Starting phenix.real_space_refine on Fri Feb 14 06:20:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vug_32127/02_2025/7vug_32127.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vug_32127/02_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_32127/02_2025/7vug_32127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vug_32127/02_2025/7vug_32127.map" model { file = "/net/cci-nas-00/data/ceres_data/7vug_32127/02_2025/7vug_32127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vug_32127/02_2025/7vug_32127.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.25, per 1000 atoms: 0.70 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: 2.25 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.99 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: 2.72 Time building geometry restraints manager: 2.57 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.790 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.220 ------------------------------------------------------------------------------- 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 9124 Z= 0.268 Angle : 0.608 6.003 12369 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 : 11.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (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 TRP 0.018 0.001 TRP R 241 HIS 0.006 0.001 HIS S 220 PHE 0.022 0.001 PHE A 196 TYR 0.022 0.002 TYR S 223 ARG 0.005 0.000 ARG B 314 *********************** 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 : 0.911 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: 0.6983 (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: 0.7780 (tp) REVERT: R 266 MET cc_start: 0.6197 (ppp) cc_final: 0.5994 (ppp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2560 time to fit residues: 68.3632 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 : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 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 304 GLN B 220 GLN B 230 ASN B 259 GLN B 268 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.140755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.127298 restraints weight = 17070.053| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.03 r_work: 0.3481 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9124 Z= 0.269 Angle : 0.620 7.390 12369 Z= 0.328 Chirality : 0.044 0.201 1402 Planarity : 0.005 0.063 1552 Dihedral : 5.297 53.533 1238 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 0.72 % Allowed : 10.55 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.26), residues: 1112 helix: 1.10 (0.27), residues: 391 sheet: -1.27 (0.30), residues: 278 loop : -1.38 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 241 HIS 0.005 0.001 HIS A 188 PHE 0.013 0.001 PHE R 303 TYR 0.024 0.002 TYR S 223 ARG 0.008 0.000 ARG R 58 *********************** 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 215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 208 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8327 (mtmt) cc_final: 0.8111 (mtmt) REVERT: B 205 ASP cc_start: 0.7203 (p0) cc_final: 0.6981 (p0) REVERT: B 213 VAL cc_start: 0.8057 (m) cc_final: 0.7585 (t) REVERT: R 32 TYR cc_start: 0.7665 (t80) cc_final: 0.7349 (t80) REVERT: R 116 ILE cc_start: 0.8136 (tp) cc_final: 0.7904 (tp) REVERT: R 205 ILE cc_start: 0.8317 (tp) cc_final: 0.8107 (tp) REVERT: R 236 ILE cc_start: 0.7611 (tp) cc_final: 0.7208 (tp) REVERT: R 266 MET cc_start: 0.6529 (ppp) cc_final: 0.5995 (ppp) REVERT: S 37 VAL cc_start: 0.8609 (m) cc_final: 0.8297 (t) REVERT: S 60 TYR cc_start: 0.7617 (m-80) cc_final: 0.7205 (m-80) REVERT: S 82 GLN cc_start: 0.7722 (tp40) cc_final: 0.7488 (tp40) REVERT: S 130 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7180 (mt0) REVERT: S 143 VAL cc_start: 0.8256 (m) cc_final: 0.7986 (p) REVERT: S 163 TYR cc_start: 0.7528 (m-80) cc_final: 0.7213 (m-80) outliers start: 7 outliers final: 3 residues processed: 210 average time/residue: 0.2579 time to fit residues: 71.6180 Evaluate side-chains 207 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 203 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 130 GLN 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 45 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN B 340 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.139852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.125322 restraints weight = 21155.407| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.39 r_work: 0.3429 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9124 Z= 0.272 Angle : 0.603 7.640 12369 Z= 0.317 Chirality : 0.043 0.205 1402 Planarity : 0.005 0.063 1552 Dihedral : 5.377 56.193 1238 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.05 % Allowed : 12.19 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.26), residues: 1112 helix: 1.03 (0.27), residues: 394 sheet: -1.41 (0.30), residues: 288 loop : -1.22 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 241 HIS 0.005 0.001 HIS S 220 PHE 0.014 0.001 PHE S 108 TYR 0.026 0.002 TYR S 223 ARG 0.009 0.001 ARG R 58 *********************** 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 230 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 1.076 Fit side-chains REVERT: A 29 LYS cc_start: 0.7771 (mmpt) cc_final: 0.7456 (mmpt) REVERT: A 32 ARG cc_start: 0.8283 (mtt-85) cc_final: 0.8032 (mtt-85) REVERT: A 209 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7988 (mtmt) REVERT: B 133 VAL cc_start: 0.8379 (OUTLIER) cc_final: 0.8106 (m) REVERT: B 147 SER cc_start: 0.8298 (m) cc_final: 0.7957 (p) REVERT: B 205 ASP cc_start: 0.7050 (p0) cc_final: 0.6813 (p0) REVERT: B 213 VAL cc_start: 0.7934 (m) cc_final: 0.7567 (t) REVERT: B 247 ASP cc_start: 0.6852 (t0) cc_final: 0.6572 (t0) REVERT: B 329 THR cc_start: 0.8133 (t) cc_final: 0.7897 (t) REVERT: R 78 PHE cc_start: 0.7675 (t80) cc_final: 0.7455 (t80) REVERT: R 116 ILE cc_start: 0.8005 (tp) cc_final: 0.7772 (tp) REVERT: R 205 ILE cc_start: 0.8172 (tp) cc_final: 0.7957 (tp) REVERT: R 236 ILE cc_start: 0.7475 (tp) cc_final: 0.7095 (tp) REVERT: S 35 HIS cc_start: 0.8519 (m-70) cc_final: 0.8217 (m-70) REVERT: S 37 VAL cc_start: 0.8534 (m) cc_final: 0.8204 (t) REVERT: S 82 GLN cc_start: 0.7633 (tp40) cc_final: 0.7338 (tp40) outliers start: 20 outliers final: 13 residues processed: 217 average time/residue: 0.2511 time to fit residues: 71.9109 Evaluate side-chains 215 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 18 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ASP 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 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 96 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3743 r_free = 0.3743 target = 0.139269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.126336 restraints weight = 15348.803| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.86 r_work: 0.3475 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9124 Z= 0.259 Angle : 0.596 7.629 12369 Z= 0.312 Chirality : 0.042 0.206 1402 Planarity : 0.005 0.063 1552 Dihedral : 5.357 57.011 1238 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.25 % Allowed : 14.24 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.26), residues: 1112 helix: 1.01 (0.26), residues: 394 sheet: -1.34 (0.30), residues: 285 loop : -1.16 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 211 HIS 0.005 0.001 HIS S 35 PHE 0.012 0.001 PHE S 108 TYR 0.027 0.002 TYR S 223 ARG 0.009 0.000 ARG R 58 *********************** 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 228 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 1.062 Fit side-chains REVERT: A 10 LYS cc_start: 0.8007 (mttm) cc_final: 0.7789 (mttm) REVERT: A 29 LYS cc_start: 0.7942 (mmpt) cc_final: 0.7623 (mmpt) REVERT: A 32 ARG cc_start: 0.8303 (mtt-85) cc_final: 0.8053 (mtt-85) REVERT: A 209 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8073 (mtmt) REVERT: B 133 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8155 (m) REVERT: B 147 SER cc_start: 0.8353 (m) cc_final: 0.8047 (p) REVERT: B 205 ASP cc_start: 0.7178 (p0) cc_final: 0.6919 (p0) REVERT: B 213 VAL cc_start: 0.7998 (m) cc_final: 0.7617 (t) REVERT: B 247 ASP cc_start: 0.7099 (t0) cc_final: 0.6874 (t0) REVERT: B 254 ASP cc_start: 0.7030 (t0) cc_final: 0.6768 (t0) REVERT: B 329 THR cc_start: 0.8214 (t) cc_final: 0.8009 (t) REVERT: R 116 ILE cc_start: 0.8112 (tp) cc_final: 0.7891 (tp) REVERT: R 205 ILE cc_start: 0.8321 (tp) cc_final: 0.8120 (tp) REVERT: R 236 ILE cc_start: 0.7616 (tp) cc_final: 0.7229 (tp) REVERT: S 35 HIS cc_start: 0.8415 (m-70) cc_final: 0.8170 (m-70) REVERT: S 82 GLN cc_start: 0.7737 (tp40) cc_final: 0.7457 (tp40) outliers start: 22 outliers final: 14 residues processed: 213 average time/residue: 0.2528 time to fit residues: 71.0469 Evaluate side-chains 219 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 341 ASP Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 252 LEU 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 38 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 94 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 5 optimal weight: 0.0060 chunk 105 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 B 259 GLN B 340 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 = 0.3752 r_free = 0.3752 target = 0.140065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125351 restraints weight = 23135.602| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.50 r_work: 0.3432 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9124 Z= 0.211 Angle : 0.570 7.676 12369 Z= 0.298 Chirality : 0.041 0.192 1402 Planarity : 0.004 0.061 1552 Dihedral : 5.262 57.615 1238 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.56 % Allowed : 14.65 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.26), residues: 1112 helix: 1.13 (0.27), residues: 394 sheet: -1.26 (0.30), residues: 285 loop : -1.06 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.004 0.001 HIS S 220 PHE 0.023 0.001 PHE S 108 TYR 0.027 0.002 TYR S 223 ARG 0.004 0.000 ARG R 58 *********************** 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 234 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.947 Fit side-chains REVERT: A 10 LYS cc_start: 0.7880 (mttm) cc_final: 0.7625 (mttm) REVERT: A 29 LYS cc_start: 0.7885 (mmpt) cc_final: 0.7546 (mmpt) REVERT: A 32 ARG cc_start: 0.8240 (mtt-85) cc_final: 0.8000 (mtt-85) REVERT: A 209 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7955 (mtmt) REVERT: B 133 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8127 (m) REVERT: B 147 SER cc_start: 0.8283 (m) cc_final: 0.7988 (p) REVERT: B 173 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7903 (p) REVERT: B 205 ASP cc_start: 0.7018 (p0) cc_final: 0.6753 (p0) REVERT: B 213 VAL cc_start: 0.7929 (m) cc_final: 0.7551 (t) REVERT: B 228 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7299 (p0) REVERT: B 247 ASP cc_start: 0.6917 (t0) cc_final: 0.6511 (t0) REVERT: B 254 ASP cc_start: 0.6815 (t0) cc_final: 0.6525 (t0) REVERT: R 116 ILE cc_start: 0.8012 (tp) cc_final: 0.7776 (tp) REVERT: R 205 ILE cc_start: 0.8201 (tp) cc_final: 0.7975 (tp) REVERT: R 236 ILE cc_start: 0.7418 (tp) cc_final: 0.7075 (tp) REVERT: S 35 HIS cc_start: 0.8359 (m-70) cc_final: 0.8155 (m-70) REVERT: S 82 GLN cc_start: 0.7658 (tp40) cc_final: 0.7388 (tp40) outliers start: 25 outliers final: 17 residues processed: 221 average time/residue: 0.2468 time to fit residues: 72.0847 Evaluate side-chains 222 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 170 ASP 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 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain S residue 37 VAL 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 80 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 91 optimal weight: 0.0030 chunk 107 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 48 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.3759 r_free = 0.3759 target = 0.140561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.127578 restraints weight = 15210.365| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.86 r_work: 0.3491 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 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 = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9124 Z= 0.200 Angle : 0.570 7.578 12369 Z= 0.298 Chirality : 0.041 0.196 1402 Planarity : 0.004 0.059 1552 Dihedral : 5.201 58.012 1238 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.26), residues: 1112 helix: 1.19 (0.27), residues: 397 sheet: -1.22 (0.30), residues: 283 loop : -1.03 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 241 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.001 PHE S 108 TYR 0.028 0.001 TYR S 223 ARG 0.008 0.000 ARG R 58 *********************** 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 228 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7474 (m-30) cc_final: 0.7244 (m-30) REVERT: A 209 LYS cc_start: 0.8390 (mtmt) cc_final: 0.8142 (mtmt) REVERT: B 133 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8162 (m) REVERT: B 147 SER cc_start: 0.8312 (m) cc_final: 0.8064 (p) REVERT: B 150 ARG cc_start: 0.8092 (mpt180) cc_final: 0.7774 (mpt180) REVERT: B 173 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.7969 (p) REVERT: B 213 VAL cc_start: 0.7943 (m) cc_final: 0.7546 (t) REVERT: B 228 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7419 (p0) REVERT: B 247 ASP cc_start: 0.7056 (t0) cc_final: 0.6626 (t0) REVERT: B 254 ASP cc_start: 0.6984 (t0) cc_final: 0.6706 (t0) REVERT: R 78 PHE cc_start: 0.7717 (t80) cc_final: 0.7460 (t80) REVERT: R 116 ILE cc_start: 0.8097 (tp) cc_final: 0.7872 (tp) REVERT: R 205 ILE cc_start: 0.8323 (tp) cc_final: 0.8106 (tp) REVERT: R 236 ILE cc_start: 0.7568 (tp) cc_final: 0.7212 (tp) REVERT: S 82 GLN cc_start: 0.7734 (tp40) cc_final: 0.7469 (tp40) REVERT: S 128 MET cc_start: 0.7773 (mtp) cc_final: 0.7543 (mtt) outliers start: 24 outliers final: 18 residues processed: 213 average time/residue: 0.2516 time to fit residues: 70.9830 Evaluate side-chains 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 170 ASP 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 292 PHE 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 R residue 266 MET Chi-restraints excluded: chain S residue 37 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.4980 chunk 35 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.0070 chunk 62 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 230 ASN ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.140096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.126571 restraints weight = 17310.115| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.05 r_work: 0.3472 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- 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 = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9124 Z= 0.221 Angle : 0.573 7.440 12369 Z= 0.301 Chirality : 0.042 0.199 1402 Planarity : 0.004 0.059 1552 Dihedral : 5.243 57.750 1238 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.87 % Allowed : 16.39 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.26), residues: 1112 helix: 1.19 (0.27), residues: 395 sheet: -1.24 (0.30), residues: 284 loop : -1.00 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 241 HIS 0.007 0.001 HIS S 35 PHE 0.023 0.001 PHE S 108 TYR 0.029 0.002 TYR S 223 ARG 0.008 0.000 ARG R 58 *********************** 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 228 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7530 (m-30) cc_final: 0.7304 (m-30) REVERT: B 133 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8186 (m) REVERT: B 147 SER cc_start: 0.8314 (m) cc_final: 0.8040 (p) REVERT: B 150 ARG cc_start: 0.8124 (mpt180) cc_final: 0.7807 (mpt180) REVERT: B 228 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7466 (p0) REVERT: B 247 ASP cc_start: 0.7115 (t0) cc_final: 0.6679 (t0) REVERT: B 254 ASP cc_start: 0.7090 (t0) cc_final: 0.6848 (t0) REVERT: R 78 PHE cc_start: 0.7705 (t80) cc_final: 0.7454 (t80) REVERT: R 116 ILE cc_start: 0.8140 (tp) cc_final: 0.7914 (tp) REVERT: R 205 ILE cc_start: 0.8343 (tp) cc_final: 0.8130 (tp) REVERT: S 82 GLN cc_start: 0.7770 (tp40) cc_final: 0.7499 (tp40) REVERT: S 128 MET cc_start: 0.7812 (mtp) cc_final: 0.7581 (mtt) outliers start: 28 outliers final: 23 residues processed: 210 average time/residue: 0.2538 time to fit residues: 70.8636 Evaluate side-chains 222 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 197 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 14 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ASP 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 274 THR 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 C residue 41 CYS Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 37 VAL 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 147 CYS Chi-restraints excluded: chain S residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 96 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3741 r_free = 0.3741 target = 0.139069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125589 restraints weight = 17378.860| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.05 r_work: 0.3453 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9124 Z= 0.270 Angle : 0.600 7.883 12369 Z= 0.314 Chirality : 0.042 0.194 1402 Planarity : 0.005 0.059 1552 Dihedral : 5.358 57.243 1238 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.28 % Allowed : 16.39 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.26), residues: 1112 helix: 1.13 (0.27), residues: 394 sheet: -1.26 (0.30), residues: 283 loop : -1.02 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 241 HIS 0.007 0.001 HIS S 35 PHE 0.015 0.001 PHE S 108 TYR 0.029 0.002 TYR S 223 ARG 0.009 0.000 ARG R 58 *********************** 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 237 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 205 time to evaluate : 0.963 Fit side-chains REVERT: A 29 LYS cc_start: 0.7974 (mmpt) cc_final: 0.7602 (mmpt) REVERT: A 209 LYS cc_start: 0.8374 (mtmt) cc_final: 0.8120 (mtmt) REVERT: B 147 SER cc_start: 0.8327 (m) cc_final: 0.8030 (p) REVERT: B 150 ARG cc_start: 0.8152 (mpt180) cc_final: 0.7829 (mpt180) REVERT: B 173 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.8020 (p) REVERT: B 197 ARG cc_start: 0.7754 (mtm110) cc_final: 0.7541 (mtm110) REVERT: B 228 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7411 (p0) REVERT: B 233 CYS cc_start: 0.7928 (t) cc_final: 0.7664 (t) REVERT: B 247 ASP cc_start: 0.7143 (t0) cc_final: 0.6873 (t0) REVERT: B 254 ASP cc_start: 0.7136 (t0) cc_final: 0.6902 (t0) REVERT: R 116 ILE cc_start: 0.8160 (tp) cc_final: 0.7753 (tp) REVERT: R 205 ILE cc_start: 0.8351 (tp) cc_final: 0.8147 (tp) REVERT: R 236 ILE cc_start: 0.7570 (tp) cc_final: 0.7207 (tp) REVERT: S 53 SER cc_start: 0.7905 (m) cc_final: 0.7641 (m) outliers start: 32 outliers final: 29 residues processed: 219 average time/residue: 0.2437 time to fit residues: 70.7916 Evaluate side-chains 230 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 14 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 220 GLN 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 B residue 329 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 37 VAL 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 147 CYS 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 72 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.0370 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- 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 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126921 restraints weight = 17724.855| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 2.08 r_work: 0.3468 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 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 = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9124 Z= 0.209 Angle : 0.576 7.745 12369 Z= 0.301 Chirality : 0.042 0.186 1402 Planarity : 0.004 0.058 1552 Dihedral : 5.260 57.760 1238 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.07 % Allowed : 17.52 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.26), residues: 1112 helix: 1.26 (0.27), residues: 396 sheet: -1.26 (0.30), residues: 282 loop : -1.01 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 241 HIS 0.005 0.001 HIS S 35 PHE 0.019 0.001 PHE S 108 TYR 0.027 0.002 TYR S 223 ARG 0.008 0.000 ARG R 58 *********************** 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 227 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.911 Fit side-chains REVERT: A 29 LYS cc_start: 0.7969 (mmpt) cc_final: 0.7596 (mmpt) REVERT: B 147 SER cc_start: 0.8346 (m) cc_final: 0.8068 (p) REVERT: B 150 ARG cc_start: 0.8159 (mpt180) cc_final: 0.7845 (mpt180) REVERT: B 173 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8008 (p) REVERT: B 197 ARG cc_start: 0.7709 (mtm110) cc_final: 0.7508 (mtm110) REVERT: B 228 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7375 (p0) REVERT: B 247 ASP cc_start: 0.7060 (t0) cc_final: 0.6683 (t0) REVERT: B 254 ASP cc_start: 0.7118 (t0) cc_final: 0.6884 (t0) REVERT: B 312 ASP cc_start: 0.7749 (t0) cc_final: 0.7476 (t0) REVERT: R 116 ILE cc_start: 0.8140 (tp) cc_final: 0.7915 (tp) REVERT: R 205 ILE cc_start: 0.8339 (tp) cc_final: 0.8113 (tp) REVERT: S 53 SER cc_start: 0.7846 (m) cc_final: 0.7575 (m) REVERT: S 128 MET cc_start: 0.7843 (mtp) cc_final: 0.7602 (mtt) REVERT: S 143 VAL cc_start: 0.8193 (OUTLIER) cc_final: 0.7965 (p) outliers start: 30 outliers final: 25 residues processed: 211 average time/residue: 0.2491 time to fit residues: 69.6632 Evaluate side-chains 223 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 28 GLU 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 170 ASP Chi-restraints excluded: chain B residue 173 THR 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 262 MET Chi-restraints excluded: chain B residue 274 THR 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 C residue 41 CYS Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 37 VAL 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 147 CYS 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 82 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 55 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 99 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.140213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.127181 restraints weight = 15290.058| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.87 r_work: 0.3490 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9124 Z= 0.215 Angle : 0.592 11.925 12369 Z= 0.306 Chirality : 0.042 0.208 1402 Planarity : 0.004 0.058 1552 Dihedral : 5.262 57.793 1238 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.07 % Allowed : 17.42 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.26), residues: 1112 helix: 1.23 (0.27), residues: 396 sheet: -1.33 (0.30), residues: 285 loop : -0.97 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 241 HIS 0.005 0.001 HIS S 35 PHE 0.021 0.001 PHE S 108 TYR 0.026 0.002 TYR S 223 ARG 0.008 0.000 ARG R 58 ********************** 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 221 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.982 Fit side-chains REVERT: A 29 LYS cc_start: 0.7949 (mmpt) cc_final: 0.7568 (mmpt) REVERT: B 147 SER cc_start: 0.8336 (m) cc_final: 0.8049 (p) REVERT: B 150 ARG cc_start: 0.8065 (mpt180) cc_final: 0.7748 (mpt180) REVERT: B 173 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7979 (p) REVERT: B 197 ARG cc_start: 0.7698 (mtm110) cc_final: 0.7491 (mtm110) REVERT: B 228 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7332 (p0) REVERT: B 247 ASP cc_start: 0.7003 (t0) cc_final: 0.6626 (t0) REVERT: B 254 ASP cc_start: 0.7039 (t0) cc_final: 0.6808 (t0) REVERT: B 312 ASP cc_start: 0.7702 (t0) cc_final: 0.7410 (t0) REVERT: R 116 ILE cc_start: 0.8117 (tp) cc_final: 0.7890 (tp) REVERT: R 205 ILE cc_start: 0.8312 (tp) cc_final: 0.8096 (tp) REVERT: S 53 SER cc_start: 0.7817 (m) cc_final: 0.7545 (m) REVERT: S 128 MET cc_start: 0.7785 (mtp) cc_final: 0.7555 (mtt) REVERT: S 143 VAL cc_start: 0.8213 (OUTLIER) cc_final: 0.7982 (p) outliers start: 30 outliers final: 26 residues processed: 208 average time/residue: 0.2510 time to fit residues: 69.0686 Evaluate side-chains 220 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 50 VAL 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 170 ASP Chi-restraints excluded: chain B residue 173 THR 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 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 B residue 329 THR Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 37 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 58 optimal weight: 0.4980 chunk 100 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3756 r_free = 0.3756 target = 0.140302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.127318 restraints weight = 15327.604| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.87 r_work: 0.3492 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9124 Z= 0.209 Angle : 0.574 8.129 12369 Z= 0.300 Chirality : 0.042 0.198 1402 Planarity : 0.004 0.058 1552 Dihedral : 5.220 57.357 1238 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.07 % Allowed : 17.52 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.26), residues: 1112 helix: 1.31 (0.27), residues: 395 sheet: -1.30 (0.29), residues: 280 loop : -1.00 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 241 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.001 PHE S 108 TYR 0.026 0.002 TYR S 223 ARG 0.008 0.000 ARG R 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5345.06 seconds wall clock time: 95 minutes 36.85 seconds (5736.85 seconds total)