp) cc_final: 0.8108 (tt) REVERT: B 258 ASP cc_start: 0.7445 (t70) cc_final: 0.6932 (t0) REVERT: S 7 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.8025 (m) REVERT: R 174 MET cc_start: 0.7316 (tpp) cc_final: 0.6910 (mmm) REVERT: R 181 MET cc_start: 0.8136 (tpt) cc_final: 0.7824 (tmm) REVERT: R 185 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7176 (mtm-85) REVERT: R 242 VAL cc_start: 0.8286 (t) cc_final: 0.8018 (p) outliers start: 33 outliers final: 22 residues processed: 228 average time/residue: 0.8754 time to fit residues: 216.3204 Evaluate side-chains 238 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 276 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 68 optimal weight: 0.0670 chunk 108 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105145 restraints weight = 12662.224| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.84 r_work: 0.3210 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8693 Z= 0.180 Angle : 0.582 9.787 11859 Z= 0.304 Chirality : 0.043 0.142 1366 Planarity : 0.004 0.050 1513 Dihedral : 4.648 49.447 1239 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.12 % Allowed : 19.76 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.47 (0.25), residues: 1131 helix: 1.81 (0.27), residues: 380 sheet: 0.02 (0.30), residues: 285 loop : -0.70 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.009 0.001 HIS A 357 PHE 0.015 0.002 PHE A 222 TYR 0.018 0.002 TYR B 59 ARG 0.009 0.000 ARG R 124 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 449) hydrogen bonds : angle 4.63837 ( 1299) SS BOND : bond 0.00238 ( 2) SS BOND : angle 0.94887 ( 4) covalent geometry : bond 0.00416 ( 8691) covalent geometry : angle 0.58229 (11855) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8495 (t) cc_final: 0.8174 (t) REVERT: A 53 LYS cc_start: 0.8048 (pttt) cc_final: 0.7847 (pttt) REVERT: A 56 ILE cc_start: 0.7724 (mt) cc_final: 0.7459 (tp) REVERT: A 258 VAL cc_start: 0.8724 (p) cc_final: 0.8472 (t) REVERT: A 299 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7171 (mt-10) REVERT: A 347 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7931 (ttp-110) REVERT: A 368 ASP cc_start: 0.7001 (m-30) cc_final: 0.6534 (m-30) REVERT: A 380 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7322 (ttp80) REVERT: B 155 ASN cc_start: 0.8057 (t0) cc_final: 0.7628 (t0) REVERT: B 158 VAL cc_start: 0.8478 (t) cc_final: 0.8227 (p) REVERT: B 175 GLN cc_start: 0.7738 (mm110) cc_final: 0.7481 (mm110) REVERT: B 190 LEU cc_start: 0.8377 (tp) cc_final: 0.8131 (tt) REVERT: B 258 ASP cc_start: 0.7453 (t70) cc_final: 0.6920 (t0) REVERT: S 7 SER cc_start: 0.8383 (OUTLIER) cc_final: 0.8132 (m) REVERT: R 186 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7765 (t) REVERT: R 242 VAL cc_start: 0.8280 (t) cc_final: 0.8013 (p) outliers start: 34 outliers final: 23 residues processed: 227 average time/residue: 0.8931 time to fit residues: 219.7741 Evaluate side-chains 231 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 276 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 0.0050 chunk 38 optimal weight: 1.9990 chunk 109 optimal weight: 0.0970 chunk 58 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.122387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106405 restraints weight = 12859.491| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.76 r_work: 0.3228 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8693 Z= 0.152 Angle : 0.571 13.010 11859 Z= 0.296 Chirality : 0.043 0.160 1366 Planarity : 0.004 0.045 1513 Dihedral : 4.566 50.643 1239 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.88 % Allowed : 20.85 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1131 helix: 1.89 (0.27), residues: 380 sheet: 0.07 (0.30), residues: 285 loop : -0.67 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.008 0.001 HIS A 357 PHE 0.014 0.002 PHE R 237 TYR 0.015 0.002 TYR A 391 ARG 0.009 0.000 ARG R 124 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 449) hydrogen bonds : angle 4.59499 ( 1299) SS BOND : bond 0.00419 ( 2) SS BOND : angle 1.15689 ( 4) covalent geometry : bond 0.00351 ( 8691) covalent geometry : angle 0.57077 (11855) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 211 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8457 (t) cc_final: 0.8157 (t) REVERT: A 53 LYS cc_start: 0.8031 (pttt) cc_final: 0.7811 (pttt) REVERT: A 56 ILE cc_start: 0.7702 (mt) cc_final: 0.7420 (tp) REVERT: A 221 LYS cc_start: 0.8044 (mppt) cc_final: 0.7822 (mppt) REVERT: A 258 VAL cc_start: 0.8723 (p) cc_final: 0.8472 (t) REVERT: A 299 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7165 (mt-10) REVERT: A 347 ARG cc_start: 0.8251 (ttm-80) cc_final: 0.8033 (ttp-110) REVERT: A 368 ASP cc_start: 0.6954 (m-30) cc_final: 0.6512 (m-30) REVERT: A 380 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7278 (ttp80) REVERT: B 155 ASN cc_start: 0.8005 (t0) cc_final: 0.7493 (t0) REVERT: B 158 VAL cc_start: 0.8470 (t) cc_final: 0.8234 (p) REVERT: B 175 GLN cc_start: 0.7693 (mm110) cc_final: 0.7423 (mm110) REVERT: B 190 LEU cc_start: 0.8332 (tp) cc_final: 0.8105 (tt) REVERT: B 258 ASP cc_start: 0.7433 (t70) cc_final: 0.6929 (t0) REVERT: B 340 ASN cc_start: 0.7413 (t0) cc_final: 0.7038 (t0) REVERT: S 7 SER cc_start: 0.8308 (p) cc_final: 0.8089 (m) REVERT: R 186 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7733 (t) REVERT: R 242 VAL cc_start: 0.8276 (t) cc_final: 0.8008 (p) outliers start: 32 outliers final: 21 residues processed: 225 average time/residue: 0.8622 time to fit residues: 210.9830 Evaluate side-chains 232 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 146 LEU Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 186 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 46 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106899 restraints weight = 12865.688| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.88 r_work: 0.3226 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8693 Z= 0.141 Angle : 0.563 11.913 11859 Z= 0.291 Chirality : 0.042 0.148 1366 Planarity : 0.004 0.045 1513 Dihedral : 4.514 51.244 1239 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.52 % Allowed : 21.58 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.62 (0.26), residues: 1131 helix: 1.92 (0.27), residues: 385 sheet: 0.11 (0.30), residues: 285 loop : -0.65 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 142 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.002 PHE R 237 TYR 0.014 0.001 TYR A 37 ARG 0.009 0.000 ARG R 124 Details of bonding type rmsd hydrogen bonds : bond 0.03932 ( 449) hydrogen bonds : angle 4.55751 ( 1299) SS BOND : bond 0.00295 ( 2) SS BOND : angle 0.74788 ( 4) covalent geometry : bond 0.00325 ( 8691) covalent geometry : angle 0.56276 (11855) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8450 (t) cc_final: 0.8138 (t) REVERT: A 53 LYS cc_start: 0.8027 (pttt) cc_final: 0.7811 (pttt) REVERT: A 56 ILE cc_start: 0.7681 (mt) cc_final: 0.7403 (tp) REVERT: A 221 LYS cc_start: 0.8019 (mppt) cc_final: 0.7779 (mppt) REVERT: A 299 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7205 (mt-10) REVERT: A 347 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.8030 (ttp-110) REVERT: A 368 ASP cc_start: 0.6965 (m-30) cc_final: 0.6539 (m-30) REVERT: A 380 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7306 (ttp80) REVERT: B 155 ASN cc_start: 0.8020 (t0) cc_final: 0.7412 (t0) REVERT: B 158 VAL cc_start: 0.8473 (t) cc_final: 0.8244 (p) REVERT: B 175 GLN cc_start: 0.7727 (mm110) cc_final: 0.7450 (mm110) REVERT: B 258 ASP cc_start: 0.7450 (t70) cc_final: 0.6952 (t0) REVERT: B 340 ASN cc_start: 0.7451 (t0) cc_final: 0.7059 (t0) REVERT: S 7 SER cc_start: 0.8379 (p) cc_final: 0.8167 (m) REVERT: R 137 VAL cc_start: 0.8288 (t) cc_final: 0.8079 (p) REVERT: R 186 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7737 (t) outliers start: 29 outliers final: 20 residues processed: 220 average time/residue: 0.8596 time to fit residues: 205.4442 Evaluate side-chains 229 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 112 SER Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 186 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 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 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.122280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.105790 restraints weight = 12880.856| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.87 r_work: 0.3217 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8693 Z= 0.165 Angle : 0.584 11.637 11859 Z= 0.303 Chirality : 0.043 0.155 1366 Planarity : 0.004 0.047 1513 Dihedral : 4.611 51.718 1239 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.39 % Allowed : 22.18 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.59 (0.26), residues: 1131 helix: 1.88 (0.27), residues: 385 sheet: 0.07 (0.30), residues: 290 loop : -0.63 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 142 HIS 0.009 0.001 HIS A 357 PHE 0.019 0.002 PHE R 237 TYR 0.016 0.002 TYR A 391 ARG 0.009 0.000 ARG R 124 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 449) hydrogen bonds : angle 4.61482 ( 1299) SS BOND : bond 0.00265 ( 2) SS BOND : angle 0.84217 ( 4) covalent geometry : bond 0.00383 ( 8691) covalent geometry : angle 0.58433 (11855) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8482 (t) cc_final: 0.8172 (t) REVERT: A 53 LYS cc_start: 0.8049 (pttt) cc_final: 0.7840 (pttt) REVERT: A 56 ILE cc_start: 0.7709 (mt) cc_final: 0.7444 (tp) REVERT: A 221 LYS cc_start: 0.8041 (mppt) cc_final: 0.7808 (mppt) REVERT: A 258 VAL cc_start: 0.8686 (p) cc_final: 0.8477 (t) REVERT: A 299 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7216 (mt-10) REVERT: A 347 ARG cc_start: 0.8244 (ttm-80) cc_final: 0.8032 (ttp-110) REVERT: A 368 ASP cc_start: 0.6989 (m-30) cc_final: 0.6569 (m-30) REVERT: A 380 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7284 (ttp80) REVERT: B 35 ASN cc_start: 0.7476 (t0) cc_final: 0.7274 (t0) REVERT: B 155 ASN cc_start: 0.8013 (t0) cc_final: 0.7454 (t0) REVERT: B 158 VAL cc_start: 0.8477 (t) cc_final: 0.8230 (p) REVERT: B 175 GLN cc_start: 0.7740 (mm110) cc_final: 0.7459 (mm110) REVERT: B 190 LEU cc_start: 0.8373 (tp) cc_final: 0.8108 (tt) REVERT: B 258 ASP cc_start: 0.7437 (t70) cc_final: 0.6938 (t0) REVERT: B 340 ASN cc_start: 0.7438 (t0) cc_final: 0.7048 (t0) REVERT: S 7 SER cc_start: 0.8381 (p) cc_final: 0.8167 (m) REVERT: R 137 VAL cc_start: 0.8307 (t) cc_final: 0.8104 (p) REVERT: R 185 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7423 (mtm-85) REVERT: R 186 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.7714 (t) REVERT: R 271 SER cc_start: 0.7666 (p) cc_final: 0.7459 (m) REVERT: R 285 LEU cc_start: 0.8160 (mt) cc_final: 0.7916 (mp) outliers start: 28 outliers final: 20 residues processed: 224 average time/residue: 0.9948 time to fit residues: 242.4854 Evaluate side-chains 234 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 276 SER Chi-restraints excluded: chain R residue 277 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.3980 chunk 110 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 24 optimal weight: 0.0000 chunk 109 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 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 = 0.123539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107112 restraints weight = 12792.099| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.87 r_work: 0.3237 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8693 Z= 0.134 Angle : 0.568 11.296 11859 Z= 0.294 Chirality : 0.043 0.146 1366 Planarity : 0.004 0.047 1513 Dihedral : 4.522 51.756 1239 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.03 % Allowed : 23.03 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.67 (0.26), residues: 1131 helix: 1.95 (0.27), residues: 385 sheet: 0.09 (0.30), residues: 290 loop : -0.57 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 142 HIS 0.007 0.001 HIS A 357 PHE 0.023 0.002 PHE R 237 TYR 0.015 0.001 TYR R 102 ARG 0.009 0.000 ARG R 124 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 449) hydrogen bonds : angle 4.56277 ( 1299) SS BOND : bond 0.00323 ( 2) SS BOND : angle 0.72264 ( 4) covalent geometry : bond 0.00310 ( 8691) covalent geometry : angle 0.56766 (11855) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2262 Ramachandran restraints generated. 1131 Oldfield, 0 Emsley, 1131 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8434 (t) cc_final: 0.8130 (t) REVERT: A 53 LYS cc_start: 0.8029 (pttt) cc_final: 0.7807 (pttt) REVERT: A 56 ILE cc_start: 0.7667 (mt) cc_final: 0.7416 (tp) REVERT: A 258 VAL cc_start: 0.8704 (p) cc_final: 0.8469 (t) REVERT: A 299 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7204 (mt-10) REVERT: A 347 ARG cc_start: 0.8227 (ttm-80) cc_final: 0.8018 (ttp-110) REVERT: A 368 ASP cc_start: 0.6953 (m-30) cc_final: 0.6535 (m-30) REVERT: A 380 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7355 (ttp80) REVERT: A 391 TYR cc_start: 0.8633 (m-80) cc_final: 0.8306 (m-80) REVERT: B 67 SER cc_start: 0.8460 (m) cc_final: 0.8235 (t) REVERT: B 155 ASN cc_start: 0.7984 (t0) cc_final: 0.7416 (t0) REVERT: B 158 VAL cc_start: 0.8471 (t) cc_final: 0.8248 (p) REVERT: B 175 GLN cc_start: 0.7721 (mm110) cc_final: 0.7455 (mm110) REVERT: B 190 LEU cc_start: 0.8346 (tp) cc_final: 0.8104 (tt) REVERT: B 258 ASP cc_start: 0.7425 (t70) cc_final: 0.6950 (t0) REVERT: B 340 ASN cc_start: 0.7288 (t0) cc_final: 0.6900 (t0) REVERT: S 7 SER cc_start: 0.8391 (p) cc_final: 0.8160 (m) REVERT: R 142 TRP cc_start: 0.8338 (m100) cc_final: 0.8086 (m100) REVERT: R 186 VAL cc_start: 0.7965 (OUTLIER) cc_final: 0.7703 (t) REVERT: R 271 SER cc_start: 0.7647 (p) cc_final: 0.7434 (m) REVERT: R 285 LEU cc_start: 0.8001 (mt) cc_final: 0.7782 (mp) outliers start: 25 outliers final: 19 residues processed: 219 average time/residue: 1.1635 time to fit residues: 277.0780 Evaluate side-chains 226 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 149 VAL Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 105 ILE Chi-restraints excluded: chain R residue 183 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 276 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 19 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 97 optimal weight: 0.5980 chunk 79 optimal weight: 0.0470 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 84 optimal weight: 0.0000 overall best weight: 0.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.124653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108294 restraints weight = 12981.652| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.90 r_work: 0.3250 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8693 Z= 0.121 Angle : 0.560 11.144 11859 Z= 0.288 Chirality : 0.042 0.166 1366 Planarity : 0.004 0.047 1513 Dihedral : 4.402 50.339 1239 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.67 % Allowed : 23.76 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1131 helix: 2.00 (0.27), residues: 385 sheet: 0.10 (0.30), residues: 289 loop : -0.54 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 142 HIS 0.006 0.001 HIS A 357 PHE 0.024 0.002 PHE R 237 TYR 0.020 0.001 TYR R 102 ARG 0.009 0.000 ARG R 124 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 449) hydrogen bonds : angle 4.49592 ( 1299) SS BOND : bond 0.00314 ( 2) SS BOND : angle 0.68321 ( 4) covalent geometry : bond 0.00274 ( 8691) covalent geometry : angle 0.55973 (11855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7285.52 seconds wall clock time: 128 minutes 43.62 seconds (7723.62 seconds total)