Starting phenix.real_space_refine on Tue Apr 29 20:32:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6l_62129/04_2025/9k6l_62129.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6l_62129/04_2025/9k6l_62129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k6l_62129/04_2025/9k6l_62129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6l_62129/04_2025/9k6l_62129.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6l_62129/04_2025/9k6l_62129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6l_62129/04_2025/9k6l_62129.cif" } resolution = 2.77 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5699 2.51 5 N 1499 2.21 5 O 1653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8914 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1819 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} 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: 2240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2240 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 7, 'TRANS': 263} Chain breaks: 1 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'SA0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.77, per 1000 atoms: 0.65 Number of scatterers: 8914 At special positions: 0 Unit cell: (90.48, 119.6, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1653 8.00 N 1499 7.00 C 5699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 69 " - pdb=" SG CYS R 79 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.48 Conformation dependent library (CDL) restraints added in 1.1 seconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 39.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.431A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.148A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.551A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.694A pdb=" N LEU A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 4.149A pdb=" N GLN A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.805A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.814A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.892A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.653A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.884A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 40 Processing helix chain 'R' and resid 43 through 73 Processing helix chain 'R' and resid 81 through 108 Processing helix chain 'R' and resid 112 through 125 Processing helix chain 'R' and resid 125 through 155 Proline residue: R 143 - end of helix Processing helix chain 'R' and resid 172 through 210 Proline residue: R 188 - end of helix removed outlier: 3.772A pdb=" N LEU R 191 " --> pdb=" O ILE R 187 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS R 210 " --> pdb=" O GLN R 206 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 248 Processing helix chain 'R' and resid 249 through 252 Processing helix chain 'R' and resid 257 through 279 Processing helix chain 'R' and resid 280 through 287 removed outlier: 3.529A pdb=" N LYS R 284 " --> pdb=" O SER R 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.829A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS A 225 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 52 removed outlier: 5.422A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.756A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.328A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.862A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.556A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.230A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 4.027A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.796A pdb=" N VAL S 5 " --> pdb=" O SER S 23 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.078A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.923A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER S 196 " --> pdb=" O ALA S 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 135 through 136 removed outlier: 6.712A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 489 hydrogen bonds defined for protein. 1401 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: 2.68 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2369 1.33 - 1.45: 1783 1.45 - 1.57: 4863 1.57 - 1.69: 0 1.69 - 1.82: 93 Bond restraints: 9108 Sorted by residual: bond pdb=" N LYS A 272 " pdb=" CA LYS A 272 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 5.04e+00 bond pdb=" CG LEU G 19 " pdb=" CD2 LEU G 19 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.81e+00 bond pdb=" C5 SA0 R 501 " pdb=" O5 SA0 R 501 " ideal model delta sigma weight residual 1.414 1.441 -0.027 2.00e-02 2.50e+03 1.78e+00 bond pdb=" CB GLU A 43 " pdb=" CG GLU A 43 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" CB GLU A 25 " pdb=" CG GLU A 25 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.70e+00 ... (remaining 9103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 12156 2.83 - 5.67: 151 5.67 - 8.50: 27 8.50 - 11.33: 4 11.33 - 14.17: 1 Bond angle restraints: 12339 Sorted by residual: angle pdb=" CA LEU G 15 " pdb=" CB LEU G 15 " pdb=" CG LEU G 15 " ideal model delta sigma weight residual 116.30 130.47 -14.17 3.50e+00 8.16e-02 1.64e+01 angle pdb=" CA GLU A 43 " pdb=" CB GLU A 43 " pdb=" CG GLU A 43 " ideal model delta sigma weight residual 114.10 122.11 -8.01 2.00e+00 2.50e-01 1.60e+01 angle pdb=" CA LYS R 254 " pdb=" CB LYS R 254 " pdb=" CG LYS R 254 " ideal model delta sigma weight residual 114.10 122.03 -7.93 2.00e+00 2.50e-01 1.57e+01 angle pdb=" C GLN A 52 " pdb=" N MET A 53 " pdb=" CA MET A 53 " ideal model delta sigma weight residual 122.54 116.13 6.41 1.65e+00 3.67e-01 1.51e+01 angle pdb=" CA MET S 93 " pdb=" CB MET S 93 " pdb=" CG MET S 93 " ideal model delta sigma weight residual 114.10 121.42 -7.32 2.00e+00 2.50e-01 1.34e+01 ... (remaining 12334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 4635 17.27 - 34.54: 559 34.54 - 51.81: 158 51.81 - 69.08: 39 69.08 - 86.35: 6 Dihedral angle restraints: 5397 sinusoidal: 2122 harmonic: 3275 Sorted by residual: dihedral pdb=" CB CYS R 69 " pdb=" SG CYS R 69 " pdb=" SG CYS R 79 " pdb=" CB CYS R 79 " ideal model delta sinusoidal sigma weight residual -86.00 0.35 -86.35 1 1.00e+01 1.00e-02 8.99e+01 dihedral pdb=" CA THR S 160 " pdb=" C THR S 160 " pdb=" N TYR S 161 " pdb=" CA TYR S 161 " ideal model delta harmonic sigma weight residual -180.00 -154.42 -25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA MET A 53 " pdb=" C MET A 53 " pdb=" N LYS A 54 " pdb=" CA LYS A 54 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 5394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1095 0.049 - 0.099: 252 0.099 - 0.148: 51 0.148 - 0.197: 9 0.197 - 0.246: 3 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CB ILE R 13 " pdb=" CA ILE R 13 " pdb=" CG1 ILE R 13 " pdb=" CG2 ILE R 13 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CG LEU R 123 " pdb=" CB LEU R 123 " pdb=" CD1 LEU R 123 " pdb=" CD2 LEU R 123 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE R 248 " pdb=" CA ILE R 248 " pdb=" CG1 ILE R 248 " pdb=" CG2 ILE R 248 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1407 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 88 " 0.025 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE R 88 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE R 88 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE R 88 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 88 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE R 88 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE R 88 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 117 " -0.020 2.00e-02 2.50e+03 1.85e-02 8.56e+00 pdb=" CG TRP R 117 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP R 117 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP R 117 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 117 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 117 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 117 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 117 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 117 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 117 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 120 " -0.025 2.00e-02 2.50e+03 1.70e-02 7.23e+00 pdb=" CG TRP R 120 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP R 120 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP R 120 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP R 120 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP R 120 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 120 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 120 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 120 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 120 " -0.007 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 150 2.65 - 3.21: 8568 3.21 - 3.78: 14646 3.78 - 4.34: 19390 4.34 - 4.90: 32174 Nonbonded interactions: 74928 Sorted by model distance: nonbonded pdb=" OG SER R 25 " pdb=" O GLY R 53 " model vdw 2.090 3.040 nonbonded pdb=" OD2 ASP R 46 " pdb=" OG1 THR R 282 " model vdw 2.174 3.040 nonbonded pdb=" OE1 GLU R 262 " pdb=" O4 SA0 R 501 " model vdw 2.181 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.206 3.040 nonbonded pdb=" N GLN B 259 " pdb=" OE1 GLN B 259 " model vdw 2.251 3.120 ... (remaining 74923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.560 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 0.044 9111 Z= 0.184 Angle : 0.774 14.168 12345 Z= 0.394 Chirality : 0.046 0.246 1410 Planarity : 0.005 0.056 1542 Dihedral : 16.438 79.200 3268 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.31 % Allowed : 32.86 % Favored : 66.84 % 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: 0.62 (0.26), residues: 1111 helix: 1.91 (0.26), residues: 413 sheet: -0.05 (0.32), residues: 282 loop : -0.74 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP R 117 HIS 0.006 0.001 HIS S 155 PHE 0.056 0.002 PHE R 88 TYR 0.028 0.002 TYR S 223 ARG 0.012 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.10971 ( 489) hydrogen bonds : angle 5.58845 ( 1401) SS BOND : bond 0.00273 ( 3) SS BOND : angle 0.74877 ( 6) covalent geometry : bond 0.00419 ( 9108) covalent geometry : angle 0.77397 (12339) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 216 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 ASP cc_start: 0.8033 (t0) cc_final: 0.7512 (t0) REVERT: A 246 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7038 (tm-30) REVERT: A 344 ILE cc_start: 0.7808 (mm) cc_final: 0.7598 (mt) REVERT: B 49 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8240 (mtt-85) REVERT: B 71 VAL cc_start: 0.8189 (t) cc_final: 0.7893 (p) REVERT: B 134 ARG cc_start: 0.7503 (mtm110) cc_final: 0.7195 (mtm180) REVERT: B 150 ARG cc_start: 0.8450 (mmt-90) cc_final: 0.8146 (mmp80) REVERT: B 161 SER cc_start: 0.8207 (p) cc_final: 0.7462 (p) REVERT: B 163 ASP cc_start: 0.7475 (m-30) cc_final: 0.7099 (m-30) REVERT: B 188 MET cc_start: 0.7953 (mmm) cc_final: 0.7584 (mmm) REVERT: B 219 ARG cc_start: 0.8348 (ttm110) cc_final: 0.8042 (ttm110) REVERT: B 230 ASN cc_start: 0.8023 (m-40) cc_final: 0.7714 (m110) REVERT: B 265 SER cc_start: 0.7697 (p) cc_final: 0.7211 (t) REVERT: B 314 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.7566 (ttm170) REVERT: G 21 MET cc_start: 0.7702 (mmm) cc_final: 0.7064 (mmm) REVERT: S 46 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6645 (mt-10) REVERT: S 127 VAL cc_start: 0.8326 (m) cc_final: 0.8024 (p) REVERT: S 191 PHE cc_start: 0.7423 (m-80) cc_final: 0.7088 (m-80) REVERT: S 208 GLU cc_start: 0.7460 (mp0) cc_final: 0.6934 (mp0) REVERT: R 11 MET cc_start: 0.7076 (tmm) cc_final: 0.6756 (tmm) REVERT: R 27 LEU cc_start: 0.7424 (tp) cc_final: 0.7147 (tm) REVERT: R 136 ILE cc_start: 0.7159 (tt) cc_final: 0.6892 (tp) REVERT: R 150 ILE cc_start: 0.6269 (pp) cc_final: 0.6020 (pt) outliers start: 3 outliers final: 3 residues processed: 217 average time/residue: 1.0900 time to fit residues: 254.8175 Evaluate side-chains 201 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 198 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN B 142 HIS B 156 GLN B 295 ASN S 39 GLN S 182 ASN R 66 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.143449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.125739 restraints weight = 12842.123| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.04 r_work: 0.3624 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9111 Z= 0.241 Angle : 0.681 9.497 12345 Z= 0.352 Chirality : 0.046 0.221 1410 Planarity : 0.005 0.059 1542 Dihedral : 5.152 57.476 1242 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 6.53 % Allowed : 28.57 % Favored : 64.90 % 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: 0.48 (0.26), residues: 1111 helix: 1.81 (0.26), residues: 414 sheet: -0.28 (0.31), residues: 284 loop : -0.70 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 120 HIS 0.006 0.001 HIS S 155 PHE 0.032 0.002 PHE R 88 TYR 0.027 0.002 TYR S 223 ARG 0.006 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 489) hydrogen bonds : angle 4.83439 ( 1401) SS BOND : bond 0.00417 ( 3) SS BOND : angle 1.10246 ( 6) covalent geometry : bond 0.00551 ( 9108) covalent geometry : angle 0.68032 (12339) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 213 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 295 ASN cc_start: 0.8171 (m-40) cc_final: 0.7955 (m-40) REVERT: A 322 THR cc_start: 0.8529 (m) cc_final: 0.8284 (p) REVERT: B 37 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7827 (OUTLIER) REVERT: B 128 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8353 (p) REVERT: B 161 SER cc_start: 0.8444 (p) cc_final: 0.8008 (p) REVERT: B 188 MET cc_start: 0.8373 (mmm) cc_final: 0.8015 (mmm) REVERT: B 230 ASN cc_start: 0.8165 (m-40) cc_final: 0.7886 (m-40) REVERT: B 265 SER cc_start: 0.7743 (p) cc_final: 0.7460 (t) REVERT: B 318 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8174 (tp) REVERT: G 21 MET cc_start: 0.8067 (mmm) cc_final: 0.7635 (mmm) REVERT: G 50 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6869 (mt) REVERT: S 46 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7321 (mt-10) REVERT: S 191 PHE cc_start: 0.8103 (m-80) cc_final: 0.7695 (m-80) REVERT: S 208 GLU cc_start: 0.7769 (mp0) cc_final: 0.7507 (mp0) REVERT: S 223 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.6537 (t80) REVERT: R 11 MET cc_start: 0.7315 (tmm) cc_final: 0.7027 (tmm) REVERT: R 27 LEU cc_start: 0.7674 (tp) cc_final: 0.7364 (tm) REVERT: R 50 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8036 (tt) REVERT: R 136 ILE cc_start: 0.7809 (tt) cc_final: 0.7589 (tp) REVERT: R 191 LEU cc_start: 0.7896 (mt) cc_final: 0.7676 (mp) outliers start: 64 outliers final: 28 residues processed: 244 average time/residue: 0.9086 time to fit residues: 240.7639 Evaluate side-chains 226 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 218 MET Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 274 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN S 39 GLN S 182 ASN R 210 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.143687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.125991 restraints weight = 12863.026| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.04 r_work: 0.3629 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9111 Z= 0.181 Angle : 0.613 8.412 12345 Z= 0.320 Chirality : 0.044 0.206 1410 Planarity : 0.005 0.058 1542 Dihedral : 5.062 57.826 1240 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 6.02 % Allowed : 28.16 % Favored : 65.82 % 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: 0.53 (0.26), residues: 1111 helix: 1.79 (0.26), residues: 418 sheet: -0.28 (0.31), residues: 269 loop : -0.60 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 120 HIS 0.010 0.001 HIS R 210 PHE 0.024 0.002 PHE R 88 TYR 0.026 0.002 TYR R 266 ARG 0.006 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 489) hydrogen bonds : angle 4.65882 ( 1401) SS BOND : bond 0.00341 ( 3) SS BOND : angle 1.03270 ( 6) covalent geometry : bond 0.00411 ( 9108) covalent geometry : angle 0.61300 (12339) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 203 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8100 (mtpp) REVERT: A 46 LYS cc_start: 0.6523 (ttpp) cc_final: 0.6152 (ttpp) REVERT: A 201 ASP cc_start: 0.8009 (t0) cc_final: 0.7653 (t0) REVERT: A 322 THR cc_start: 0.8536 (m) cc_final: 0.8293 (p) REVERT: B 18 ILE cc_start: 0.8383 (pp) cc_final: 0.8122 (pt) REVERT: B 37 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7807 (tt) REVERT: B 114 CYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7657 (p) REVERT: B 128 THR cc_start: 0.8620 (p) cc_final: 0.8346 (p) REVERT: B 188 MET cc_start: 0.8325 (mmm) cc_final: 0.7941 (mmm) REVERT: B 230 ASN cc_start: 0.8178 (m-40) cc_final: 0.7868 (m-40) REVERT: B 246 ASP cc_start: 0.7818 (m-30) cc_final: 0.7419 (m-30) REVERT: B 262 MET cc_start: 0.7104 (mmm) cc_final: 0.6802 (mmm) REVERT: B 265 SER cc_start: 0.7737 (p) cc_final: 0.7453 (t) REVERT: B 318 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8071 (tp) REVERT: G 21 MET cc_start: 0.8076 (mmm) cc_final: 0.7672 (mmm) REVERT: G 50 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7008 (mt) REVERT: S 46 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7307 (mt-10) REVERT: S 108 PHE cc_start: 0.8506 (m-80) cc_final: 0.8231 (m-80) REVERT: S 191 PHE cc_start: 0.8121 (m-80) cc_final: 0.7729 (m-80) REVERT: S 208 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: S 223 TYR cc_start: 0.6998 (OUTLIER) cc_final: 0.6506 (t80) REVERT: R 27 LEU cc_start: 0.7674 (tp) cc_final: 0.7436 (tm) REVERT: R 136 ILE cc_start: 0.7778 (tt) cc_final: 0.7532 (tp) REVERT: R 150 ILE cc_start: 0.6861 (pp) cc_final: 0.6606 (pt) REVERT: R 191 LEU cc_start: 0.7902 (mt) cc_final: 0.7668 (mp) outliers start: 59 outliers final: 33 residues processed: 237 average time/residue: 0.9455 time to fit residues: 242.9410 Evaluate side-chains 231 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 191 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 187 VAL Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 40 ARG Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 108 SER Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 210 HIS Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 260 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.8980 chunk 79 optimal weight: 0.0570 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 95 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 88 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 182 ASN R 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.145558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.127990 restraints weight = 12877.388| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.06 r_work: 0.3653 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9111 Z= 0.130 Angle : 0.574 8.255 12345 Z= 0.300 Chirality : 0.042 0.182 1410 Planarity : 0.005 0.059 1542 Dihedral : 4.970 59.127 1240 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 5.82 % Allowed : 28.78 % Favored : 65.41 % 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: 0.57 (0.26), residues: 1111 helix: 1.90 (0.26), residues: 418 sheet: -0.40 (0.32), residues: 266 loop : -0.56 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 120 HIS 0.008 0.001 HIS R 210 PHE 0.044 0.002 PHE R 88 TYR 0.025 0.002 TYR R 266 ARG 0.006 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 489) hydrogen bonds : angle 4.55895 ( 1401) SS BOND : bond 0.00323 ( 3) SS BOND : angle 0.92759 ( 6) covalent geometry : bond 0.00291 ( 9108) covalent geometry : angle 0.57343 (12339) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 204 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8224 (mtpp) REVERT: A 46 LYS cc_start: 0.6556 (ttpp) cc_final: 0.6151 (ttpp) REVERT: A 201 ASP cc_start: 0.8043 (t0) cc_final: 0.7604 (t0) REVERT: A 246 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7279 (tm-30) REVERT: B 18 ILE cc_start: 0.8395 (pp) cc_final: 0.8151 (pt) REVERT: B 37 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7775 (tt) REVERT: B 114 CYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7581 (p) REVERT: B 128 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8331 (p) REVERT: B 188 MET cc_start: 0.8244 (mmm) cc_final: 0.7850 (mmm) REVERT: B 230 ASN cc_start: 0.8116 (m-40) cc_final: 0.7796 (m-40) REVERT: B 246 ASP cc_start: 0.7841 (m-30) cc_final: 0.7411 (m-30) REVERT: B 262 MET cc_start: 0.7042 (mmm) cc_final: 0.6776 (mmm) REVERT: B 265 SER cc_start: 0.7720 (p) cc_final: 0.7398 (t) REVERT: G 21 MET cc_start: 0.8014 (mmm) cc_final: 0.7624 (mmm) REVERT: G 50 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6802 (mt) REVERT: S 46 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7288 (mt-10) REVERT: S 108 PHE cc_start: 0.8564 (m-80) cc_final: 0.8363 (m-80) REVERT: S 180 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7684 (ttp) REVERT: S 208 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: S 223 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6475 (t80) REVERT: R 27 LEU cc_start: 0.7606 (tp) cc_final: 0.7349 (tm) REVERT: R 136 ILE cc_start: 0.7605 (tt) cc_final: 0.7344 (tp) REVERT: R 219 MET cc_start: 0.6816 (mpp) cc_final: 0.6594 (mmm) outliers start: 57 outliers final: 27 residues processed: 234 average time/residue: 0.9108 time to fit residues: 231.3443 Evaluate side-chains 229 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 210 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS S 39 GLN S 182 ASN R 210 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.141354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123780 restraints weight = 12756.625| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.99 r_work: 0.3602 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 9111 Z= 0.316 Angle : 0.668 8.563 12345 Z= 0.347 Chirality : 0.047 0.230 1410 Planarity : 0.005 0.053 1542 Dihedral : 5.220 59.383 1240 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 7.96 % Allowed : 27.04 % Favored : 65.00 % 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: 0.28 (0.25), residues: 1111 helix: 1.53 (0.25), residues: 419 sheet: -0.44 (0.31), residues: 265 loop : -0.67 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 120 HIS 0.016 0.002 HIS R 210 PHE 0.036 0.003 PHE R 88 TYR 0.028 0.002 TYR R 266 ARG 0.006 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 489) hydrogen bonds : angle 4.69089 ( 1401) SS BOND : bond 0.00479 ( 3) SS BOND : angle 1.18123 ( 6) covalent geometry : bond 0.00724 ( 9108) covalent geometry : angle 0.66745 (12339) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 193 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6698 (ttpp) cc_final: 0.6171 (ttpp) REVERT: A 199 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7984 (mtp) REVERT: A 201 ASP cc_start: 0.8042 (t0) cc_final: 0.7526 (t0) REVERT: A 322 THR cc_start: 0.8493 (m) cc_final: 0.8293 (p) REVERT: B 37 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7903 (tt) REVERT: B 114 CYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7776 (p) REVERT: B 128 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8311 (p) REVERT: B 188 MET cc_start: 0.8327 (mmm) cc_final: 0.7957 (mmm) REVERT: B 262 MET cc_start: 0.7204 (mmm) cc_final: 0.6840 (mmm) REVERT: B 265 SER cc_start: 0.7733 (p) cc_final: 0.7502 (t) REVERT: B 318 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8114 (tp) REVERT: G 21 MET cc_start: 0.8202 (mmm) cc_final: 0.7878 (mmm) REVERT: G 50 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7534 (mt) REVERT: S 46 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7314 (mt-10) REVERT: S 87 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7393 (mtp180) REVERT: S 180 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7707 (ttp) REVERT: S 208 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: S 223 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6588 (t80) REVERT: R 27 LEU cc_start: 0.7848 (tp) cc_final: 0.7625 (tm) REVERT: R 50 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8004 (tt) REVERT: R 136 ILE cc_start: 0.7897 (tt) cc_final: 0.7678 (tp) REVERT: R 190 ILE cc_start: 0.7953 (mm) cc_final: 0.7735 (tp) outliers start: 78 outliers final: 37 residues processed: 236 average time/residue: 0.9533 time to fit residues: 243.4174 Evaluate side-chains 235 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 180 MET Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 274 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.0470 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS S 182 ASN R 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.143766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.126001 restraints weight = 12667.673| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.03 r_work: 0.3630 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9111 Z= 0.169 Angle : 0.604 8.304 12345 Z= 0.314 Chirality : 0.044 0.199 1410 Planarity : 0.005 0.056 1542 Dihedral : 5.075 57.646 1240 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 5.51 % Allowed : 30.31 % Favored : 64.18 % 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: 1111 helix: 1.79 (0.25), residues: 418 sheet: -0.51 (0.32), residues: 266 loop : -0.57 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 120 HIS 0.012 0.001 HIS R 210 PHE 0.031 0.002 PHE R 88 TYR 0.026 0.002 TYR R 266 ARG 0.006 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03686 ( 489) hydrogen bonds : angle 4.61945 ( 1401) SS BOND : bond 0.00359 ( 3) SS BOND : angle 1.09938 ( 6) covalent geometry : bond 0.00387 ( 9108) covalent geometry : angle 0.60413 (12339) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7365 (pm20) cc_final: 0.7153 (pt0) REVERT: A 10 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8140 (mtpp) REVERT: A 46 LYS cc_start: 0.6656 (ttpp) cc_final: 0.6202 (ttpp) REVERT: A 201 ASP cc_start: 0.8038 (t0) cc_final: 0.7497 (t0) REVERT: A 246 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 258 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8132 (ptmm) REVERT: A 322 THR cc_start: 0.8486 (m) cc_final: 0.8263 (p) REVERT: B 37 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7879 (tt) REVERT: B 114 CYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7655 (p) REVERT: B 128 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8262 (p) REVERT: B 188 MET cc_start: 0.8292 (mmm) cc_final: 0.7867 (mmm) REVERT: B 262 MET cc_start: 0.7099 (mmm) cc_final: 0.6851 (mmm) REVERT: B 265 SER cc_start: 0.7731 (p) cc_final: 0.7464 (t) REVERT: G 21 MET cc_start: 0.8130 (mmm) cc_final: 0.7818 (mmm) REVERT: G 50 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7507 (mt) REVERT: S 46 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7352 (mt-10) REVERT: S 83 MET cc_start: 0.8081 (mtm) cc_final: 0.7640 (ttm) REVERT: S 87 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7308 (mtp180) REVERT: S 191 PHE cc_start: 0.8167 (m-80) cc_final: 0.7729 (m-80) REVERT: S 208 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: S 223 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6527 (t80) REVERT: R 27 LEU cc_start: 0.7803 (tp) cc_final: 0.7565 (tm) REVERT: R 50 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7971 (tt) REVERT: R 136 ILE cc_start: 0.7782 (tt) cc_final: 0.7538 (tp) outliers start: 54 outliers final: 29 residues processed: 227 average time/residue: 0.9755 time to fit residues: 239.6280 Evaluate side-chains 227 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 210 HIS Chi-restraints excluded: chain R residue 231 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 15 optimal weight: 0.0020 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS S 182 ASN R 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.144739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.126913 restraints weight = 12741.539| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.06 r_work: 0.3638 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9111 Z= 0.151 Angle : 0.594 8.251 12345 Z= 0.308 Chirality : 0.043 0.201 1410 Planarity : 0.005 0.057 1542 Dihedral : 5.009 58.130 1240 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 5.92 % Allowed : 29.49 % Favored : 64.59 % 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: 0.51 (0.26), residues: 1111 helix: 1.88 (0.25), residues: 420 sheet: -0.50 (0.31), residues: 271 loop : -0.59 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 120 HIS 0.022 0.001 HIS R 210 PHE 0.028 0.002 PHE R 88 TYR 0.026 0.002 TYR R 266 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 489) hydrogen bonds : angle 4.58083 ( 1401) SS BOND : bond 0.00289 ( 3) SS BOND : angle 0.95222 ( 6) covalent geometry : bond 0.00347 ( 9108) covalent geometry : angle 0.59340 (12339) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 199 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7631 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 258 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8118 (ptmm) REVERT: A 322 THR cc_start: 0.8467 (m) cc_final: 0.8258 (p) REVERT: B 37 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7874 (tt) REVERT: B 114 CYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7661 (p) REVERT: B 128 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8271 (p) REVERT: B 188 MET cc_start: 0.8235 (mmm) cc_final: 0.7875 (mmm) REVERT: B 262 MET cc_start: 0.7059 (mmm) cc_final: 0.6828 (mmm) REVERT: B 265 SER cc_start: 0.7746 (p) cc_final: 0.7457 (t) REVERT: B 266 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.7554 (t-170) REVERT: G 21 MET cc_start: 0.8154 (mmm) cc_final: 0.7841 (mmm) REVERT: G 50 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7455 (mt) REVERT: S 46 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7305 (mt-10) REVERT: S 83 MET cc_start: 0.8016 (mtm) cc_final: 0.7761 (ttm) REVERT: S 87 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7252 (mtp180) REVERT: S 208 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: S 223 TYR cc_start: 0.6918 (OUTLIER) cc_final: 0.6493 (t80) REVERT: R 16 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7156 (pp) REVERT: R 27 LEU cc_start: 0.7745 (tp) cc_final: 0.7523 (tm) REVERT: R 136 ILE cc_start: 0.7770 (tt) cc_final: 0.7524 (tp) outliers start: 58 outliers final: 31 residues processed: 232 average time/residue: 0.9741 time to fit residues: 245.0021 Evaluate side-chains 236 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 195 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 210 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 0.0970 chunk 100 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS S 182 ASN R 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.144314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.126628 restraints weight = 12902.906| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.05 r_work: 0.3636 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9111 Z= 0.173 Angle : 0.614 8.324 12345 Z= 0.317 Chirality : 0.044 0.214 1410 Planarity : 0.005 0.057 1542 Dihedral : 5.029 57.980 1240 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.51 % Allowed : 30.51 % Favored : 63.98 % 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: 1111 helix: 1.86 (0.25), residues: 420 sheet: -0.45 (0.31), residues: 279 loop : -0.64 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 120 HIS 0.016 0.001 HIS R 210 PHE 0.027 0.002 PHE R 88 TYR 0.026 0.002 TYR R 266 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 489) hydrogen bonds : angle 4.56564 ( 1401) SS BOND : bond 0.00328 ( 3) SS BOND : angle 0.90602 ( 6) covalent geometry : bond 0.00398 ( 9108) covalent geometry : angle 0.61384 (12339) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 198 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7309 (tm-30) REVERT: A 258 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8121 (ptmm) REVERT: A 322 THR cc_start: 0.8484 (m) cc_final: 0.8268 (p) REVERT: B 18 ILE cc_start: 0.8292 (pp) cc_final: 0.8087 (pt) REVERT: B 37 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7896 (tt) REVERT: B 114 CYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7699 (p) REVERT: B 128 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8285 (p) REVERT: B 188 MET cc_start: 0.8253 (mmm) cc_final: 0.7846 (mmm) REVERT: B 262 MET cc_start: 0.7082 (mmm) cc_final: 0.6837 (mmm) REVERT: B 266 HIS cc_start: 0.7617 (OUTLIER) cc_final: 0.7351 (t-90) REVERT: G 21 MET cc_start: 0.8160 (mmm) cc_final: 0.7847 (mmm) REVERT: G 50 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7452 (mt) REVERT: S 87 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7295 (mtp180) REVERT: S 208 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: S 223 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.6500 (t80) REVERT: R 16 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7175 (pp) REVERT: R 27 LEU cc_start: 0.7760 (tp) cc_final: 0.7528 (tm) REVERT: R 50 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7758 (tt) REVERT: R 136 ILE cc_start: 0.7756 (tt) cc_final: 0.7511 (tp) outliers start: 54 outliers final: 33 residues processed: 229 average time/residue: 1.0565 time to fit residues: 261.8714 Evaluate side-chains 239 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 172 SER Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 270 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 0.0270 chunk 74 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 0.3980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS S 182 ASN R 210 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.144993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.127425 restraints weight = 12697.916| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.03 r_work: 0.3652 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9111 Z= 0.141 Angle : 0.611 8.263 12345 Z= 0.314 Chirality : 0.043 0.218 1410 Planarity : 0.005 0.057 1542 Dihedral : 4.994 58.524 1240 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.20 % Allowed : 31.22 % Favored : 63.57 % 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: 1111 helix: 1.96 (0.25), residues: 420 sheet: -0.43 (0.31), residues: 279 loop : -0.66 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 120 HIS 0.013 0.001 HIS R 210 PHE 0.032 0.002 PHE S 200 TYR 0.025 0.002 TYR R 266 ARG 0.010 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 489) hydrogen bonds : angle 4.56073 ( 1401) SS BOND : bond 0.00307 ( 3) SS BOND : angle 0.88888 ( 6) covalent geometry : bond 0.00322 ( 9108) covalent geometry : angle 0.61064 (12339) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 201 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8258 (mtpp) REVERT: A 246 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7276 (tm-30) REVERT: A 258 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8104 (ptmm) REVERT: A 340 VAL cc_start: 0.7897 (t) cc_final: 0.7641 (p) REVERT: B 18 ILE cc_start: 0.8315 (pp) cc_final: 0.8091 (pt) REVERT: B 37 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7886 (tt) REVERT: B 114 CYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7672 (p) REVERT: B 128 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8269 (p) REVERT: B 188 MET cc_start: 0.8210 (mmm) cc_final: 0.7852 (mmm) REVERT: B 262 MET cc_start: 0.7011 (mmm) cc_final: 0.6800 (mmm) REVERT: G 21 MET cc_start: 0.8154 (mmm) cc_final: 0.7851 (mmm) REVERT: G 50 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7412 (mt) REVERT: S 87 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7269 (mtp180) REVERT: S 189 ASP cc_start: 0.7650 (t0) cc_final: 0.7439 (t0) REVERT: S 208 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: S 223 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.6512 (t80) REVERT: R 16 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.7148 (pp) REVERT: R 27 LEU cc_start: 0.7690 (tp) cc_final: 0.7481 (tm) REVERT: R 50 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7756 (tt) REVERT: R 69 CYS cc_start: 0.6481 (OUTLIER) cc_final: 0.6258 (t) REVERT: R 136 ILE cc_start: 0.7637 (tt) cc_final: 0.7394 (tp) outliers start: 51 outliers final: 31 residues processed: 230 average time/residue: 0.9800 time to fit residues: 243.7308 Evaluate side-chains 236 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 69 CYS Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 210 HIS Chi-restraints excluded: chain R residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 109 optimal weight: 0.5980 chunk 41 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 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 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN R 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.144906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.127499 restraints weight = 12847.114| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.04 r_work: 0.3648 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9111 Z= 0.159 Angle : 0.617 8.332 12345 Z= 0.318 Chirality : 0.043 0.211 1410 Planarity : 0.005 0.057 1542 Dihedral : 5.000 58.388 1240 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.39 % Allowed : 32.76 % Favored : 62.86 % 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: 0.54 (0.26), residues: 1111 helix: 1.98 (0.25), residues: 420 sheet: -0.50 (0.31), residues: 271 loop : -0.65 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 120 HIS 0.018 0.001 HIS R 210 PHE 0.038 0.002 PHE S 200 TYR 0.026 0.002 TYR R 266 ARG 0.010 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 489) hydrogen bonds : angle 4.57310 ( 1401) SS BOND : bond 0.00314 ( 3) SS BOND : angle 0.90780 ( 6) covalent geometry : bond 0.00364 ( 9108) covalent geometry : angle 0.61726 (12339) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 197 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8247 (mtpp) REVERT: A 246 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7245 (tm-30) REVERT: A 258 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8119 (ptmm) REVERT: A 340 VAL cc_start: 0.7902 (t) cc_final: 0.7661 (p) REVERT: B 18 ILE cc_start: 0.8312 (pp) cc_final: 0.8085 (pt) REVERT: B 37 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7876 (tt) REVERT: B 114 CYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7708 (p) REVERT: B 128 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8272 (p) REVERT: B 170 ASP cc_start: 0.7683 (t0) cc_final: 0.7364 (p0) REVERT: B 188 MET cc_start: 0.8235 (mmm) cc_final: 0.7859 (mmm) REVERT: B 262 MET cc_start: 0.7050 (mmm) cc_final: 0.6836 (mmm) REVERT: G 21 MET cc_start: 0.8172 (mmm) cc_final: 0.7897 (mmm) REVERT: S 87 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7285 (mtp180) REVERT: S 189 ASP cc_start: 0.7626 (t0) cc_final: 0.7423 (t0) REVERT: S 208 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: S 223 TYR cc_start: 0.6834 (OUTLIER) cc_final: 0.6507 (t80) REVERT: R 16 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7138 (pp) REVERT: R 27 LEU cc_start: 0.7700 (tp) cc_final: 0.7472 (tm) REVERT: R 136 ILE cc_start: 0.7635 (tt) cc_final: 0.7385 (tp) outliers start: 43 outliers final: 29 residues processed: 222 average time/residue: 0.9245 time to fit residues: 222.1302 Evaluate side-chains 230 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 126 ILE Chi-restraints excluded: chain S residue 208 GLU Chi-restraints excluded: chain S residue 223 TYR Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 49 LEU Chi-restraints excluded: chain R residue 64 MET Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 83 ILE Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 183 VAL Chi-restraints excluded: chain R residue 244 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 0.0870 chunk 44 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 0.0000 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 182 ASN R 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.145187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.127830 restraints weight = 12750.659| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.04 r_work: 0.3655 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9111 Z= 0.147 Angle : 0.621 8.303 12345 Z= 0.317 Chirality : 0.043 0.196 1410 Planarity : 0.004 0.057 1542 Dihedral : 4.967 58.774 1240 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.98 % Allowed : 33.47 % Favored : 62.55 % 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: 0.57 (0.26), residues: 1111 helix: 2.03 (0.25), residues: 419 sheet: -0.57 (0.31), residues: 273 loop : -0.60 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 120 HIS 0.009 0.001 HIS R 210 PHE 0.031 0.002 PHE S 200 TYR 0.025 0.002 TYR R 266 ARG 0.010 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 489) hydrogen bonds : angle 4.59249 ( 1401) SS BOND : bond 0.00309 ( 3) SS BOND : angle 0.93109 ( 6) covalent geometry : bond 0.00337 ( 9108) covalent geometry : angle 0.62116 (12339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7889.01 seconds wall clock time: 136 minutes 24.43 seconds (8184.43 seconds total)