Starting phenix.real_space_refine on Fri Aug 22 22:03:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wst_37824/08_2025/8wst_37824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wst_37824/08_2025/8wst_37824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wst_37824/08_2025/8wst_37824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wst_37824/08_2025/8wst_37824.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wst_37824/08_2025/8wst_37824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wst_37824/08_2025/8wst_37824.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.001 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 59 5.16 5 C 5261 2.51 5 N 1432 2.21 5 O 1534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8286 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1876 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2590 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "L" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 129 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 973 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 123} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2280 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 14, 'TRANS': 272} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 2.07, per 1000 atoms: 0.25 Number of scatterers: 8286 At special positions: 0 Unit cell: (83.22, 100.01, 133.59, 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 59 16.00 O 1534 8.00 N 1432 7.00 C 5261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 184 " distance=1.99 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: 0.61 Conformation dependent library (CDL) restraints added in 424.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1986 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 40.9% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.590A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 4.135A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 154 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.118A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 203 Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 5 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 23 removed outlier: 3.505A pdb=" N ARG G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.623A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 32 through 62 removed outlier: 3.980A pdb=" N LEU R 37 " --> pdb=" O ASP R 33 " (cutoff:3.500A) Proline residue: R 38 - end of helix removed outlier: 4.224A pdb=" N ILE R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY R 42 " --> pdb=" O PRO R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 85 Processing helix chain 'R' and resid 85 through 96 removed outlier: 3.671A pdb=" N LEU R 89 " --> pdb=" O GLY R 85 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N GLN R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP R 93 " --> pdb=" O LEU R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 142 through 145 Processing helix chain 'R' and resid 146 through 165 removed outlier: 3.593A pdb=" N ALA R 165 " --> pdb=" O SER R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 171 removed outlier: 3.552A pdb=" N TRP R 169 " --> pdb=" O ALA R 165 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL R 170 " --> pdb=" O LEU R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 181 removed outlier: 4.328A pdb=" N VAL R 181 " --> pdb=" O LYS R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 206 Processing helix chain 'R' and resid 208 through 231 removed outlier: 3.809A pdb=" N LEU R 212 " --> pdb=" O PHE R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 235 Processing helix chain 'R' and resid 247 through 249 No H-bonds generated for 'chain 'R' and resid 247 through 249' Processing helix chain 'R' and resid 250 through 276 Proline residue: R 266 - end of helix removed outlier: 3.561A pdb=" N LEU R 272 " --> pdb=" O HIS R 268 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN R 276 " --> pdb=" O LEU R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 296 removed outlier: 4.047A pdb=" N TYR R 296 " --> pdb=" O ILE R 292 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 308 removed outlier: 3.620A pdb=" N SER R 300 " --> pdb=" O TYR R 296 " (cutoff:3.500A) Proline residue: R 303 - end of helix Processing helix chain 'R' and resid 313 through 317 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.260A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N PHE A 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.999A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.759A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.969A 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: 6.908A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.797A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.631A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.432A 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: 3.951A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.895A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 7 through 9 Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.588A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.162A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 172 through 175 408 hydrogen bonds defined for protein. 1137 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: 1.23 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2705 1.35 - 1.46: 1989 1.46 - 1.58: 3681 1.58 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 8457 Sorted by residual: bond pdb=" N GLU R 182 " pdb=" CA GLU R 182 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.29e-02 6.01e+03 8.19e+00 bond pdb=" N VAL A 86 " pdb=" CA VAL A 86 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.07e+00 bond pdb=" N GLN A 89 " pdb=" CA GLN A 89 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.29e-02 6.01e+03 6.50e+00 bond pdb=" N SER R 183 " pdb=" CA SER R 183 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.27e+00 bond pdb=" N VAL R 181 " pdb=" CA VAL R 181 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.25e-02 6.40e+03 5.75e+00 ... (remaining 8452 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 11274 1.29 - 2.57: 138 2.57 - 3.86: 46 3.86 - 5.14: 8 5.14 - 6.43: 5 Bond angle restraints: 11471 Sorted by residual: angle pdb=" C CYS R 184 " pdb=" CA CYS R 184 " pdb=" CB CYS R 184 " ideal model delta sigma weight residual 110.88 105.02 5.86 1.60e+00 3.91e-01 1.34e+01 angle pdb=" N ASP A 85 " pdb=" CA ASP A 85 " pdb=" C ASP A 85 " ideal model delta sigma weight residual 107.99 101.56 6.43 1.77e+00 3.19e-01 1.32e+01 angle pdb=" N CYS R 184 " pdb=" CA CYS R 184 " pdb=" C CYS R 184 " ideal model delta sigma weight residual 108.63 103.01 5.62 1.60e+00 3.91e-01 1.23e+01 angle pdb=" N SER R 183 " pdb=" CA SER R 183 " pdb=" C SER R 183 " ideal model delta sigma weight residual 109.07 114.41 -5.34 1.52e+00 4.33e-01 1.23e+01 angle pdb=" C GLU R 182 " pdb=" N SER R 183 " pdb=" CA SER R 183 " ideal model delta sigma weight residual 121.75 116.01 5.74 1.73e+00 3.34e-01 1.10e+01 ... (remaining 11466 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 4890 17.50 - 35.00: 125 35.00 - 52.49: 28 52.49 - 69.99: 5 69.99 - 87.49: 4 Dihedral angle restraints: 5052 sinusoidal: 1979 harmonic: 3073 Sorted by residual: dihedral pdb=" CB CYS R 106 " pdb=" SG CYS R 106 " pdb=" SG CYS R 184 " pdb=" CB CYS R 184 " ideal model delta sinusoidal sigma weight residual 93.00 153.36 -60.36 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" C CYS R 184 " pdb=" N CYS R 184 " pdb=" CA CYS R 184 " pdb=" CB CYS R 184 " ideal model delta harmonic sigma weight residual -122.60 -111.35 -11.25 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" N CYS R 184 " pdb=" C CYS R 184 " pdb=" CA CYS R 184 " pdb=" CB CYS R 184 " ideal model delta harmonic sigma weight residual 122.80 114.64 8.16 0 2.50e+00 1.60e-01 1.06e+01 ... (remaining 5049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1220 0.082 - 0.163: 81 0.163 - 0.245: 2 0.245 - 0.327: 0 0.327 - 0.408: 1 Chirality restraints: 1304 Sorted by residual: chirality pdb=" CA CYS R 184 " pdb=" N CYS R 184 " pdb=" C CYS R 184 " pdb=" CB CYS R 184 " both_signs ideal model delta sigma weight residual False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA VAL R 181 " pdb=" N VAL R 181 " pdb=" C VAL R 181 " pdb=" CB VAL R 181 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA VAL A 86 " pdb=" N VAL A 86 " pdb=" C VAL A 86 " pdb=" CB VAL A 86 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 1301 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS R 184 " -0.007 2.00e-02 2.50e+03 1.33e-02 1.76e+00 pdb=" C CYS R 184 " 0.023 2.00e-02 2.50e+03 pdb=" O CYS R 184 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA R 185 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 180 " -0.006 2.00e-02 2.50e+03 1.22e-02 1.48e+00 pdb=" C GLY R 180 " 0.021 2.00e-02 2.50e+03 pdb=" O GLY R 180 " -0.008 2.00e-02 2.50e+03 pdb=" N VAL R 181 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 203 " 0.006 2.00e-02 2.50e+03 1.10e-02 1.22e+00 pdb=" C ILE R 203 " -0.019 2.00e-02 2.50e+03 pdb=" O ILE R 203 " 0.007 2.00e-02 2.50e+03 pdb=" N THR R 204 " 0.006 2.00e-02 2.50e+03 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 225 2.71 - 3.25: 8403 3.25 - 3.80: 13293 3.80 - 4.35: 17161 4.35 - 4.90: 29572 Nonbonded interactions: 68654 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.158 3.040 nonbonded pdb=" OD1 ASP B 247 " pdb=" OH TYR N 32 " model vdw 2.199 3.040 nonbonded pdb=" O LEU R 164 " pdb=" OH TYR R 200 " model vdw 2.244 3.040 nonbonded pdb=" O PHE N 29 " pdb=" NH2 ARG N 72 " model vdw 2.264 3.120 nonbonded pdb=" NH1 ARG B 283 " pdb=" OD1 ASP B 298 " model vdw 2.269 3.120 ... (remaining 68649 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.120 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8460 Z= 0.128 Angle : 0.450 6.429 11477 Z= 0.260 Chirality : 0.041 0.408 1304 Planarity : 0.002 0.028 1460 Dihedral : 8.866 87.491 3057 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.22 % Allowed : 3.77 % Favored : 96.01 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.41 (0.28), residues: 1041 helix: 3.55 (0.27), residues: 383 sheet: 1.45 (0.36), residues: 217 loop : -0.12 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.008 0.001 TYR R 148 PHE 0.006 0.001 PHE A 228 TRP 0.005 0.001 TRP A 96 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 8457) covalent geometry : angle 0.44919 (11471) SS BOND : bond 0.02177 ( 3) SS BOND : angle 1.41833 ( 6) hydrogen bonds : bond 0.16969 ( 408) hydrogen bonds : angle 6.21704 ( 1137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.322 Fit side-chains REVERT: A 21 LYS cc_start: 0.7531 (ttpp) cc_final: 0.7306 (ttmm) REVERT: A 221 THR cc_start: 0.7341 (p) cc_final: 0.7068 (p) REVERT: B 325 MET cc_start: 0.8336 (mmt) cc_final: 0.8102 (mmt) REVERT: N 5 GLN cc_start: 0.5573 (mm-40) cc_final: 0.5205 (mm110) REVERT: N 49 SER cc_start: 0.7623 (p) cc_final: 0.7056 (t) REVERT: R 98 GLU cc_start: 0.6329 (tt0) cc_final: 0.6076 (tt0) REVERT: R 140 ARG cc_start: 0.5925 (tpp80) cc_final: 0.5404 (tpt90) REVERT: R 247 MET cc_start: 0.5781 (mmm) cc_final: 0.5440 (mmt) outliers start: 2 outliers final: 0 residues processed: 198 average time/residue: 0.6033 time to fit residues: 125.8970 Evaluate side-chains 112 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 75 GLN B 220 GLN B 237 ASN B 268 ASN B 340 ASN R 230 GLN R 268 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.195947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157376 restraints weight = 8336.289| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 1.91 r_work: 0.3636 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8460 Z= 0.135 Angle : 0.559 8.791 11477 Z= 0.290 Chirality : 0.042 0.142 1304 Planarity : 0.004 0.052 1460 Dihedral : 4.038 20.026 1152 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.55 % Allowed : 10.31 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.27), residues: 1041 helix: 2.87 (0.27), residues: 393 sheet: 1.20 (0.33), residues: 233 loop : -0.25 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 314 TYR 0.012 0.001 TYR N 115 PHE 0.012 0.001 PHE A 215 TRP 0.013 0.002 TRP B 82 HIS 0.006 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8457) covalent geometry : angle 0.55850 (11471) SS BOND : bond 0.00223 ( 3) SS BOND : angle 0.75154 ( 6) hydrogen bonds : bond 0.04560 ( 408) hydrogen bonds : angle 4.83755 ( 1137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.322 Fit side-chains REVERT: A 28 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.5662 (mt-10) REVERT: A 132 ARG cc_start: 0.7330 (ptm160) cc_final: 0.6786 (tpt90) REVERT: A 221 THR cc_start: 0.7474 (p) cc_final: 0.7184 (p) REVERT: B 59 TYR cc_start: 0.8101 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: B 195 ASP cc_start: 0.7108 (p0) cc_final: 0.6841 (p0) REVERT: B 217 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7716 (pmt) REVERT: N 49 SER cc_start: 0.7634 (p) cc_final: 0.7010 (t) REVERT: N 52 SER cc_start: 0.5968 (t) cc_final: 0.5758 (t) REVERT: R 140 ARG cc_start: 0.6276 (tpp80) cc_final: 0.5537 (tpt90) REVERT: R 228 TYR cc_start: 0.7435 (t80) cc_final: 0.7217 (t80) REVERT: R 247 MET cc_start: 0.5986 (mmm) cc_final: 0.5714 (mmt) outliers start: 32 outliers final: 11 residues processed: 138 average time/residue: 0.5187 time to fit residues: 76.1092 Evaluate side-chains 110 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 0.0000 chunk 56 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 52 ASN R 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.194245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.155044 restraints weight = 8267.866| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.03 r_work: 0.3595 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8460 Z= 0.123 Angle : 0.529 9.050 11477 Z= 0.275 Chirality : 0.042 0.135 1304 Planarity : 0.004 0.038 1460 Dihedral : 4.104 19.268 1152 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.33 % Allowed : 11.53 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.27), residues: 1041 helix: 2.87 (0.26), residues: 387 sheet: 1.02 (0.32), residues: 229 loop : -0.39 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 19 TYR 0.012 0.001 TYR A 191 PHE 0.012 0.001 PHE B 151 TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8457) covalent geometry : angle 0.52940 (11471) SS BOND : bond 0.00262 ( 3) SS BOND : angle 0.62813 ( 6) hydrogen bonds : bond 0.04097 ( 408) hydrogen bonds : angle 4.62700 ( 1137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.313 Fit side-chains REVERT: A 23 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7863 (mp) REVERT: A 28 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5569 (mt-10) REVERT: A 132 ARG cc_start: 0.7381 (ptm160) cc_final: 0.6642 (tpt170) REVERT: B 59 TYR cc_start: 0.8172 (OUTLIER) cc_final: 0.7403 (m-80) REVERT: B 195 ASP cc_start: 0.7116 (p0) cc_final: 0.6907 (p0) REVERT: B 217 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7800 (pmt) REVERT: R 140 ARG cc_start: 0.6369 (tpp80) cc_final: 0.5611 (tpt90) REVERT: R 157 LEU cc_start: 0.6750 (tt) cc_final: 0.6493 (tp) REVERT: R 228 TYR cc_start: 0.7453 (t80) cc_final: 0.7210 (t80) REVERT: R 232 LYS cc_start: 0.5657 (mmpt) cc_final: 0.5371 (mmtm) REVERT: R 247 MET cc_start: 0.6061 (mmm) cc_final: 0.5790 (mmt) outliers start: 30 outliers final: 15 residues processed: 122 average time/residue: 0.6029 time to fit residues: 77.9196 Evaluate side-chains 116 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 64 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.191663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.152962 restraints weight = 8417.171| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.10 r_work: 0.3569 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8460 Z= 0.141 Angle : 0.546 7.663 11477 Z= 0.287 Chirality : 0.043 0.140 1304 Planarity : 0.004 0.040 1460 Dihedral : 4.382 19.960 1152 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.88 % Allowed : 12.31 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.26), residues: 1041 helix: 2.50 (0.26), residues: 395 sheet: 0.85 (0.32), residues: 218 loop : -0.69 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 152 TYR 0.016 0.002 TYR A 191 PHE 0.014 0.002 PHE B 199 TRP 0.017 0.002 TRP B 82 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8457) covalent geometry : angle 0.54564 (11471) SS BOND : bond 0.00077 ( 3) SS BOND : angle 0.66893 ( 6) hydrogen bonds : bond 0.04217 ( 408) hydrogen bonds : angle 4.63129 ( 1137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.361 Fit side-chains REVERT: A 23 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7806 (mp) REVERT: A 28 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.5448 (mt-10) REVERT: A 132 ARG cc_start: 0.7303 (ptm160) cc_final: 0.6594 (tpt170) REVERT: B 195 ASP cc_start: 0.7094 (p0) cc_final: 0.6813 (p0) REVERT: B 217 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7904 (pmt) REVERT: R 140 ARG cc_start: 0.6446 (tpp80) cc_final: 0.5678 (tpt90) REVERT: R 228 TYR cc_start: 0.7527 (t80) cc_final: 0.7256 (t80) REVERT: R 232 LYS cc_start: 0.5639 (mmpt) cc_final: 0.5244 (mmtm) REVERT: R 282 LEU cc_start: 0.6599 (OUTLIER) cc_final: 0.6192 (tp) outliers start: 35 outliers final: 17 residues processed: 127 average time/residue: 0.5769 time to fit residues: 77.6738 Evaluate side-chains 126 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.189243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.145759 restraints weight = 8349.653| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.77 r_work: 0.3578 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8460 Z= 0.175 Angle : 0.595 10.133 11477 Z= 0.314 Chirality : 0.044 0.147 1304 Planarity : 0.004 0.042 1460 Dihedral : 4.736 21.464 1152 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.66 % Allowed : 13.64 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.26), residues: 1041 helix: 2.19 (0.25), residues: 395 sheet: 0.64 (0.33), residues: 222 loop : -0.81 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 188 TYR 0.023 0.002 TYR A 191 PHE 0.016 0.002 PHE B 151 TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8457) covalent geometry : angle 0.59459 (11471) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.75177 ( 6) hydrogen bonds : bond 0.04584 ( 408) hydrogen bonds : angle 4.78080 ( 1137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 0.250 Fit side-chains REVERT: A 18 MET cc_start: 0.7525 (mtt) cc_final: 0.7234 (tmm) REVERT: A 21 LYS cc_start: 0.8054 (ttpp) cc_final: 0.7588 (ttmm) REVERT: A 28 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5600 (mt-10) REVERT: A 53 MET cc_start: 0.6771 (mtt) cc_final: 0.6490 (mmt) REVERT: A 132 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6615 (tpt170) REVERT: B 23 LYS cc_start: 0.7347 (tptm) cc_final: 0.7109 (ttpp) REVERT: B 101 MET cc_start: 0.8591 (ptm) cc_final: 0.8326 (ptm) REVERT: B 217 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7928 (pmt) REVERT: B 259 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: G 47 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7466 (pt0) REVERT: N 79 LEU cc_start: 0.4353 (tp) cc_final: 0.4088 (tp) REVERT: R 140 ARG cc_start: 0.6391 (tpp80) cc_final: 0.5675 (tpt90) REVERT: R 195 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6348 (tm) REVERT: R 228 TYR cc_start: 0.7588 (t80) cc_final: 0.7309 (t80) REVERT: R 232 LYS cc_start: 0.5720 (mmpt) cc_final: 0.5377 (mmtm) REVERT: R 282 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6252 (tp) outliers start: 33 outliers final: 16 residues processed: 124 average time/residue: 0.6017 time to fit residues: 78.9708 Evaluate side-chains 124 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 282 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 6 optimal weight: 2.9990 chunk 44 optimal weight: 0.0170 chunk 55 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.190476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.152728 restraints weight = 8255.889| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.00 r_work: 0.3562 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8460 Z= 0.127 Angle : 0.526 8.983 11477 Z= 0.277 Chirality : 0.042 0.143 1304 Planarity : 0.004 0.041 1460 Dihedral : 4.428 19.922 1152 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.77 % Allowed : 14.19 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.26), residues: 1041 helix: 2.50 (0.25), residues: 393 sheet: 0.62 (0.33), residues: 220 loop : -0.77 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.015 0.001 TYR A 191 PHE 0.016 0.001 PHE B 199 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8457) covalent geometry : angle 0.52633 (11471) SS BOND : bond 0.00122 ( 3) SS BOND : angle 0.68678 ( 6) hydrogen bonds : bond 0.03987 ( 408) hydrogen bonds : angle 4.56320 ( 1137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.280 Fit side-chains REVERT: A 18 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7199 (tmt) REVERT: A 28 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5601 (mt-10) REVERT: A 132 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.6604 (tpt170) REVERT: B 23 LYS cc_start: 0.7271 (tptm) cc_final: 0.7044 (ttpp) REVERT: B 135 VAL cc_start: 0.6926 (t) cc_final: 0.6603 (p) REVERT: B 175 GLN cc_start: 0.7622 (mm110) cc_final: 0.7411 (mp-120) REVERT: B 217 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7977 (pp-130) REVERT: G 47 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7456 (pt0) REVERT: N 79 LEU cc_start: 0.4427 (tp) cc_final: 0.4190 (tp) REVERT: R 140 ARG cc_start: 0.6385 (tpp80) cc_final: 0.5688 (tpt90) REVERT: R 232 LYS cc_start: 0.5748 (mmpt) cc_final: 0.5406 (mmtm) REVERT: R 282 LEU cc_start: 0.6573 (OUTLIER) cc_final: 0.6203 (tp) outliers start: 34 outliers final: 16 residues processed: 133 average time/residue: 0.5586 time to fit residues: 78.5647 Evaluate side-chains 128 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 0.0040 chunk 6 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN R 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.188116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.150305 restraints weight = 8328.659| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.88 r_work: 0.3521 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3392 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8460 Z= 0.187 Angle : 0.608 9.141 11477 Z= 0.320 Chirality : 0.045 0.153 1304 Planarity : 0.005 0.044 1460 Dihedral : 4.836 22.252 1152 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.43 % Allowed : 13.64 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.25), residues: 1041 helix: 2.05 (0.25), residues: 399 sheet: 0.48 (0.32), residues: 222 loop : -0.91 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 188 TYR 0.024 0.002 TYR A 191 PHE 0.018 0.002 PHE B 199 TRP 0.019 0.002 TRP B 82 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 8457) covalent geometry : angle 0.60762 (11471) SS BOND : bond 0.00113 ( 3) SS BOND : angle 0.72551 ( 6) hydrogen bonds : bond 0.04655 ( 408) hydrogen bonds : angle 4.80746 ( 1137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.333 Fit side-chains REVERT: A 18 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7325 (tmm) REVERT: A 21 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7635 (ttmm) REVERT: A 28 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.5667 (mt-10) REVERT: A 132 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6650 (tpt170) REVERT: B 23 LYS cc_start: 0.7361 (tptm) cc_final: 0.7153 (ttpp) REVERT: B 217 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7958 (pmt) REVERT: B 259 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7859 (mt0) REVERT: G 47 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7486 (pt0) REVERT: N 79 LEU cc_start: 0.4656 (tp) cc_final: 0.4375 (tp) REVERT: R 195 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6363 (tm) REVERT: R 212 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7736 (mp) REVERT: R 228 TYR cc_start: 0.7580 (t80) cc_final: 0.7334 (t80) REVERT: R 232 LYS cc_start: 0.5749 (mmpt) cc_final: 0.5427 (mmtm) REVERT: R 282 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6179 (tp) outliers start: 40 outliers final: 18 residues processed: 119 average time/residue: 0.5807 time to fit residues: 73.2347 Evaluate side-chains 122 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 212 LEU Chi-restraints excluded: chain R residue 225 TRP Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 282 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.189500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.150805 restraints weight = 8249.040| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.10 r_work: 0.3548 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8460 Z= 0.134 Angle : 0.543 8.773 11477 Z= 0.286 Chirality : 0.043 0.147 1304 Planarity : 0.004 0.043 1460 Dihedral : 4.569 20.826 1152 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.97 % Rotamer: Outliers : 3.22 % Allowed : 14.30 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.26), residues: 1041 helix: 2.29 (0.25), residues: 399 sheet: 0.46 (0.32), residues: 222 loop : -0.87 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.017 0.001 TYR A 191 PHE 0.017 0.001 PHE B 199 TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8457) covalent geometry : angle 0.54321 (11471) SS BOND : bond 0.00090 ( 3) SS BOND : angle 0.71230 ( 6) hydrogen bonds : bond 0.04092 ( 408) hydrogen bonds : angle 4.62315 ( 1137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.332 Fit side-chains REVERT: A 18 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.7203 (tmt) REVERT: A 21 LYS cc_start: 0.8109 (ttpp) cc_final: 0.7602 (ttmm) REVERT: A 28 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5600 (mt-10) REVERT: A 132 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6642 (tpt170) REVERT: B 23 LYS cc_start: 0.7259 (tptm) cc_final: 0.7051 (ttpp) REVERT: B 217 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7984 (pp-130) REVERT: G 47 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: N 79 LEU cc_start: 0.4560 (tp) cc_final: 0.4287 (tp) REVERT: R 54 LEU cc_start: 0.7289 (tt) cc_final: 0.7088 (tt) REVERT: R 140 ARG cc_start: 0.6431 (tpp80) cc_final: 0.5807 (tpt90) REVERT: R 195 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6316 (tm) REVERT: R 228 TYR cc_start: 0.7574 (t80) cc_final: 0.7306 (t80) REVERT: R 232 LYS cc_start: 0.5797 (mmpt) cc_final: 0.5450 (mmtm) REVERT: R 282 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6094 (tp) outliers start: 29 outliers final: 17 residues processed: 119 average time/residue: 0.5881 time to fit residues: 74.4048 Evaluate side-chains 120 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 86 MET Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 225 TRP Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 84 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.191234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.153388 restraints weight = 8242.121| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.94 r_work: 0.3578 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8460 Z= 0.108 Angle : 0.508 8.574 11477 Z= 0.267 Chirality : 0.041 0.143 1304 Planarity : 0.004 0.041 1460 Dihedral : 4.296 19.268 1152 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.25 % Rotamer: Outliers : 3.10 % Allowed : 14.52 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.26), residues: 1041 helix: 2.65 (0.25), residues: 393 sheet: 0.48 (0.32), residues: 233 loop : -0.73 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 19 TYR 0.012 0.001 TYR A 191 PHE 0.016 0.001 PHE B 199 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8457) covalent geometry : angle 0.50789 (11471) SS BOND : bond 0.00184 ( 3) SS BOND : angle 0.59355 ( 6) hydrogen bonds : bond 0.03668 ( 408) hydrogen bonds : angle 4.43668 ( 1137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.259 Fit side-chains REVERT: A 18 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7244 (tmt) REVERT: A 21 LYS cc_start: 0.8143 (ttpp) cc_final: 0.7642 (ttmm) REVERT: A 28 GLU cc_start: 0.6369 (OUTLIER) cc_final: 0.5597 (mt-10) REVERT: A 132 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6688 (tpt170) REVERT: B 23 LYS cc_start: 0.7238 (tptm) cc_final: 0.7031 (ttpp) REVERT: B 172 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7230 (mm-30) REVERT: B 217 MET cc_start: 0.8215 (ppp) cc_final: 0.7989 (pp-130) REVERT: G 47 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7458 (pt0) REVERT: R 54 LEU cc_start: 0.7427 (tt) cc_final: 0.7220 (tt) REVERT: R 140 ARG cc_start: 0.6415 (tpp80) cc_final: 0.5870 (tpt90) REVERT: R 195 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6371 (tm) REVERT: R 200 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6665 (t80) REVERT: R 225 TRP cc_start: 0.6492 (OUTLIER) cc_final: 0.6276 (t-100) REVERT: R 228 TYR cc_start: 0.7512 (t80) cc_final: 0.7238 (t80) REVERT: R 232 LYS cc_start: 0.5855 (mmpt) cc_final: 0.5481 (mmtm) REVERT: R 282 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6220 (tt) outliers start: 28 outliers final: 13 residues processed: 119 average time/residue: 0.5589 time to fit residues: 70.6707 Evaluate side-chains 120 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 200 TYR Chi-restraints excluded: chain R residue 225 TRP Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.0060 chunk 26 optimal weight: 0.0770 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 overall best weight: 0.7556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN R 230 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.189701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.152819 restraints weight = 8268.476| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.82 r_work: 0.3559 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8460 Z= 0.123 Angle : 0.527 8.439 11477 Z= 0.277 Chirality : 0.042 0.145 1304 Planarity : 0.004 0.041 1460 Dihedral : 4.381 20.012 1152 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 3.10 % Allowed : 14.41 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.26), residues: 1041 helix: 2.63 (0.25), residues: 393 sheet: 0.53 (0.32), residues: 230 loop : -0.70 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.017 0.001 TYR R 148 PHE 0.016 0.001 PHE B 199 TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8457) covalent geometry : angle 0.52713 (11471) SS BOND : bond 0.00152 ( 3) SS BOND : angle 0.89758 ( 6) hydrogen bonds : bond 0.03859 ( 408) hydrogen bonds : angle 4.46437 ( 1137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2082 Ramachandran restraints generated. 1041 Oldfield, 0 Emsley, 1041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.321 Fit side-chains REVERT: A 18 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7275 (tmt) REVERT: A 28 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5603 (mt-10) REVERT: A 132 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6686 (tpt170) REVERT: B 23 LYS cc_start: 0.7279 (tptm) cc_final: 0.7069 (ttpp) REVERT: B 59 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7365 (m-80) REVERT: B 172 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7234 (mm-30) REVERT: B 197 ARG cc_start: 0.7291 (mmm-85) cc_final: 0.6978 (mmm-85) REVERT: B 217 MET cc_start: 0.8231 (ppp) cc_final: 0.8018 (pp-130) REVERT: G 47 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7474 (pt0) REVERT: R 54 LEU cc_start: 0.7434 (tt) cc_final: 0.7232 (tt) REVERT: R 140 ARG cc_start: 0.6413 (tpp80) cc_final: 0.5834 (tpt90) REVERT: R 195 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6349 (tm) REVERT: R 200 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6759 (t80) REVERT: R 225 TRP cc_start: 0.6545 (OUTLIER) cc_final: 0.6285 (t-100) REVERT: R 228 TYR cc_start: 0.7550 (t80) cc_final: 0.7256 (t80) REVERT: R 232 LYS cc_start: 0.5867 (mmpt) cc_final: 0.5491 (mmtm) outliers start: 28 outliers final: 14 residues processed: 115 average time/residue: 0.6022 time to fit residues: 73.1625 Evaluate side-chains 116 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 106 CYS Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 200 TYR Chi-restraints excluded: chain R residue 225 TRP Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 chunk 63 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.190229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144187 restraints weight = 8407.779| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.03 r_work: 0.3558 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8460 Z= 0.118 Angle : 0.525 8.462 11477 Z= 0.276 Chirality : 0.042 0.144 1304 Planarity : 0.004 0.040 1460 Dihedral : 4.347 19.812 1152 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.97 % Rotamer: Outliers : 3.10 % Allowed : 14.75 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.26), residues: 1041 helix: 2.67 (0.25), residues: 393 sheet: 0.53 (0.32), residues: 230 loop : -0.68 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 46 TYR 0.024 0.001 TYR R 148 PHE 0.016 0.001 PHE B 199 TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8457) covalent geometry : angle 0.52483 (11471) SS BOND : bond 0.00191 ( 3) SS BOND : angle 1.05819 ( 6) hydrogen bonds : bond 0.03773 ( 408) hydrogen bonds : angle 4.44690 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3995.37 seconds wall clock time: 68 minutes 34.10 seconds (4114.10 seconds total)