Starting phenix.real_space_refine on Wed Mar 12 19:08:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wst_37824/03_2025/8wst_37824.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wst_37824/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wst_37824/03_2025/8wst_37824.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wst_37824/03_2025/8wst_37824.map" model { file = "/net/cci-nas-00/data/ceres_data/8wst_37824/03_2025/8wst_37824.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wst_37824/03_2025/8wst_37824.cif" } resolution = 2.4 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= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 5.39, per 1000 atoms: 0.65 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: 1.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.92 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: 2.29 Time building geometry restraints manager: 2.31 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: 1.150 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: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.300 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:16.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.440 ------------------------------------------------------------------------------- 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 0.037 8457 Z= 0.140 Angle : 0.449 6.429 11471 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 : 4.97 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 (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: 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 TRP 0.005 0.001 TRP A 96 HIS 0.004 0.001 HIS A 209 PHE 0.006 0.001 PHE A 228 TYR 0.008 0.001 TYR R 148 ARG 0.002 0.000 ARG B 214 *********************** 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 : 0.912 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: 1.3190 time to fit residues: 275.9664 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 : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 4.9990 chunk 77 optimal weight: 0.0370 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 0.0170 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.4696 ------------------------------------------------------------------------------- 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 = 0.4310 r_free = 0.4310 target = 0.199146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.162251 restraints weight = 8308.211| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 1.95 r_work: 0.3674 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8457 Z= 0.165 Angle : 0.530 7.218 11471 Z= 0.275 Chirality : 0.042 0.143 1304 Planarity : 0.004 0.044 1460 Dihedral : 3.785 18.752 1152 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.10 % Allowed : 10.86 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.27), residues: 1041 helix: 3.12 (0.27), residues: 387 sheet: 1.28 (0.34), residues: 226 loop : -0.25 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS A 209 PHE 0.010 0.001 PHE B 199 TYR 0.012 0.001 TYR R 148 ARG 0.007 0.001 ARG B 137 *********************** 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 148 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.865 Fit side-chains REVERT: A 28 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.5630 (mt-10) REVERT: A 132 ARG cc_start: 0.7297 (ptm160) cc_final: 0.6672 (tpt90) REVERT: A 221 THR cc_start: 0.7422 (p) cc_final: 0.7135 (p) REVERT: B 59 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7245 (m-80) REVERT: B 217 MET cc_start: 0.7878 (ppp) cc_final: 0.7636 (pmt) REVERT: N 49 SER cc_start: 0.7604 (p) cc_final: 0.6991 (t) REVERT: R 140 ARG cc_start: 0.6297 (tpp80) cc_final: 0.5569 (tpt90) REVERT: R 228 TYR cc_start: 0.7392 (t80) cc_final: 0.7169 (t80) REVERT: R 247 MET cc_start: 0.5918 (mmm) cc_final: 0.5642 (mmt) outliers start: 28 outliers final: 8 residues processed: 136 average time/residue: 1.3052 time to fit residues: 189.8760 Evaluate side-chains 116 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN 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 263 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 chunk 95 optimal weight: 0.0050 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 237 ASN B 268 ASN R 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.194926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.155767 restraints weight = 8399.280| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.98 r_work: 0.3620 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8457 Z= 0.183 Angle : 0.537 9.126 11471 Z= 0.278 Chirality : 0.042 0.136 1304 Planarity : 0.004 0.036 1460 Dihedral : 4.051 19.244 1152 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.66 % Allowed : 10.98 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.27), residues: 1041 helix: 2.80 (0.26), residues: 393 sheet: 1.07 (0.32), residues: 231 loop : -0.39 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.012 0.001 PHE B 151 TYR 0.011 0.001 TYR A 191 ARG 0.005 0.000 ARG B 19 *********************** 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 145 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.886 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7793 (mp) REVERT: A 28 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.5572 (mt-10) REVERT: A 132 ARG cc_start: 0.7373 (ptm160) cc_final: 0.6809 (tpt90) REVERT: A 221 THR cc_start: 0.7453 (p) cc_final: 0.7139 (p) REVERT: B 59 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7388 (m-80) REVERT: B 217 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7715 (pmt) REVERT: R 140 ARG cc_start: 0.6364 (tpp80) cc_final: 0.5605 (tpt90) REVERT: R 228 TYR cc_start: 0.7437 (t80) cc_final: 0.7194 (t80) REVERT: R 232 LYS cc_start: 0.5771 (OUTLIER) cc_final: 0.5350 (mmtm) REVERT: R 247 MET cc_start: 0.6083 (mmm) cc_final: 0.5814 (mmt) outliers start: 33 outliers final: 13 residues processed: 131 average time/residue: 1.4144 time to fit residues: 196.2562 Evaluate side-chains 113 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL 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 232 LYS 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 59 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 70 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN R 52 ASN R 230 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.188592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.149742 restraints weight = 8267.334| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.14 r_work: 0.3534 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 8457 Z= 0.338 Angle : 0.649 9.257 11471 Z= 0.345 Chirality : 0.047 0.150 1304 Planarity : 0.005 0.043 1460 Dihedral : 4.902 21.197 1152 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.32 % Allowed : 11.42 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1041 helix: 2.09 (0.25), residues: 392 sheet: 0.71 (0.33), residues: 222 loop : -0.76 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.007 0.002 HIS A 209 PHE 0.017 0.002 PHE N 29 TYR 0.026 0.002 TYR A 191 ARG 0.005 0.001 ARG A 188 *********************** 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 150 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 0.934 Fit side-chains REVERT: A 28 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5705 (mt-10) REVERT: A 132 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6560 (tpt170) REVERT: A 221 THR cc_start: 0.7495 (p) cc_final: 0.7195 (p) REVERT: B 217 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7950 (pmt) REVERT: B 230 ASN cc_start: 0.8055 (p0) cc_final: 0.7811 (m110) REVERT: B 262 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7563 (ttm) REVERT: B 304 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7856 (mtm180) REVERT: G 47 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: N 79 LEU cc_start: 0.4332 (tp) cc_final: 0.4124 (tp) REVERT: R 140 ARG cc_start: 0.6488 (tpp80) cc_final: 0.5694 (tpt90) REVERT: R 228 TYR cc_start: 0.7594 (t80) cc_final: 0.7341 (t80) REVERT: R 232 LYS cc_start: 0.5806 (OUTLIER) cc_final: 0.5469 (mmtm) REVERT: R 282 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6230 (tp) outliers start: 39 outliers final: 14 residues processed: 135 average time/residue: 1.1887 time to fit residues: 170.9374 Evaluate side-chains 122 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.821 ------------------------------------------------------------------------------- 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 171 THR Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 47 THR 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 232 LYS 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 45 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.190692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.152920 restraints weight = 8281.957| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.94 r_work: 0.3544 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8457 Z= 0.202 Angle : 0.540 9.472 11471 Z= 0.283 Chirality : 0.043 0.141 1304 Planarity : 0.004 0.040 1460 Dihedral : 4.505 20.124 1152 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.10 % Allowed : 13.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1041 helix: 2.33 (0.26), residues: 394 sheet: 0.74 (0.33), residues: 218 loop : -0.87 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.015 0.001 PHE B 199 TYR 0.016 0.001 TYR A 191 ARG 0.004 0.000 ARG B 19 *********************** 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 148 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 111 time to evaluate : 1.040 Fit side-chains REVERT: A 18 MET cc_start: 0.7678 (mtt) cc_final: 0.7317 (tmm) REVERT: A 28 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5639 (mt-10) REVERT: A 132 ARG cc_start: 0.7372 (ptm160) cc_final: 0.6649 (tpt170) REVERT: B 217 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7892 (pmt) REVERT: B 230 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7788 (m110) REVERT: N 79 LEU cc_start: 0.4281 (tp) cc_final: 0.4051 (tp) REVERT: R 140 ARG cc_start: 0.6456 (tpp80) cc_final: 0.5734 (tpt90) REVERT: R 228 TYR cc_start: 0.7557 (t80) cc_final: 0.7299 (t80) REVERT: R 232 LYS cc_start: 0.5817 (OUTLIER) cc_final: 0.5474 (mmtm) REVERT: R 282 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6272 (tp) outliers start: 37 outliers final: 20 residues processed: 131 average time/residue: 1.2273 time to fit residues: 171.0462 Evaluate side-chains 126 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG 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 171 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 232 LYS 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 217 MET Chi-restraints excluded: chain B residue 230 ASN 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 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 232 LYS 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 101 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.190297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.151921 restraints weight = 8266.458| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.02 r_work: 0.3551 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8457 Z= 0.207 Angle : 0.537 8.894 11471 Z= 0.282 Chirality : 0.043 0.143 1304 Planarity : 0.004 0.042 1460 Dihedral : 4.490 20.418 1152 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.32 % Allowed : 14.08 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1041 helix: 2.39 (0.25), residues: 394 sheet: 0.67 (0.32), residues: 220 loop : -0.88 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 PHE 0.015 0.001 PHE B 199 TYR 0.016 0.001 TYR A 191 ARG 0.003 0.000 ARG B 19 *********************** 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 144 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 105 time to evaluate : 1.006 Fit side-chains REVERT: A 18 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7265 (tmm) REVERT: A 21 LYS cc_start: 0.8081 (ttpp) cc_final: 0.7598 (ttmm) REVERT: A 28 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.5625 (mt-10) REVERT: A 132 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6650 (tpt170) REVERT: A 221 THR cc_start: 0.7501 (p) cc_final: 0.7234 (p) REVERT: B 217 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7973 (pp-130) REVERT: B 230 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7782 (m110) REVERT: B 304 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7916 (mtm180) REVERT: G 47 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7476 (pt0) REVERT: N 79 LEU cc_start: 0.4414 (tp) cc_final: 0.4209 (tp) REVERT: R 140 ARG cc_start: 0.6423 (tpp80) cc_final: 0.5698 (tpt90) REVERT: R 195 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6356 (tm) REVERT: R 228 TYR cc_start: 0.7565 (t80) cc_final: 0.7347 (t80) REVERT: R 232 LYS cc_start: 0.5831 (OUTLIER) cc_final: 0.5482 (mmtm) REVERT: R 282 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6236 (tp) outliers start: 39 outliers final: 17 residues processed: 127 average time/residue: 1.6735 time to fit residues: 225.4436 Evaluate side-chains 126 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 112 SER Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 195 LYS 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 217 MET Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG 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 161 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 195 LEU Chi-restraints excluded: chain R residue 232 LYS 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 99 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4220 r_free = 0.4220 target = 0.190061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.152061 restraints weight = 8285.088| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 2.02 r_work: 0.3559 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8457 Z= 0.194 Angle : 0.527 8.596 11471 Z= 0.276 Chirality : 0.042 0.142 1304 Planarity : 0.004 0.042 1460 Dihedral : 4.437 20.515 1152 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.10 % Allowed : 14.41 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1041 helix: 2.40 (0.25), residues: 399 sheet: 0.64 (0.32), residues: 218 loop : -0.91 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 169 HIS 0.005 0.001 HIS A 209 PHE 0.015 0.001 PHE B 199 TYR 0.015 0.001 TYR A 191 ARG 0.004 0.000 ARG B 19 *********************** 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 151 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.849 Fit side-chains REVERT: A 18 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7191 (tmt) REVERT: A 28 GLU cc_start: 0.6388 (OUTLIER) cc_final: 0.5599 (mt-10) REVERT: A 132 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6630 (tpt170) REVERT: B 172 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7223 (mm-30) REVERT: B 195 ASP cc_start: 0.7057 (p0) cc_final: 0.6729 (p0) REVERT: B 217 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7972 (pp-130) REVERT: B 230 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7758 (m110) REVERT: G 47 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7467 (pt0) REVERT: N 79 LEU cc_start: 0.4383 (tp) cc_final: 0.4178 (tp) REVERT: R 140 ARG cc_start: 0.6405 (tpp80) cc_final: 0.5713 (tpt90) REVERT: R 195 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6280 (tm) REVERT: R 200 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.6775 (t80) REVERT: R 228 TYR cc_start: 0.7552 (t80) cc_final: 0.7344 (t80) REVERT: R 232 LYS cc_start: 0.5806 (OUTLIER) cc_final: 0.5452 (mmtm) REVERT: R 282 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6136 (tp) outliers start: 37 outliers final: 19 residues processed: 137 average time/residue: 1.2368 time to fit residues: 180.3335 Evaluate side-chains 132 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 112 SER Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 195 LYS 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 217 MET Chi-restraints excluded: chain B residue 230 ASN 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 200 TYR Chi-restraints excluded: chain R residue 232 LYS 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 72 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.1344 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.189599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146234 restraints weight = 8401.721| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.83 r_work: 0.3588 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8457 Z= 0.235 Angle : 0.551 8.510 11471 Z= 0.291 Chirality : 0.043 0.145 1304 Planarity : 0.004 0.043 1460 Dihedral : 4.587 21.229 1152 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.03 % Favored : 95.87 % Rotamer: Outliers : 3.99 % Allowed : 14.86 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.26), residues: 1041 helix: 2.30 (0.25), residues: 399 sheet: 0.50 (0.32), residues: 220 loop : -0.89 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 169 HIS 0.005 0.001 HIS A 209 PHE 0.016 0.002 PHE B 199 TYR 0.018 0.002 TYR A 191 ARG 0.003 0.000 ARG A 188 *********************** 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 139 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 103 time to evaluate : 0.975 Fit side-chains REVERT: A 18 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7199 (tmm) REVERT: A 28 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.5600 (mt-10) REVERT: A 132 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6656 (tpt170) REVERT: B 172 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7217 (mm-30) REVERT: B 195 ASP cc_start: 0.7100 (p0) cc_final: 0.6807 (p0) REVERT: B 217 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7954 (pp-130) REVERT: B 304 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7868 (mtm180) REVERT: G 47 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7450 (pt0) REVERT: N 79 LEU cc_start: 0.4582 (tp) cc_final: 0.4332 (tp) REVERT: R 140 ARG cc_start: 0.6368 (tpp80) cc_final: 0.5686 (tpt90) REVERT: R 195 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6318 (tm) REVERT: R 228 TYR cc_start: 0.7554 (t80) cc_final: 0.7319 (t80) REVERT: R 232 LYS cc_start: 0.5854 (OUTLIER) cc_final: 0.5500 (mmtm) REVERT: R 282 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.6146 (tp) outliers start: 36 outliers final: 20 residues processed: 123 average time/residue: 1.3286 time to fit residues: 173.5617 Evaluate side-chains 131 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 171 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG 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 106 CYS 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 232 LYS 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 55 optimal weight: 3.9990 chunk 72 optimal weight: 0.4980 chunk 74 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.189607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152120 restraints weight = 8371.701| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.90 r_work: 0.3536 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8457 Z= 0.213 Angle : 0.546 8.493 11471 Z= 0.287 Chirality : 0.043 0.145 1304 Planarity : 0.004 0.043 1460 Dihedral : 4.542 20.743 1152 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.03 % Favored : 95.87 % Rotamer: Outliers : 3.99 % Allowed : 15.08 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1041 helix: 2.33 (0.25), residues: 399 sheet: 0.53 (0.32), residues: 220 loop : -0.87 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 169 HIS 0.005 0.001 HIS A 209 PHE 0.016 0.001 PHE B 199 TYR 0.017 0.001 TYR A 191 ARG 0.003 0.000 ARG A 208 *********************** 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 142 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 106 time to evaluate : 0.872 Fit side-chains REVERT: A 18 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7313 (tmt) REVERT: A 28 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5676 (mt-10) REVERT: A 132 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6668 (tpt170) REVERT: B 59 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: B 172 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: B 217 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.8022 (pp-130) REVERT: G 47 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7480 (pt0) REVERT: N 79 LEU cc_start: 0.4474 (tp) cc_final: 0.4234 (tp) REVERT: R 140 ARG cc_start: 0.6476 (tpp80) cc_final: 0.5770 (tpt90) REVERT: R 195 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6327 (tm) REVERT: R 200 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.6835 (t80) REVERT: R 225 TRP cc_start: 0.6590 (OUTLIER) cc_final: 0.6303 (t-100) REVERT: R 228 TYR cc_start: 0.7573 (t80) cc_final: 0.7321 (t80) REVERT: R 232 LYS cc_start: 0.5845 (OUTLIER) cc_final: 0.5490 (mmtm) REVERT: R 282 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6124 (tp) outliers start: 36 outliers final: 20 residues processed: 127 average time/residue: 1.2843 time to fit residues: 173.0302 Evaluate side-chains 134 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 171 THR Chi-restraints excluded: chain A residue 195 LYS 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 159 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 172 GLU 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 42 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain R residue 106 CYS 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 200 TYR Chi-restraints excluded: chain R residue 225 TRP Chi-restraints excluded: chain R residue 232 LYS 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 57 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 99 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 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 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 = 0.4226 r_free = 0.4226 target = 0.190670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.148701 restraints weight = 8350.489| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.72 r_work: 0.3615 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8457 Z= 0.166 Angle : 0.506 8.280 11471 Z= 0.267 Chirality : 0.042 0.142 1304 Planarity : 0.004 0.042 1460 Dihedral : 4.309 19.462 1152 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.25 % Rotamer: Outliers : 3.10 % Allowed : 15.96 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1041 helix: 2.65 (0.25), residues: 393 sheet: 0.60 (0.33), residues: 220 loop : -0.74 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 169 HIS 0.003 0.001 HIS A 209 PHE 0.015 0.001 PHE B 199 TYR 0.014 0.001 TYR R 289 ARG 0.004 0.000 ARG B 19 ********************** 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 133 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.953 Fit side-chains REVERT: A 18 MET cc_start: 0.7507 (mtt) cc_final: 0.7204 (tmt) REVERT: A 28 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.5535 (mt-10) REVERT: A 132 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6727 (tpt170) REVERT: A 221 THR cc_start: 0.7338 (p) cc_final: 0.7081 (p) REVERT: B 59 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: B 172 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: B 217 MET cc_start: 0.8224 (ppp) cc_final: 0.8004 (pp-130) REVERT: G 47 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7451 (pt0) REVERT: R 140 ARG cc_start: 0.6340 (tpp80) cc_final: 0.5686 (tpt90) REVERT: R 195 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6352 (tm) REVERT: R 225 TRP cc_start: 0.6475 (OUTLIER) cc_final: 0.6210 (t-100) REVERT: R 228 TYR cc_start: 0.7565 (t80) cc_final: 0.7261 (t80) REVERT: R 232 LYS cc_start: 0.5948 (OUTLIER) cc_final: 0.5577 (mmtm) REVERT: R 282 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6293 (tt) outliers start: 28 outliers final: 15 residues processed: 123 average time/residue: 1.1757 time to fit residues: 154.1428 Evaluate side-chains 127 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 47 SER Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 159 THR 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 42 GLU 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 225 TRP Chi-restraints excluded: chain R residue 232 LYS 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 52 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4204 r_free = 0.4204 target = 0.188261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141040 restraints weight = 8465.871| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.73 r_work: 0.3547 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8457 Z= 0.256 Angle : 0.578 8.219 11471 Z= 0.305 Chirality : 0.044 0.159 1304 Planarity : 0.004 0.042 1460 Dihedral : 4.669 20.960 1152 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.29 % Rotamer: Outliers : 2.88 % Allowed : 16.08 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1041 helix: 2.28 (0.25), residues: 399 sheet: 0.44 (0.33), residues: 221 loop : -0.81 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 169 HIS 0.005 0.001 HIS A 209 PHE 0.016 0.002 PHE B 199 TYR 0.024 0.002 TYR R 148 ARG 0.003 0.000 ARG A 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8673.16 seconds wall clock time: 150 minutes 10.29 seconds (9010.29 seconds total)