Starting phenix.real_space_refine on Sat Aug 23 01:29:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xzj_38798/08_2025/8xzj_38798.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xzj_38798/08_2025/8xzj_38798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xzj_38798/08_2025/8xzj_38798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xzj_38798/08_2025/8xzj_38798.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xzj_38798/08_2025/8xzj_38798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xzj_38798/08_2025/8xzj_38798.map" } resolution = 3.0 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= 0.002 sd= 0.006 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 73 5.16 5 C 5804 2.51 5 N 1536 2.21 5 O 1693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 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: 9106 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2410 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "L" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 112 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 3, 'TRANS': 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'NAL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.12, per 1000 atoms: 0.23 Number of scatterers: 9106 At special positions: 0 Unit cell: (100.44, 132.06, 114.39, 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 73 16.00 O 1693 8.00 N 1536 7.00 C 5804 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 19 " - pdb=" SG CYS R 281 " distance=2.16 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.11 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.02 Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 6 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 282.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 15 sheets defined 39.2% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'R' and resid 26 through 55 Proline residue: R 32 - end of helix Processing helix chain 'R' and resid 64 through 78 Processing helix chain 'R' and resid 81 through 91 removed outlier: 3.848A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 132 removed outlier: 4.346A pdb=" N PHE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 3.855A pdb=" N LEU R 142 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG R 143 " --> pdb=" O ARG R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 161 Processing helix chain 'R' and resid 161 through 167 removed outlier: 3.843A pdb=" N MET R 165 " --> pdb=" O ALA R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 210 Processing helix chain 'R' and resid 210 through 216 removed outlier: 3.705A pdb=" N THR R 215 " --> pdb=" O VAL R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 232 removed outlier: 3.697A pdb=" N GLY R 230 " --> pdb=" O GLN R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 274 Proline residue: R 263 - end of helix removed outlier: 4.199A pdb=" N THR R 269 " --> pdb=" O HIS R 265 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU R 270 " --> pdb=" O LEU R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 311 Proline residue: R 292 - end of helix removed outlier: 3.728A pdb=" N SER R 298 " --> pdb=" O CYS R 294 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N TYR R 299 " --> pdb=" O THR R 295 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL R 300 " --> pdb=" O CYS R 296 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN R 301 " --> pdb=" O ILE R 297 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) Proline residue: R 306 - end of helix removed outlier: 3.704A pdb=" N ALA R 310 " --> pdb=" O PRO R 306 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 325 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.520A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 5.023A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.231A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.207A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.873A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.137A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 208 through 212 Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.451A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.623A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.542A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.839A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.278A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.610A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.515A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.621A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.991A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.991A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.427A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 4.055A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1272 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: 1.37 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2196 1.33 - 1.45: 1991 1.45 - 1.57: 5015 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 9307 Sorted by residual: bond pdb=" N ARG L 2 " pdb=" CA ARG L 2 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.24e+01 bond pdb=" N PRO S 224 " pdb=" CD PRO S 224 " ideal model delta sigma weight residual 1.474 1.428 0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" N VAL R 79 " pdb=" CA VAL R 79 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.09e-02 8.42e+03 1.05e+01 bond pdb=" N VAL R 80 " pdb=" CA VAL R 80 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.65e+00 bond pdb=" C4A NAL L 11 " pdb=" C8A NAL L 11 " ideal model delta sigma weight residual 1.419 1.480 -0.061 2.00e-02 2.50e+03 9.34e+00 ... (remaining 9302 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 11898 1.94 - 3.88: 648 3.88 - 5.82: 53 5.82 - 7.75: 12 7.75 - 9.69: 2 Bond angle restraints: 12613 Sorted by residual: angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.23 103.54 9.69 1.24e+00 6.50e-01 6.11e+01 angle pdb=" C ASP R 313 " pdb=" N PRO R 314 " pdb=" CA PRO R 314 " ideal model delta sigma weight residual 119.32 126.59 -7.27 1.14e+00 7.69e-01 4.07e+01 angle pdb=" N LEU R 266 " pdb=" CA LEU R 266 " pdb=" C LEU R 266 " ideal model delta sigma weight residual 113.97 107.43 6.54 1.28e+00 6.10e-01 2.61e+01 angle pdb=" N GLN R 226 " pdb=" CA GLN R 226 " pdb=" C GLN R 226 " ideal model delta sigma weight residual 113.97 107.48 6.49 1.28e+00 6.10e-01 2.57e+01 angle pdb=" N LEU R 308 " pdb=" CA LEU R 308 " pdb=" C LEU R 308 " ideal model delta sigma weight residual 111.36 116.79 -5.43 1.09e+00 8.42e-01 2.48e+01 ... (remaining 12608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 5235 17.12 - 34.24: 178 34.24 - 51.35: 61 51.35 - 68.47: 19 68.47 - 85.59: 6 Dihedral angle restraints: 5499 sinusoidal: 2130 harmonic: 3369 Sorted by residual: dihedral pdb=" CB CYS L 1 " pdb=" SG CYS L 1 " pdb=" SG CYS L 6 " pdb=" CB CYS L 6 " ideal model delta sinusoidal sigma weight residual 93.00 176.96 -83.96 1 1.00e+01 1.00e-02 8.59e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 152.48 27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CD ARG R 91 " pdb=" NE ARG R 91 " pdb=" CZ ARG R 91 " pdb=" NH1 ARG R 91 " ideal model delta sinusoidal sigma weight residual 0.00 -41.70 41.70 1 1.00e+01 1.00e-02 2.43e+01 ... (remaining 5496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 916 0.047 - 0.094: 303 0.094 - 0.141: 135 0.141 - 0.188: 58 0.188 - 0.235: 12 Chirality restraints: 1424 Sorted by residual: chirality pdb=" CA ILE B 338 " pdb=" N ILE B 338 " pdb=" C ILE B 338 " pdb=" CB ILE B 338 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL A 50 " pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CB VAL A 50 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA VAL R 300 " pdb=" N VAL R 300 " pdb=" C VAL R 300 " pdb=" CB VAL R 300 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 1421 not shown) Planarity restraints: 1588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 91 " 0.723 9.50e-02 1.11e+02 3.24e-01 6.39e+01 pdb=" NE ARG R 91 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG R 91 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG R 91 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 91 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 8 " 0.022 2.00e-02 2.50e+03 4.50e-02 2.03e+01 pdb=" C LYS L 8 " -0.078 2.00e-02 2.50e+03 pdb=" O LYS L 8 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY L 9 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 75 " 0.015 2.00e-02 2.50e+03 3.10e-02 9.59e+00 pdb=" C GLN B 75 " -0.054 2.00e-02 2.50e+03 pdb=" O GLN B 75 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP B 76 " 0.018 2.00e-02 2.50e+03 ... (remaining 1585 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1984 2.78 - 3.31: 8657 3.31 - 3.84: 15376 3.84 - 4.37: 19249 4.37 - 4.90: 32319 Nonbonded interactions: 77585 Sorted by model distance: nonbonded pdb=" CD1 ILE R 68 " pdb=" O TYR R 309 " model vdw 2.252 3.460 nonbonded pdb=" O PRO R 280 " pdb=" N ASP R 282 " model vdw 2.272 3.120 nonbonded pdb=" OD1 ASP R 23 " pdb=" NZ LYS L 8 " model vdw 2.287 3.120 nonbonded pdb=" OD2 ASP R 75 " pdb=" ND2 ASN R 305 " model vdw 2.330 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.348 3.040 ... (remaining 77580 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.340 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:5.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 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 : 0.011 0.132 9312 Z= 0.634 Angle : 0.967 12.631 12623 Z= 0.667 Chirality : 0.064 0.235 1424 Planarity : 0.010 0.324 1588 Dihedral : 11.329 85.590 3312 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.84 % Favored : 97.89 % Rotamer: Outliers : 2.72 % Allowed : 2.32 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.36 (0.24), residues: 1139 helix: 0.19 (0.24), residues: 400 sheet: 0.82 (0.29), residues: 288 loop : 0.09 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 314 TYR 0.034 0.002 TYR B 105 PHE 0.024 0.001 PHE B 199 TRP 0.013 0.002 TRP R 95 HIS 0.009 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.01056 ( 9307) covalent geometry : angle 0.94483 (12613) SS BOND : bond 0.06887 ( 5) SS BOND : angle 7.42354 ( 10) hydrogen bonds : bond 0.18179 ( 457) hydrogen bonds : angle 7.50522 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: R 78 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7687 (t80) REVERT: R 293 TYR cc_start: 0.6553 (m-80) cc_final: 0.6161 (m-80) REVERT: A 32 ARG cc_start: 0.7145 (mtm-85) cc_final: 0.6692 (mtm180) REVERT: A 186 GLU cc_start: 0.6466 (mt-10) cc_final: 0.6221 (mt-10) REVERT: B 156 GLN cc_start: 0.8012 (mt0) cc_final: 0.7779 (mt0) REVERT: B 176 GLN cc_start: 0.8320 (mt0) cc_final: 0.8024 (mt0) REVERT: B 219 ARG cc_start: 0.7075 (mtt-85) cc_final: 0.6774 (mtm110) REVERT: B 294 CYS cc_start: 0.7664 (m) cc_final: 0.7318 (m) REVERT: B 325 MET cc_start: 0.8126 (mmt) cc_final: 0.7790 (mmm) REVERT: G 59 ASN cc_start: 0.7839 (t0) cc_final: 0.7583 (t0) REVERT: S 23 SER cc_start: 0.8030 (t) cc_final: 0.7778 (m) REVERT: S 85 SER cc_start: 0.8182 (m) cc_final: 0.7971 (p) REVERT: S 87 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6829 (mtt-85) REVERT: L 8 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6644 (pttm) outliers start: 27 outliers final: 8 residues processed: 240 average time/residue: 0.5071 time to fit residues: 129.3188 Evaluate side-chains 143 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 78 PHE Chi-restraints excluded: chain R residue 109 ILE Chi-restraints excluded: chain R residue 165 MET Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 75 GLN B 91 HIS B 293 ASN S 39 GLN S 130 GLN S 159 ASN S 167 GLN S 182 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.122346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.097971 restraints weight = 14703.476| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.76 r_work: 0.3247 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9312 Z= 0.154 Angle : 0.590 7.652 12623 Z= 0.315 Chirality : 0.043 0.145 1424 Planarity : 0.004 0.051 1588 Dihedral : 6.275 59.157 1281 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 1.67 % Favored : 98.16 % Rotamer: Outliers : 3.43 % Allowed : 10.69 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.12 (0.25), residues: 1139 helix: 1.50 (0.26), residues: 410 sheet: 0.75 (0.30), residues: 264 loop : 0.18 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 143 TYR 0.015 0.002 TYR R 114 PHE 0.023 0.002 PHE R 110 TRP 0.012 0.002 TRP B 297 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9307) covalent geometry : angle 0.58721 (12613) SS BOND : bond 0.00271 ( 5) SS BOND : angle 2.05307 ( 10) hydrogen bonds : bond 0.04497 ( 457) hydrogen bonds : angle 4.95323 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.242 Fit side-chains REVERT: R 41 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6739 (mt) REVERT: R 93 TYR cc_start: 0.4437 (m-80) cc_final: 0.3990 (m-80) REVERT: R 162 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7224 (ptt) REVERT: R 236 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6326 (mtm-85) REVERT: R 272 MET cc_start: 0.6679 (mtm) cc_final: 0.5901 (ptt) REVERT: R 293 TYR cc_start: 0.6642 (m-80) cc_final: 0.6132 (m-80) REVERT: A 253 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8078 (mm) REVERT: A 274 PHE cc_start: 0.7091 (t80) cc_final: 0.6651 (t80) REVERT: B 19 ARG cc_start: 0.7694 (ttp-110) cc_final: 0.6854 (tpp-160) REVERT: B 212 ASP cc_start: 0.8088 (t0) cc_final: 0.7846 (t0) REVERT: B 217 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8268 (pmt) REVERT: B 219 ARG cc_start: 0.7697 (mtt-85) cc_final: 0.7322 (mtm110) REVERT: B 254 ASP cc_start: 0.7409 (t70) cc_final: 0.7130 (t0) REVERT: B 325 MET cc_start: 0.8478 (mmt) cc_final: 0.7808 (mmm) REVERT: G 59 ASN cc_start: 0.7962 (t0) cc_final: 0.7726 (t0) REVERT: S 87 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7359 (mtt90) REVERT: L 8 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6864 (pttm) outliers start: 34 outliers final: 11 residues processed: 169 average time/residue: 0.5652 time to fit residues: 101.1690 Evaluate side-chains 142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 208 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 236 ARG Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 chunk 39 optimal weight: 0.0070 chunk 59 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 112 ASN R 180 GLN A 333 GLN B 75 GLN B 293 ASN B 340 ASN S 159 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.121195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095708 restraints weight = 14646.573| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.81 r_work: 0.3224 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9312 Z= 0.154 Angle : 0.572 7.779 12623 Z= 0.299 Chirality : 0.042 0.145 1424 Planarity : 0.004 0.051 1588 Dihedral : 5.440 50.622 1270 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.28 % Favored : 97.63 % Rotamer: Outliers : 3.73 % Allowed : 12.10 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.24 (0.25), residues: 1139 helix: 1.91 (0.26), residues: 404 sheet: 0.68 (0.30), residues: 260 loop : 0.04 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 148 TYR 0.012 0.002 TYR R 264 PHE 0.028 0.002 PHE R 110 TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 9307) covalent geometry : angle 0.56930 (12613) SS BOND : bond 0.00232 ( 5) SS BOND : angle 2.02626 ( 10) hydrogen bonds : bond 0.04025 ( 457) hydrogen bonds : angle 4.69333 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 136 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: R 36 MET cc_start: 0.6731 (tpp) cc_final: 0.3780 (tmm) REVERT: R 93 TYR cc_start: 0.4658 (m-80) cc_final: 0.4338 (m-80) REVERT: R 162 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.6926 (ptt) REVERT: R 165 MET cc_start: 0.6788 (tpt) cc_final: 0.6585 (tpt) REVERT: R 272 MET cc_start: 0.6718 (mtm) cc_final: 0.5963 (ptt) REVERT: R 287 LEU cc_start: 0.7559 (mp) cc_final: 0.7099 (tt) REVERT: R 293 TYR cc_start: 0.6736 (m-80) cc_final: 0.6255 (m-80) REVERT: A 32 ARG cc_start: 0.7203 (mtm-85) cc_final: 0.6745 (mtm180) REVERT: A 46 LYS cc_start: 0.6916 (mtmm) cc_final: 0.6680 (mtpm) REVERT: A 184 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7752 (tt) REVERT: A 270 LYS cc_start: 0.7598 (mttt) cc_final: 0.7110 (mmpt) REVERT: A 274 PHE cc_start: 0.7043 (t80) cc_final: 0.6717 (t80) REVERT: B 19 ARG cc_start: 0.7770 (ttp-110) cc_final: 0.6873 (tpp-160) REVERT: B 57 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8512 (mttt) REVERT: B 217 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8367 (pmt) REVERT: B 219 ARG cc_start: 0.7757 (mtt-85) cc_final: 0.7334 (mtm110) REVERT: B 254 ASP cc_start: 0.7371 (t70) cc_final: 0.7057 (t0) REVERT: B 322 ASP cc_start: 0.8330 (m-30) cc_final: 0.8110 (m-30) REVERT: G 37 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7664 (mt) REVERT: S 87 ARG cc_start: 0.7621 (mtt180) cc_final: 0.7322 (mtt90) REVERT: L 8 LYS cc_start: 0.7173 (OUTLIER) cc_final: 0.6695 (pttm) outliers start: 37 outliers final: 14 residues processed: 159 average time/residue: 0.5480 time to fit residues: 92.8518 Evaluate side-chains 144 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 ASN A 311 ASN B 176 GLN B 293 ASN B 340 ASN S 159 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.118913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.094089 restraints weight = 14585.787| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.83 r_work: 0.3153 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9312 Z= 0.229 Angle : 0.625 9.237 12623 Z= 0.328 Chirality : 0.045 0.151 1424 Planarity : 0.005 0.053 1588 Dihedral : 5.570 57.430 1270 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.19 % Favored : 97.72 % Rotamer: Outliers : 3.73 % Allowed : 12.90 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.90 (0.25), residues: 1139 helix: 1.61 (0.26), residues: 405 sheet: 0.48 (0.31), residues: 264 loop : -0.13 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.013 0.002 TYR R 182 PHE 0.027 0.002 PHE R 110 TRP 0.016 0.002 TRP B 82 HIS 0.006 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 9307) covalent geometry : angle 0.62308 (12613) SS BOND : bond 0.00482 ( 5) SS BOND : angle 1.88335 ( 10) hydrogen bonds : bond 0.04179 ( 457) hydrogen bonds : angle 4.95744 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.247 Fit side-chains REVERT: R 162 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7039 (ptt) REVERT: R 182 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.6670 (p90) REVERT: R 272 MET cc_start: 0.6721 (mtm) cc_final: 0.5945 (ptt) REVERT: R 293 TYR cc_start: 0.6883 (m-80) cc_final: 0.6409 (m-80) REVERT: A 184 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7910 (tp) REVERT: A 270 LYS cc_start: 0.7601 (mttt) cc_final: 0.7312 (mmtm) REVERT: A 274 PHE cc_start: 0.7264 (t80) cc_final: 0.6924 (t80) REVERT: A 311 ASN cc_start: 0.7889 (t0) cc_final: 0.7673 (t0) REVERT: B 57 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8651 (mttt) REVERT: B 217 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8319 (pmt) REVERT: B 219 ARG cc_start: 0.7774 (mtt-85) cc_final: 0.7351 (mtm110) REVERT: B 254 ASP cc_start: 0.7404 (t70) cc_final: 0.7114 (t0) REVERT: S 87 ARG cc_start: 0.7565 (mtt180) cc_final: 0.7259 (mtt90) outliers start: 37 outliers final: 15 residues processed: 156 average time/residue: 0.5524 time to fit residues: 91.6297 Evaluate side-chains 139 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 219 THR Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS B 75 GLN B 293 ASN B 340 ASN G 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.120481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.096185 restraints weight = 14529.475| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.72 r_work: 0.3212 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9312 Z= 0.134 Angle : 0.541 8.874 12623 Z= 0.285 Chirality : 0.041 0.142 1424 Planarity : 0.004 0.052 1588 Dihedral : 4.473 27.770 1261 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.28 % Favored : 97.63 % Rotamer: Outliers : 2.72 % Allowed : 15.02 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.06 (0.26), residues: 1139 helix: 1.76 (0.27), residues: 407 sheet: 0.57 (0.31), residues: 271 loop : -0.08 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.012 0.001 TYR S 178 PHE 0.024 0.001 PHE R 110 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9307) covalent geometry : angle 0.53951 (12613) SS BOND : bond 0.00301 ( 5) SS BOND : angle 1.55744 ( 10) hydrogen bonds : bond 0.03578 ( 457) hydrogen bonds : angle 4.62907 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: R 54 PHE cc_start: 0.6352 (m-10) cc_final: 0.6119 (m-10) REVERT: R 148 VAL cc_start: 0.7270 (t) cc_final: 0.7068 (p) REVERT: R 162 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.7041 (ptt) REVERT: R 182 TYR cc_start: 0.7179 (p90) cc_final: 0.6754 (p90) REVERT: R 272 MET cc_start: 0.6830 (mtm) cc_final: 0.6068 (ttp) REVERT: R 288 MET cc_start: 0.6254 (OUTLIER) cc_final: 0.6024 (mmt) REVERT: R 293 TYR cc_start: 0.6828 (m-80) cc_final: 0.6482 (m-80) REVERT: A 184 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7849 (tp) REVERT: A 270 LYS cc_start: 0.7600 (mttt) cc_final: 0.7124 (mmpt) REVERT: A 274 PHE cc_start: 0.7280 (t80) cc_final: 0.6915 (t80) REVERT: B 217 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8295 (pmt) REVERT: B 219 ARG cc_start: 0.7770 (mtt-85) cc_final: 0.7334 (mtm110) REVERT: S 87 ARG cc_start: 0.7592 (mtt180) cc_final: 0.7259 (mtt90) REVERT: S 142 SER cc_start: 0.6999 (p) cc_final: 0.6490 (t) REVERT: S 159 ASN cc_start: 0.8716 (m-40) cc_final: 0.8492 (m110) REVERT: S 174 GLN cc_start: 0.8466 (tt0) cc_final: 0.8207 (pt0) REVERT: L 8 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6229 (ttpt) outliers start: 27 outliers final: 9 residues processed: 144 average time/residue: 0.5369 time to fit residues: 82.3209 Evaluate side-chains 135 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain L residue 8 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 87 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 27 optimal weight: 0.0040 chunk 25 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 0.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 176 GLN B 293 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.120519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.096349 restraints weight = 14576.963| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.71 r_work: 0.3216 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9312 Z= 0.129 Angle : 0.532 8.867 12623 Z= 0.278 Chirality : 0.041 0.144 1424 Planarity : 0.004 0.051 1588 Dihedral : 4.311 27.633 1260 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.46 % Favored : 97.45 % Rotamer: Outliers : 2.62 % Allowed : 15.83 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.11 (0.26), residues: 1139 helix: 1.89 (0.27), residues: 407 sheet: 0.47 (0.31), residues: 268 loop : -0.05 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.012 0.001 TYR S 178 PHE 0.025 0.001 PHE R 110 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9307) covalent geometry : angle 0.53085 (12613) SS BOND : bond 0.00280 ( 5) SS BOND : angle 1.43550 ( 10) hydrogen bonds : bond 0.03470 ( 457) hydrogen bonds : angle 4.53528 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.347 Fit side-chains REVERT: R 36 MET cc_start: 0.6428 (tpp) cc_final: 0.3594 (tmm) REVERT: R 101 PHE cc_start: 0.4343 (OUTLIER) cc_final: 0.4131 (m-10) REVERT: R 139 ARG cc_start: 0.7430 (pmt-80) cc_final: 0.5706 (mtm-85) REVERT: R 162 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.6973 (ptt) REVERT: R 182 TYR cc_start: 0.7193 (p90) cc_final: 0.6886 (p90) REVERT: R 272 MET cc_start: 0.6821 (mtm) cc_final: 0.6090 (ttp) REVERT: R 288 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.6119 (mmt) REVERT: R 293 TYR cc_start: 0.6806 (m-80) cc_final: 0.6467 (m-80) REVERT: A 184 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7856 (tt) REVERT: A 270 LYS cc_start: 0.7578 (mttt) cc_final: 0.7133 (mmpt) REVERT: A 274 PHE cc_start: 0.7315 (t80) cc_final: 0.6963 (t80) REVERT: B 217 MET cc_start: 0.8493 (pmm) cc_final: 0.8256 (pmt) REVERT: B 219 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.7356 (mtm110) REVERT: S 142 SER cc_start: 0.7114 (p) cc_final: 0.6796 (m) REVERT: S 159 ASN cc_start: 0.8719 (m-40) cc_final: 0.8491 (m110) REVERT: S 174 GLN cc_start: 0.8448 (tt0) cc_final: 0.8229 (pt0) outliers start: 26 outliers final: 12 residues processed: 142 average time/residue: 0.4867 time to fit residues: 74.0175 Evaluate side-chains 137 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 156 LEU Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 18 optimal weight: 7.9990 chunk 72 optimal weight: 0.0060 chunk 21 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 83 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 0.0070 overall best weight: 0.8616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.120657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.096515 restraints weight = 14633.248| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.71 r_work: 0.3214 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 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 0.035 9312 Z= 0.129 Angle : 0.537 9.571 12623 Z= 0.280 Chirality : 0.041 0.202 1424 Planarity : 0.004 0.052 1588 Dihedral : 4.273 27.397 1260 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.19 % Favored : 97.72 % Rotamer: Outliers : 2.92 % Allowed : 16.13 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.12 (0.26), residues: 1139 helix: 1.95 (0.27), residues: 407 sheet: 0.45 (0.30), residues: 268 loop : -0.08 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.027 0.001 TYR R 93 PHE 0.023 0.001 PHE R 110 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9307) covalent geometry : angle 0.53585 (12613) SS BOND : bond 0.00252 ( 5) SS BOND : angle 1.37680 ( 10) hydrogen bonds : bond 0.03437 ( 457) hydrogen bonds : angle 4.50153 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.405 Fit side-chains REVERT: R 36 MET cc_start: 0.6479 (tpp) cc_final: 0.3580 (tmm) REVERT: R 101 PHE cc_start: 0.4346 (OUTLIER) cc_final: 0.4129 (m-10) REVERT: R 139 ARG cc_start: 0.7388 (pmt-80) cc_final: 0.5713 (mtm-85) REVERT: R 162 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6931 (ptt) REVERT: R 182 TYR cc_start: 0.7211 (p90) cc_final: 0.6955 (p90) REVERT: R 272 MET cc_start: 0.6820 (mtm) cc_final: 0.6063 (ttp) REVERT: R 288 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.6240 (mmt) REVERT: R 293 TYR cc_start: 0.6787 (m-80) cc_final: 0.6439 (m-80) REVERT: A 184 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7873 (tt) REVERT: A 270 LYS cc_start: 0.7559 (mttt) cc_final: 0.7127 (mmpt) REVERT: A 274 PHE cc_start: 0.7248 (t80) cc_final: 0.6908 (t80) REVERT: B 217 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8221 (pmt) REVERT: B 219 ARG cc_start: 0.7773 (mtt-85) cc_final: 0.7363 (mtm110) REVERT: B 267 ASP cc_start: 0.7286 (m-30) cc_final: 0.6925 (p0) REVERT: S 142 SER cc_start: 0.7006 (p) cc_final: 0.6670 (m) REVERT: S 159 ASN cc_start: 0.8711 (m-40) cc_final: 0.8502 (m110) outliers start: 29 outliers final: 15 residues processed: 142 average time/residue: 0.6409 time to fit residues: 97.0896 Evaluate side-chains 138 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 101 PHE Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 75 GLN B 176 GLN B 293 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.118824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094196 restraints weight = 14453.677| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.70 r_work: 0.3163 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9312 Z= 0.208 Angle : 0.602 11.102 12623 Z= 0.311 Chirality : 0.045 0.399 1424 Planarity : 0.004 0.053 1588 Dihedral : 4.583 27.864 1260 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.72 % Favored : 97.19 % Rotamer: Outliers : 3.23 % Allowed : 16.63 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.93 (0.26), residues: 1139 helix: 1.75 (0.27), residues: 407 sheet: 0.28 (0.30), residues: 270 loop : -0.11 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 139 TYR 0.039 0.002 TYR R 93 PHE 0.027 0.002 PHE R 286 TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 9307) covalent geometry : angle 0.60078 (12613) SS BOND : bond 0.00318 ( 5) SS BOND : angle 1.48047 ( 10) hydrogen bonds : bond 0.03815 ( 457) hydrogen bonds : angle 4.76711 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.396 Fit side-chains REVERT: R 36 MET cc_start: 0.6630 (tpp) cc_final: 0.3759 (tmm) REVERT: R 54 PHE cc_start: 0.6553 (OUTLIER) cc_final: 0.6052 (m-10) REVERT: R 139 ARG cc_start: 0.7407 (pmt-80) cc_final: 0.5758 (mtm-85) REVERT: R 162 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6866 (ptt) REVERT: R 272 MET cc_start: 0.6839 (mtm) cc_final: 0.6050 (ttp) REVERT: R 288 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.6147 (mmt) REVERT: R 293 TYR cc_start: 0.6872 (m-80) cc_final: 0.6546 (m-80) REVERT: A 184 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7926 (tp) REVERT: A 270 LYS cc_start: 0.7568 (mttt) cc_final: 0.7176 (mmpt) REVERT: A 274 PHE cc_start: 0.7364 (t80) cc_final: 0.7025 (t80) REVERT: A 311 ASN cc_start: 0.7877 (t0) cc_final: 0.7640 (t0) REVERT: B 177 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8301 (m) REVERT: B 217 MET cc_start: 0.8500 (pmm) cc_final: 0.8227 (pmt) REVERT: B 219 ARG cc_start: 0.7782 (mtt-85) cc_final: 0.7341 (mtm110) outliers start: 32 outliers final: 15 residues processed: 144 average time/residue: 0.5608 time to fit residues: 86.5568 Evaluate side-chains 142 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 54 PHE Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 84 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 293 ASN S 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.121092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.096834 restraints weight = 14515.540| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.73 r_work: 0.3222 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9312 Z= 0.118 Angle : 0.533 11.947 12623 Z= 0.277 Chirality : 0.041 0.145 1424 Planarity : 0.004 0.052 1588 Dihedral : 4.283 27.335 1260 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.19 % Favored : 97.72 % Rotamer: Outliers : 2.22 % Allowed : 17.74 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.12 (0.26), residues: 1139 helix: 1.92 (0.27), residues: 414 sheet: 0.41 (0.30), residues: 273 loop : -0.06 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.037 0.001 TYR R 93 PHE 0.024 0.001 PHE R 110 TRP 0.012 0.001 TRP B 297 HIS 0.003 0.001 HIS R 231 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9307) covalent geometry : angle 0.53196 (12613) SS BOND : bond 0.00245 ( 5) SS BOND : angle 1.40952 ( 10) hydrogen bonds : bond 0.03355 ( 457) hydrogen bonds : angle 4.47957 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.395 Fit side-chains REVERT: R 36 MET cc_start: 0.6484 (tpp) cc_final: 0.3623 (tmm) REVERT: R 139 ARG cc_start: 0.7374 (pmt-80) cc_final: 0.5728 (mtm-85) REVERT: R 153 LEU cc_start: 0.6874 (pp) cc_final: 0.6506 (mm) REVERT: R 162 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6843 (ptt) REVERT: R 182 TYR cc_start: 0.6998 (p90) cc_final: 0.6262 (p90) REVERT: R 272 MET cc_start: 0.6669 (mtm) cc_final: 0.6024 (ttp) REVERT: R 288 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.6139 (mmt) REVERT: R 293 TYR cc_start: 0.6765 (m-80) cc_final: 0.6445 (m-80) REVERT: A 184 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7886 (tt) REVERT: A 270 LYS cc_start: 0.7625 (mttt) cc_final: 0.7195 (mmpt) REVERT: A 274 PHE cc_start: 0.7306 (t80) cc_final: 0.6967 (t80) REVERT: B 177 THR cc_start: 0.8493 (p) cc_final: 0.8224 (m) REVERT: B 217 MET cc_start: 0.8461 (pmm) cc_final: 0.8214 (pmt) REVERT: B 219 ARG cc_start: 0.7803 (mtt-85) cc_final: 0.7355 (mtm110) REVERT: G 21 MET cc_start: 0.6730 (mmp) cc_final: 0.6444 (tpp) REVERT: S 159 ASN cc_start: 0.8701 (m-40) cc_final: 0.8501 (m110) outliers start: 22 outliers final: 11 residues processed: 134 average time/residue: 0.6379 time to fit residues: 91.1607 Evaluate side-chains 132 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 19 optimal weight: 0.0570 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN B 176 GLN B 293 ASN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.117675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.093020 restraints weight = 14524.191| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.71 r_work: 0.3142 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 9312 Z= 0.267 Angle : 0.648 12.030 12623 Z= 0.337 Chirality : 0.046 0.158 1424 Planarity : 0.005 0.053 1588 Dihedral : 4.779 27.920 1260 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.46 % Favored : 97.37 % Rotamer: Outliers : 2.32 % Allowed : 17.64 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.74 (0.26), residues: 1139 helix: 1.59 (0.26), residues: 406 sheet: 0.19 (0.30), residues: 279 loop : -0.22 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 139 TYR 0.042 0.002 TYR R 93 PHE 0.033 0.002 PHE R 286 TRP 0.016 0.002 TRP B 82 HIS 0.008 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 9307) covalent geometry : angle 0.64680 (12613) SS BOND : bond 0.00346 ( 5) SS BOND : angle 1.65890 ( 10) hydrogen bonds : bond 0.04105 ( 457) hydrogen bonds : angle 4.92463 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.400 Fit side-chains REVERT: R 139 ARG cc_start: 0.7384 (pmt-80) cc_final: 0.5773 (mtm-85) REVERT: R 153 LEU cc_start: 0.6978 (pp) cc_final: 0.6563 (mm) REVERT: R 162 MET cc_start: 0.7120 (OUTLIER) cc_final: 0.6852 (ptt) REVERT: R 182 TYR cc_start: 0.6957 (p90) cc_final: 0.6200 (p90) REVERT: R 272 MET cc_start: 0.6752 (mtm) cc_final: 0.6134 (ttp) REVERT: R 288 MET cc_start: 0.6341 (OUTLIER) cc_final: 0.6093 (mmt) REVERT: R 293 TYR cc_start: 0.6965 (m-80) cc_final: 0.6624 (m-80) REVERT: A 184 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7960 (tp) REVERT: A 270 LYS cc_start: 0.7622 (mttt) cc_final: 0.7163 (mmpt) REVERT: A 274 PHE cc_start: 0.7348 (t80) cc_final: 0.7038 (t80) REVERT: A 311 ASN cc_start: 0.7980 (t0) cc_final: 0.7745 (t0) REVERT: B 217 MET cc_start: 0.8391 (pmm) cc_final: 0.8152 (pmt) REVERT: B 219 ARG cc_start: 0.7826 (mtt-85) cc_final: 0.7386 (mtm110) outliers start: 23 outliers final: 13 residues processed: 136 average time/residue: 0.6051 time to fit residues: 88.0156 Evaluate side-chains 139 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 65 ASP Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 148 VAL Chi-restraints excluded: chain R residue 162 MET Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 248 SER Chi-restraints excluded: chain R residue 288 MET Chi-restraints excluded: chain R residue 297 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 201 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 67 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 107 optimal weight: 0.0040 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN S 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.121135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.096997 restraints weight = 14337.738| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.71 r_work: 0.3228 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9312 Z= 0.115 Angle : 0.541 12.338 12623 Z= 0.280 Chirality : 0.041 0.146 1424 Planarity : 0.004 0.053 1588 Dihedral : 4.316 27.317 1260 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.02 % Favored : 97.81 % Rotamer: Outliers : 1.61 % Allowed : 18.45 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.01 (0.26), residues: 1139 helix: 1.89 (0.27), residues: 413 sheet: 0.35 (0.30), residues: 271 loop : -0.19 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.032 0.001 TYR R 93 PHE 0.027 0.001 PHE R 110 TRP 0.012 0.001 TRP B 297 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9307) covalent geometry : angle 0.54022 (12613) SS BOND : bond 0.00226 ( 5) SS BOND : angle 1.38792 ( 10) hydrogen bonds : bond 0.03378 ( 457) hydrogen bonds : angle 4.50912 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3360.42 seconds wall clock time: 58 minutes 1.95 seconds (3481.95 seconds total)