Starting phenix.real_space_refine on Sat Aug 23 05:04:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vug_32127/08_2025/7vug_32127.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vug_32127/08_2025/7vug_32127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vug_32127/08_2025/7vug_32127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vug_32127/08_2025/7vug_32127.map" model { file = "/net/cci-nas-00/data/ceres_data/7vug_32127/08_2025/7vug_32127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vug_32127/08_2025/7vug_32127.cif" } resolution = 3.2 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1050 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 61 5.16 5 Cl 1 4.86 5 C 5711 2.51 5 N 1503 2.21 5 O 1648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 8924 Number of models: 1 Model: "" Number of chains: 6 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: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" 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: "R" Number of atoms: 2324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 282, 2313 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 12, 'TRANS': 269} Conformer: "B" Number of residues, atoms: 282, 2313 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 12, 'TRANS': 269} bond proxies already assigned to first conformer: 2369 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7ZQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.65, per 1000 atoms: 0.30 Number of scatterers: 8924 At special positions: 0 Unit cell: (88.4, 121.68, 125.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 61 16.00 O 1648 8.00 N 1503 7.00 C 5711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 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: 0.83 Conformation dependent library (CDL) restraints added in 410.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 16 sheets defined 38.2% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 44 through 54 removed outlier: 3.617A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.380A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.080A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.578A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 23 through 25 No H-bonds generated for 'chain 'R' and resid 23 through 25' Processing helix chain 'R' and resid 26 through 52 removed outlier: 4.209A pdb=" N VAL R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL R 31 " --> pdb=" O PHE R 27 " (cutoff:3.500A) Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 53 through 58 Processing helix chain 'R' and resid 60 through 81 removed outlier: 3.697A pdb=" N ASN R 64 " --> pdb=" O LYS R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 88 Processing helix chain 'R' and resid 99 through 132 removed outlier: 3.808A pdb=" N THR R 119 " --> pdb=" O SER R 115 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL R 120 " --> pdb=" O ILE R 116 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 135 through 140 Processing helix chain 'R' and resid 141 through 160 removed outlier: 3.592A pdb=" N LYS R 147 " --> pdb=" O ALA R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 166 removed outlier: 3.714A pdb=" N TRP R 165 " --> pdb=" O PRO R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 192 Processing helix chain 'R' and resid 192 through 212 Processing helix chain 'R' and resid 220 through 242 removed outlier: 3.842A pdb=" N ILE R 236 " --> pdb=" O THR R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 254 removed outlier: 4.229A pdb=" N ILE R 248 " --> pdb=" O ARG R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 287 removed outlier: 3.523A pdb=" N VAL R 263 " --> pdb=" O ASN R 259 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE R 282 " --> pdb=" O THR R 278 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 304 Processing helix chain 'S' and resid 52 through 56 removed outlier: 4.044A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 186 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 186 removed outlier: 6.355A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.263A 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 50 removed outlier: 5.716A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.803A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP B 83 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.736A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.610A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.123A 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: 4.232A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.261A 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: 3.892A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.267A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.591A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.591A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'S' and resid 45 through 51 removed outlier: 6.584A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.699A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 143 through 147 Processing sheet with id=AB7, first strand: chain 'S' and resid 165 through 167 405 hydrogen bonds defined for protein. 1143 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: 1.64 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1426 1.31 - 1.43: 2494 1.43 - 1.56: 5115 1.56 - 1.68: 0 1.68 - 1.81: 89 Bond restraints: 9124 Sorted by residual: bond pdb=" C9 7ZQ R 401 " pdb=" N2 7ZQ R 401 " ideal model delta sigma weight residual 1.341 1.444 -0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" C7 7ZQ R 401 " pdb=" N1 7ZQ R 401 " ideal model delta sigma weight residual 1.344 1.444 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.16e+00 bond pdb=" C3 7ZQ R 401 " pdb="CL1 7ZQ R 401 " ideal model delta sigma weight residual 1.732 1.784 -0.052 2.00e-02 2.50e+03 6.64e+00 bond pdb=" N LYS A 277 " pdb=" CA LYS A 277 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.32e-02 5.74e+03 6.37e+00 ... (remaining 9119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 11742 1.20 - 2.40: 479 2.40 - 3.60: 101 3.60 - 4.80: 32 4.80 - 6.00: 15 Bond angle restraints: 12369 Sorted by residual: angle pdb=" CA ILE A 278 " pdb=" C ILE A 278 " pdb=" O ILE A 278 " ideal model delta sigma weight residual 121.17 118.05 3.12 1.06e+00 8.90e-01 8.67e+00 angle pdb=" CA TYR S 223 " pdb=" CB TYR S 223 " pdb=" CG TYR S 223 " ideal model delta sigma weight residual 113.90 108.64 5.26 1.80e+00 3.09e-01 8.54e+00 angle pdb=" C GLU A 275 " pdb=" N GLU A 276 " pdb=" CA GLU A 276 " ideal model delta sigma weight residual 120.44 123.99 -3.55 1.36e+00 5.41e-01 6.81e+00 angle pdb=" CA LYS R 301 " pdb=" C LYS R 301 " pdb=" O LYS R 301 " ideal model delta sigma weight residual 121.00 118.26 2.74 1.05e+00 9.07e-01 6.80e+00 angle pdb=" CA LYS A 279 " pdb=" C LYS A 279 " pdb=" O LYS A 279 " ideal model delta sigma weight residual 120.82 118.16 2.66 1.05e+00 9.07e-01 6.41e+00 ... (remaining 12364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 4864 17.41 - 34.83: 441 34.83 - 52.24: 74 52.24 - 69.65: 14 69.65 - 87.06: 3 Dihedral angle restraints: 5396 sinusoidal: 2107 harmonic: 3289 Sorted by residual: dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 146.54 -53.54 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CA ASN R 93 " pdb=" C ASN R 93 " pdb=" N MET R 94 " pdb=" CA MET R 94 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA GLU S 222 " pdb=" C GLU S 222 " pdb=" N TYR S 223 " pdb=" CA TYR S 223 " ideal model delta harmonic sigma weight residual -180.00 -155.14 -24.86 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 5393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 899 0.034 - 0.068: 344 0.068 - 0.103: 111 0.103 - 0.137: 38 0.137 - 0.171: 10 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CG LEU S 4 " pdb=" CB LEU S 4 " pdb=" CD1 LEU S 4 " pdb=" CD2 LEU S 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.89e-01 ... (remaining 1399 not shown) Planarity restraints: 1552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP R 166 " 0.041 5.00e-02 4.00e+02 6.28e-02 6.30e+00 pdb=" N PRO R 167 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 167 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 167 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO S 224 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP R 84 " 0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C ASP R 84 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP R 84 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE R 85 " 0.012 2.00e-02 2.50e+03 ... (remaining 1549 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 164 2.66 - 3.22: 8576 3.22 - 3.78: 14085 3.78 - 4.34: 18997 4.34 - 4.90: 31814 Nonbonded interactions: 73636 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.099 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.199 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP C 48 " model vdw 2.221 3.040 nonbonded pdb=" NH2 ARG R 244 " pdb=" O2 7ZQ R 401 " model vdw 2.223 3.120 nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.228 3.120 ... (remaining 73631 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=0.50 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.420 Find NCS groups from input model: 0.050 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 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 : 0.004 0.103 9125 Z= 0.195 Angle : 0.608 6.003 12371 Z= 0.331 Chirality : 0.043 0.171 1402 Planarity : 0.005 0.063 1552 Dihedral : 13.558 87.063 3271 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.26), residues: 1112 helix: 1.16 (0.28), residues: 388 sheet: -1.25 (0.31), residues: 280 loop : -1.42 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.022 0.002 TYR S 223 PHE 0.022 0.001 PHE A 196 TRP 0.018 0.001 TRP R 241 HIS 0.006 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 9124) covalent geometry : angle 0.60806 (12369) SS BOND : bond 0.00534 ( 1) SS BOND : angle 1.04510 ( 2) hydrogen bonds : bond 0.16210 ( 396) hydrogen bonds : angle 7.56333 ( 1143) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.339 Fit side-chains REVERT: A 29 LYS cc_start: 0.7742 (mmpt) cc_final: 0.7473 (mmpt) REVERT: A 209 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7695 (mtmt) REVERT: B 213 VAL cc_start: 0.7793 (m) cc_final: 0.7230 (t) REVERT: R 32 TYR cc_start: 0.7288 (t80) cc_final: 0.6986 (t80) REVERT: R 116 ILE cc_start: 0.7860 (tp) cc_final: 0.7637 (tp) REVERT: R 153 TYR cc_start: 0.7838 (m-80) cc_final: 0.7446 (m-80) REVERT: R 200 PHE cc_start: 0.7065 (m-10) cc_final: 0.6686 (m-80) REVERT: R 205 ILE cc_start: 0.8009 (tp) cc_final: 0.7779 (tp) REVERT: R 266 MET cc_start: 0.6197 (ppp) cc_final: 0.5995 (ppp) REVERT: R 276 LEU cc_start: 0.6846 (tp) cc_final: 0.6646 (tp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1164 time to fit residues: 31.2162 Evaluate side-chains 187 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.0470 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 220 GLN B 230 ASN B 259 GLN B 268 ASN B 340 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.126437 restraints weight = 22570.001| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.48 r_work: 0.3445 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9125 Z= 0.178 Angle : 0.612 7.255 12371 Z= 0.324 Chirality : 0.043 0.206 1402 Planarity : 0.005 0.063 1552 Dihedral : 5.254 53.077 1238 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.61 % Allowed : 10.86 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.26), residues: 1112 helix: 1.13 (0.27), residues: 392 sheet: -1.35 (0.30), residues: 283 loop : -1.33 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 58 TYR 0.025 0.002 TYR S 223 PHE 0.012 0.001 PHE B 278 TRP 0.012 0.002 TRP R 241 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9124) covalent geometry : angle 0.61167 (12369) SS BOND : bond 0.00906 ( 1) SS BOND : angle 0.71008 ( 2) hydrogen bonds : bond 0.04424 ( 396) hydrogen bonds : angle 5.92294 ( 1143) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 208 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7983 (mtmt) REVERT: B 205 ASP cc_start: 0.7041 (p0) cc_final: 0.6826 (p0) REVERT: B 213 VAL cc_start: 0.7976 (m) cc_final: 0.7513 (t) REVERT: R 32 TYR cc_start: 0.7510 (t80) cc_final: 0.7219 (t80) REVERT: R 116 ILE cc_start: 0.8001 (tp) cc_final: 0.7744 (tp) REVERT: R 153 TYR cc_start: 0.8006 (m-80) cc_final: 0.7276 (m-80) REVERT: R 205 ILE cc_start: 0.8155 (tp) cc_final: 0.7929 (tp) REVERT: R 236 ILE cc_start: 0.7392 (tp) cc_final: 0.6968 (tp) REVERT: R 266 MET cc_start: 0.6235 (ppp) cc_final: 0.5683 (ppp) REVERT: S 37 VAL cc_start: 0.8513 (m) cc_final: 0.8191 (t) REVERT: S 60 TYR cc_start: 0.7437 (m-80) cc_final: 0.7006 (m-80) REVERT: S 82 GLN cc_start: 0.7642 (tp40) cc_final: 0.7395 (tp40) REVERT: S 143 VAL cc_start: 0.8190 (m) cc_final: 0.7914 (p) REVERT: S 163 TYR cc_start: 0.7399 (m-80) cc_final: 0.7193 (m-80) outliers start: 6 outliers final: 3 residues processed: 210 average time/residue: 0.1222 time to fit residues: 33.9079 Evaluate side-chains 204 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 203 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.0020 chunk 101 optimal weight: 0.0870 chunk 95 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 99 optimal weight: 0.4980 overall best weight: 0.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.142563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.129708 restraints weight = 15326.080| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.86 r_work: 0.3503 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9125 Z= 0.132 Angle : 0.571 7.799 12371 Z= 0.299 Chirality : 0.042 0.189 1402 Planarity : 0.004 0.060 1552 Dihedral : 5.181 55.995 1238 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.54 % Allowed : 12.40 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.62 (0.26), residues: 1112 helix: 1.20 (0.27), residues: 394 sheet: -1.39 (0.29), residues: 289 loop : -1.12 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 58 TYR 0.023 0.001 TYR S 223 PHE 0.012 0.001 PHE S 108 TRP 0.013 0.001 TRP R 241 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9124) covalent geometry : angle 0.57081 (12369) SS BOND : bond 0.00517 ( 1) SS BOND : angle 0.56306 ( 2) hydrogen bonds : bond 0.03708 ( 396) hydrogen bonds : angle 5.47381 ( 1143) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.355 Fit side-chains REVERT: A 10 LYS cc_start: 0.8018 (mttm) cc_final: 0.7796 (mttm) REVERT: A 29 LYS cc_start: 0.7841 (mmpt) cc_final: 0.7539 (mmpt) REVERT: A 32 ARG cc_start: 0.8344 (mtt-85) cc_final: 0.8121 (mtt-85) REVERT: A 209 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8102 (mtmt) REVERT: B 101 MET cc_start: 0.7308 (mtp) cc_final: 0.7097 (mtp) REVERT: B 133 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8130 (m) REVERT: B 147 SER cc_start: 0.8305 (m) cc_final: 0.8046 (p) REVERT: B 205 ASP cc_start: 0.7161 (p0) cc_final: 0.6908 (p0) REVERT: B 213 VAL cc_start: 0.8017 (m) cc_final: 0.7581 (t) REVERT: B 247 ASP cc_start: 0.6998 (t0) cc_final: 0.6693 (t0) REVERT: B 254 ASP cc_start: 0.7137 (t0) cc_final: 0.6888 (t0) REVERT: R 32 TYR cc_start: 0.7618 (t80) cc_final: 0.7317 (t80) REVERT: R 153 TYR cc_start: 0.8062 (m-80) cc_final: 0.7586 (m-80) REVERT: R 205 ILE cc_start: 0.8312 (tp) cc_final: 0.8069 (tp) REVERT: S 35 HIS cc_start: 0.8504 (m-70) cc_final: 0.8291 (m-70) REVERT: S 37 VAL cc_start: 0.8606 (m) cc_final: 0.8274 (t) REVERT: S 82 GLN cc_start: 0.7734 (tp40) cc_final: 0.7453 (tp40) outliers start: 15 outliers final: 9 residues processed: 207 average time/residue: 0.1273 time to fit residues: 34.6281 Evaluate side-chains 206 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 0.0770 chunk 7 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 0.0070 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 230 ASN B 259 GLN B 340 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.142851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.128569 restraints weight = 21581.114| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.40 r_work: 0.3469 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9125 Z= 0.121 Angle : 0.556 7.878 12371 Z= 0.290 Chirality : 0.041 0.182 1402 Planarity : 0.004 0.057 1552 Dihedral : 5.109 56.855 1238 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.54 % Allowed : 14.65 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.26), residues: 1112 helix: 1.24 (0.27), residues: 396 sheet: -1.26 (0.29), residues: 286 loop : -1.09 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 58 TYR 0.023 0.001 TYR S 223 PHE 0.010 0.001 PHE S 108 TRP 0.011 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9124) covalent geometry : angle 0.55642 (12369) SS BOND : bond 0.00431 ( 1) SS BOND : angle 0.63932 ( 2) hydrogen bonds : bond 0.03434 ( 396) hydrogen bonds : angle 5.24489 ( 1143) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.328 Fit side-chains REVERT: A 10 LYS cc_start: 0.7919 (mttm) cc_final: 0.7684 (mttm) REVERT: A 29 LYS cc_start: 0.7786 (mmpt) cc_final: 0.7461 (mmpt) REVERT: A 32 ARG cc_start: 0.8234 (mtt-85) cc_final: 0.7995 (mtt-85) REVERT: A 209 LYS cc_start: 0.8258 (mtmt) cc_final: 0.8024 (mtmt) REVERT: B 147 SER cc_start: 0.8276 (m) cc_final: 0.7993 (p) REVERT: B 173 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7896 (p) REVERT: B 205 ASP cc_start: 0.7004 (p0) cc_final: 0.6719 (p0) REVERT: B 213 VAL cc_start: 0.7935 (m) cc_final: 0.7383 (t) REVERT: B 247 ASP cc_start: 0.6835 (t0) cc_final: 0.6493 (t0) REVERT: B 254 ASP cc_start: 0.6942 (t0) cc_final: 0.6676 (t0) REVERT: R 32 TYR cc_start: 0.7554 (t80) cc_final: 0.7174 (t80) REVERT: R 205 ILE cc_start: 0.8207 (tp) cc_final: 0.7957 (tp) REVERT: R 236 ILE cc_start: 0.7290 (tp) cc_final: 0.6894 (tp) REVERT: S 82 GLN cc_start: 0.7629 (tp40) cc_final: 0.7332 (tp40) REVERT: S 143 VAL cc_start: 0.8081 (m) cc_final: 0.7813 (p) outliers start: 15 outliers final: 10 residues processed: 208 average time/residue: 0.1223 time to fit residues: 33.5459 Evaluate side-chains 206 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 97 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.141385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.126521 restraints weight = 22847.593| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.57 r_work: 0.3431 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9125 Z= 0.157 Angle : 0.577 7.588 12371 Z= 0.301 Chirality : 0.042 0.194 1402 Planarity : 0.004 0.057 1552 Dihedral : 5.192 58.598 1238 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.15 % Allowed : 14.86 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.26), residues: 1112 helix: 1.21 (0.27), residues: 395 sheet: -1.28 (0.29), residues: 288 loop : -1.04 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 58 TYR 0.027 0.002 TYR S 223 PHE 0.014 0.001 PHE S 108 TRP 0.014 0.002 TRP R 241 HIS 0.008 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9124) covalent geometry : angle 0.57721 (12369) SS BOND : bond 0.00566 ( 1) SS BOND : angle 1.05671 ( 2) hydrogen bonds : bond 0.03574 ( 396) hydrogen bonds : angle 5.17909 ( 1143) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.381 Fit side-chains REVERT: A 29 LYS cc_start: 0.7799 (mmpt) cc_final: 0.7452 (mmpt) REVERT: A 32 ARG cc_start: 0.8262 (mtt-85) cc_final: 0.8054 (mtt-85) REVERT: A 209 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7990 (mtmt) REVERT: B 133 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8118 (m) REVERT: B 147 SER cc_start: 0.8277 (m) cc_final: 0.7952 (p) REVERT: B 205 ASP cc_start: 0.7074 (p0) cc_final: 0.6801 (p0) REVERT: B 213 VAL cc_start: 0.7946 (m) cc_final: 0.7568 (t) REVERT: B 228 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7250 (p0) REVERT: B 247 ASP cc_start: 0.6891 (t0) cc_final: 0.6526 (t0) REVERT: B 254 ASP cc_start: 0.7008 (t0) cc_final: 0.6708 (t0) REVERT: B 329 THR cc_start: 0.8145 (OUTLIER) cc_final: 0.7908 (t) REVERT: R 116 ILE cc_start: 0.8009 (tp) cc_final: 0.7764 (tp) REVERT: R 205 ILE cc_start: 0.8213 (tp) cc_final: 0.7988 (tp) REVERT: S 82 GLN cc_start: 0.7635 (tp40) cc_final: 0.7323 (tp40) outliers start: 21 outliers final: 13 residues processed: 223 average time/residue: 0.1156 time to fit residues: 34.3607 Evaluate side-chains 221 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 97 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B 36 ASN B 230 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.140527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127543 restraints weight = 15234.880| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.88 r_work: 0.3489 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9125 Z= 0.173 Angle : 0.586 7.661 12371 Z= 0.307 Chirality : 0.042 0.200 1402 Planarity : 0.004 0.057 1552 Dihedral : 5.228 57.484 1238 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.46 % Allowed : 16.09 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.26), residues: 1112 helix: 1.16 (0.27), residues: 395 sheet: -1.22 (0.30), residues: 283 loop : -1.01 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 58 TYR 0.029 0.002 TYR S 223 PHE 0.010 0.001 PHE A 196 TRP 0.012 0.002 TRP B 211 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9124) covalent geometry : angle 0.58587 (12369) SS BOND : bond 0.00604 ( 1) SS BOND : angle 1.05817 ( 2) hydrogen bonds : bond 0.03610 ( 396) hydrogen bonds : angle 5.15070 ( 1143) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.342 Fit side-chains REVERT: A 29 LYS cc_start: 0.7940 (mmpt) cc_final: 0.7601 (mmpt) REVERT: A 32 ARG cc_start: 0.8336 (mtt-85) cc_final: 0.8129 (mtt-85) REVERT: A 209 LYS cc_start: 0.8320 (mtmt) cc_final: 0.8084 (mtmt) REVERT: B 133 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8168 (m) REVERT: B 147 SER cc_start: 0.8312 (m) cc_final: 0.8011 (p) REVERT: B 173 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8001 (p) REVERT: B 205 ASP cc_start: 0.7171 (p0) cc_final: 0.6903 (p0) REVERT: B 213 VAL cc_start: 0.7980 (m) cc_final: 0.7591 (t) REVERT: B 228 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7421 (p0) REVERT: B 247 ASP cc_start: 0.7097 (t0) cc_final: 0.6829 (t0) REVERT: B 254 ASP cc_start: 0.7064 (t0) cc_final: 0.6794 (t0) REVERT: R 32 TYR cc_start: 0.7633 (t80) cc_final: 0.7236 (t80) REVERT: R 205 ILE cc_start: 0.8319 (tp) cc_final: 0.8111 (tp) REVERT: R 236 ILE cc_start: 0.7553 (tp) cc_final: 0.7181 (tp) REVERT: R 237 PHE cc_start: 0.8201 (t80) cc_final: 0.7953 (t80) REVERT: S 53 SER cc_start: 0.7910 (m) cc_final: 0.7686 (m) REVERT: S 82 GLN cc_start: 0.7707 (tp40) cc_final: 0.7412 (tp40) REVERT: S 128 MET cc_start: 0.7778 (mtp) cc_final: 0.7577 (mtt) outliers start: 24 outliers final: 18 residues processed: 217 average time/residue: 0.1182 time to fit residues: 34.0506 Evaluate side-chains 226 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 0.3980 chunk 22 optimal weight: 0.4980 chunk 24 optimal weight: 0.1980 chunk 97 optimal weight: 0.2980 chunk 18 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.142065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.129047 restraints weight = 15431.157| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.91 r_work: 0.3507 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9125 Z= 0.114 Angle : 0.555 7.870 12371 Z= 0.289 Chirality : 0.041 0.181 1402 Planarity : 0.004 0.056 1552 Dihedral : 5.063 57.557 1238 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.46 % Allowed : 16.50 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.26), residues: 1112 helix: 1.31 (0.27), residues: 397 sheet: -1.22 (0.29), residues: 284 loop : -0.96 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 58 TYR 0.026 0.001 TYR S 223 PHE 0.012 0.001 PHE R 90 TRP 0.014 0.001 TRP R 241 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9124) covalent geometry : angle 0.55443 (12369) SS BOND : bond 0.00392 ( 1) SS BOND : angle 0.93877 ( 2) hydrogen bonds : bond 0.03282 ( 396) hydrogen bonds : angle 5.05528 ( 1143) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 202 time to evaluate : 0.358 Fit side-chains REVERT: A 20 ASP cc_start: 0.7506 (m-30) cc_final: 0.7258 (m-30) REVERT: A 29 LYS cc_start: 0.7966 (mmpt) cc_final: 0.7620 (mmpt) REVERT: B 59 TYR cc_start: 0.8476 (m-80) cc_final: 0.7961 (m-80) REVERT: B 133 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8151 (m) REVERT: B 147 SER cc_start: 0.8335 (m) cc_final: 0.8080 (p) REVERT: B 150 ARG cc_start: 0.8050 (mpt180) cc_final: 0.7833 (mpt180) REVERT: B 173 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7945 (p) REVERT: B 197 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7471 (mtm110) REVERT: B 213 VAL cc_start: 0.7958 (m) cc_final: 0.7414 (t) REVERT: B 228 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7370 (p0) REVERT: B 247 ASP cc_start: 0.6937 (t0) cc_final: 0.6591 (t0) REVERT: B 254 ASP cc_start: 0.7148 (t0) cc_final: 0.6893 (t0) REVERT: R 32 TYR cc_start: 0.7593 (t80) cc_final: 0.7244 (t80) REVERT: R 205 ILE cc_start: 0.8301 (tp) cc_final: 0.8075 (tp) REVERT: R 237 PHE cc_start: 0.8199 (t80) cc_final: 0.7960 (t80) REVERT: S 53 SER cc_start: 0.7733 (m) cc_final: 0.7500 (m) REVERT: S 82 GLN cc_start: 0.7724 (tp40) cc_final: 0.7451 (tp40) REVERT: S 128 MET cc_start: 0.7749 (mtp) cc_final: 0.7531 (mtt) REVERT: S 222 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5661 (mp0) outliers start: 24 outliers final: 16 residues processed: 212 average time/residue: 0.1203 time to fit residues: 33.6937 Evaluate side-chains 218 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 105 optimal weight: 0.0970 chunk 44 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.140582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.125158 restraints weight = 27291.550| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.83 r_work: 0.3419 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9125 Z= 0.154 Angle : 0.576 7.515 12371 Z= 0.300 Chirality : 0.042 0.193 1402 Planarity : 0.004 0.055 1552 Dihedral : 5.153 57.838 1238 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.77 % Allowed : 16.29 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.26), residues: 1112 helix: 1.26 (0.27), residues: 397 sheet: -1.25 (0.29), residues: 284 loop : -0.98 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.029 0.002 TYR S 223 PHE 0.014 0.001 PHE A 199 TRP 0.014 0.002 TRP B 63 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 9124) covalent geometry : angle 0.57613 (12369) SS BOND : bond 0.00600 ( 1) SS BOND : angle 1.18966 ( 2) hydrogen bonds : bond 0.03452 ( 396) hydrogen bonds : angle 5.05669 ( 1143) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7390 (m-30) cc_final: 0.7149 (m-30) REVERT: A 29 LYS cc_start: 0.7896 (mmpt) cc_final: 0.7554 (mmpt) REVERT: B 147 SER cc_start: 0.8291 (m) cc_final: 0.7996 (p) REVERT: B 150 ARG cc_start: 0.8037 (mpt180) cc_final: 0.7804 (mpt180) REVERT: B 197 ARG cc_start: 0.7617 (mtm110) cc_final: 0.7391 (mtm110) REVERT: B 213 VAL cc_start: 0.7905 (m) cc_final: 0.7510 (t) REVERT: B 228 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7303 (p0) REVERT: B 247 ASP cc_start: 0.6933 (t0) cc_final: 0.6571 (t0) REVERT: B 254 ASP cc_start: 0.6997 (t0) cc_final: 0.6746 (t0) REVERT: R 32 TYR cc_start: 0.7589 (t80) cc_final: 0.7201 (t80) REVERT: R 205 ILE cc_start: 0.8237 (tp) cc_final: 0.8011 (tp) REVERT: R 236 ILE cc_start: 0.7461 (tp) cc_final: 0.7094 (tp) REVERT: S 53 SER cc_start: 0.7715 (m) cc_final: 0.7470 (m) REVERT: S 82 GLN cc_start: 0.7683 (tp40) cc_final: 0.7398 (tp40) REVERT: S 128 MET cc_start: 0.7584 (mtp) cc_final: 0.7336 (mtt) REVERT: S 221 LEU cc_start: 0.7535 (tt) cc_final: 0.7134 (tt) REVERT: S 222 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.5644 (mp0) outliers start: 27 outliers final: 22 residues processed: 215 average time/residue: 0.1199 time to fit residues: 34.0561 Evaluate side-chains 217 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 135 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.126514 restraints weight = 18040.315| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.11 r_work: 0.3471 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9125 Z= 0.169 Angle : 0.592 7.952 12371 Z= 0.307 Chirality : 0.042 0.199 1402 Planarity : 0.004 0.056 1552 Dihedral : 5.218 58.591 1238 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.77 % Allowed : 16.29 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.26), residues: 1112 helix: 1.24 (0.27), residues: 397 sheet: -1.20 (0.30), residues: 281 loop : -1.03 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.031 0.002 TYR S 223 PHE 0.016 0.001 PHE A 199 TRP 0.014 0.002 TRP R 241 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9124) covalent geometry : angle 0.59149 (12369) SS BOND : bond 0.00568 ( 1) SS BOND : angle 1.21413 ( 2) hydrogen bonds : bond 0.03540 ( 396) hydrogen bonds : angle 5.07412 ( 1143) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7970 (mmpt) cc_final: 0.7628 (mmpt) REVERT: B 61 MET cc_start: 0.7625 (ptm) cc_final: 0.7325 (ptm) REVERT: B 147 SER cc_start: 0.8340 (m) cc_final: 0.8074 (p) REVERT: B 150 ARG cc_start: 0.8090 (mpt180) cc_final: 0.7838 (mpt180) REVERT: B 187 VAL cc_start: 0.7942 (OUTLIER) cc_final: 0.7617 (t) REVERT: B 197 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7600 (mtm110) REVERT: B 213 VAL cc_start: 0.7973 (m) cc_final: 0.7583 (t) REVERT: B 228 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7420 (p0) REVERT: B 233 CYS cc_start: 0.7896 (t) cc_final: 0.7626 (t) REVERT: B 247 ASP cc_start: 0.7105 (t0) cc_final: 0.6728 (t0) REVERT: B 254 ASP cc_start: 0.7123 (t0) cc_final: 0.6869 (t0) REVERT: B 312 ASP cc_start: 0.7761 (t0) cc_final: 0.7476 (t0) REVERT: R 32 TYR cc_start: 0.7675 (t80) cc_final: 0.7304 (t80) REVERT: R 205 ILE cc_start: 0.8358 (tp) cc_final: 0.8146 (tp) REVERT: S 53 SER cc_start: 0.7852 (m) cc_final: 0.7588 (m) REVERT: S 82 GLN cc_start: 0.7771 (tp40) cc_final: 0.7488 (tp40) REVERT: S 128 MET cc_start: 0.7836 (mtp) cc_final: 0.7630 (mtt) REVERT: S 221 LEU cc_start: 0.7591 (tt) cc_final: 0.7227 (tt) REVERT: S 222 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5827 (mp0) outliers start: 27 outliers final: 21 residues processed: 215 average time/residue: 0.1203 time to fit residues: 34.3554 Evaluate side-chains 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 120 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 231 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 0.2980 chunk 49 optimal weight: 0.1980 chunk 63 optimal weight: 0.0980 chunk 89 optimal weight: 0.6980 chunk 105 optimal weight: 0.3980 chunk 14 optimal weight: 0.0770 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.2138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.143665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130710 restraints weight = 15359.851| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.90 r_work: 0.3524 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9125 Z= 0.105 Angle : 0.555 8.304 12371 Z= 0.286 Chirality : 0.041 0.179 1402 Planarity : 0.004 0.055 1552 Dihedral : 4.956 55.228 1238 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.43 % Allowed : 17.93 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.26), residues: 1112 helix: 1.39 (0.27), residues: 396 sheet: -1.15 (0.29), residues: 279 loop : -0.97 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 32 TYR 0.025 0.001 TYR S 223 PHE 0.015 0.001 PHE A 199 TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9124) covalent geometry : angle 0.55511 (12369) SS BOND : bond 0.00359 ( 1) SS BOND : angle 1.20541 ( 2) hydrogen bonds : bond 0.03132 ( 396) hydrogen bonds : angle 4.91920 ( 1143) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7950 (mmpt) cc_final: 0.7594 (mmpt) REVERT: B 147 SER cc_start: 0.8288 (m) cc_final: 0.8066 (p) REVERT: B 150 ARG cc_start: 0.7933 (mpt180) cc_final: 0.7725 (mpt180) REVERT: B 197 ARG cc_start: 0.7734 (mtm110) cc_final: 0.7531 (mtm110) REVERT: B 228 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7400 (p0) REVERT: B 247 ASP cc_start: 0.6885 (t0) cc_final: 0.6537 (t0) REVERT: B 254 ASP cc_start: 0.7114 (t0) cc_final: 0.6889 (t0) REVERT: B 308 LEU cc_start: 0.8075 (mt) cc_final: 0.7871 (mp) REVERT: B 312 ASP cc_start: 0.7671 (t0) cc_final: 0.7405 (t0) REVERT: R 205 ILE cc_start: 0.8330 (tp) cc_final: 0.8059 (tp) REVERT: R 236 ILE cc_start: 0.7338 (tp) cc_final: 0.6949 (tp) REVERT: S 35 HIS cc_start: 0.8589 (m-70) cc_final: 0.8348 (m-70) REVERT: S 53 SER cc_start: 0.7682 (m) cc_final: 0.7416 (m) REVERT: S 82 GLN cc_start: 0.7764 (tp40) cc_final: 0.7481 (tp40) REVERT: S 128 MET cc_start: 0.7700 (mtp) cc_final: 0.7468 (mtt) REVERT: S 143 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7844 (p) REVERT: S 219 GLN cc_start: 0.8184 (pp30) cc_final: 0.7525 (pp30) REVERT: S 221 LEU cc_start: 0.7419 (tt) cc_final: 0.6870 (tt) REVERT: S 222 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5602 (mp0) outliers start: 14 outliers final: 11 residues processed: 194 average time/residue: 0.1265 time to fit residues: 32.0459 Evaluate side-chains 200 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain S residue 51 ILE Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 222 GLU Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 33 optimal weight: 0.0670 chunk 24 optimal weight: 0.0570 chunk 44 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.0670 chunk 31 optimal weight: 0.2980 overall best weight: 0.1974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.145204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130738 restraints weight = 21389.940| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.42 r_work: 0.3497 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9125 Z= 0.101 Angle : 0.544 8.467 12371 Z= 0.280 Chirality : 0.041 0.174 1402 Planarity : 0.004 0.054 1552 Dihedral : 4.841 54.524 1238 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.64 % Allowed : 18.14 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.26), residues: 1112 helix: 1.47 (0.27), residues: 396 sheet: -1.20 (0.29), residues: 281 loop : -0.89 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 32 TYR 0.025 0.001 TYR S 223 PHE 0.017 0.001 PHE A 199 TRP 0.014 0.001 TRP R 241 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 9124) covalent geometry : angle 0.54334 (12369) SS BOND : bond 0.00438 ( 1) SS BOND : angle 1.21438 ( 2) hydrogen bonds : bond 0.03021 ( 396) hydrogen bonds : angle 4.84035 ( 1143) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2771.61 seconds wall clock time: 48 minutes 27.96 seconds (2907.96 seconds total)