Starting phenix.real_space_refine on Mon May 12 10:20:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k6l_62129/05_2025/9k6l_62129.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k6l_62129/05_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_62129/05_2025/9k6l_62129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k6l_62129/05_2025/9k6l_62129.map" model { file = "/net/cci-nas-00/data/ceres_data/9k6l_62129/05_2025/9k6l_62129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k6l_62129/05_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-5687/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: 5.55, per 1000 atoms: 0.62 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: 2.49 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: 1.03 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: 2.71 Time building geometry restraints manager: 2.85 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: 1.050 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.710 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:10.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.370 ------------------------------------------------------------------------------- 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 : 0.999 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: 1.0366 time to fit residues: 242.3818 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 : 1.226 ------------------------------------------------------------------------------- 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 = 40)----------------| | 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: 0.3465 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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: 0.7769 (tm-30) cc_final: 0.7363 (tm-30) REVERT: A 295 ASN cc_start: 0.8172 (m-40) cc_final: 0.7955 (m-40) REVERT: A 322 THR cc_start: 0.8530 (m) cc_final: 0.8283 (p) REVERT: B 37 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7825 (OUTLIER) REVERT: B 128 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8353 (p) REVERT: B 161 SER cc_start: 0.8446 (p) cc_final: 0.8007 (p) REVERT: B 188 MET cc_start: 0.8372 (mmm) cc_final: 0.8012 (mmm) REVERT: B 230 ASN cc_start: 0.8164 (m-40) cc_final: 0.7885 (m-40) REVERT: B 265 SER cc_start: 0.7736 (p) cc_final: 0.7452 (t) REVERT: B 318 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8172 (tp) REVERT: G 21 MET cc_start: 0.8066 (mmm) cc_final: 0.7636 (mmm) REVERT: G 50 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6868 (mt) REVERT: S 46 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7317 (mt-10) REVERT: S 191 PHE cc_start: 0.8106 (m-80) cc_final: 0.7694 (m-80) REVERT: S 208 GLU cc_start: 0.7772 (mp0) cc_final: 0.7507 (mp0) REVERT: S 223 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6535 (t80) REVERT: R 11 MET cc_start: 0.7313 (tmm) cc_final: 0.7026 (tmm) REVERT: R 27 LEU cc_start: 0.7675 (tp) cc_final: 0.7364 (tm) REVERT: R 50 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8034 (tt) REVERT: R 136 ILE cc_start: 0.7812 (tt) cc_final: 0.7591 (tp) REVERT: R 191 LEU cc_start: 0.7898 (mt) cc_final: 0.7678 (mp) outliers start: 64 outliers final: 28 residues processed: 244 average time/residue: 0.9129 time to fit residues: 241.6811 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 : 0.960 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.8980 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3975 r_free = 0.3975 target = 0.143706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.126037 restraints weight = 12849.860| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.03 r_work: 0.3629 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1613 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= 0.182 Angle : 0.615 8.409 12345 Z= 0.321 Chirality : 0.044 0.209 1410 Planarity : 0.005 0.058 1542 Dihedral : 5.063 57.763 1240 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.60 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: 1.78 (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 0.025 0.002 TYR R 266 ARG 0.006 0.001 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03777 ( 489) hydrogen bonds : angle 4.65829 ( 1401) SS BOND : bond 0.00349 ( 3) SS BOND : angle 1.03667 ( 6) covalent geometry : bond 0.00414 ( 9108) covalent geometry : angle 0.61462 (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 : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8104 (mtpp) REVERT: A 46 LYS cc_start: 0.6514 (ttpp) cc_final: 0.6141 (ttpp) REVERT: A 201 ASP cc_start: 0.8009 (t0) cc_final: 0.7647 (t0) REVERT: A 246 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7313 (tm-30) REVERT: A 322 THR cc_start: 0.8529 (m) cc_final: 0.8289 (p) REVERT: B 18 ILE cc_start: 0.8383 (pp) cc_final: 0.8122 (pt) REVERT: B 37 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7815 (tt) REVERT: B 114 CYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7660 (p) REVERT: B 128 THR cc_start: 0.8619 (p) cc_final: 0.8345 (p) REVERT: B 188 MET cc_start: 0.8323 (mmm) cc_final: 0.7937 (mmm) REVERT: B 230 ASN cc_start: 0.8170 (m-40) cc_final: 0.7862 (m-40) REVERT: B 246 ASP cc_start: 0.7811 (m-30) cc_final: 0.7411 (m-30) REVERT: B 262 MET cc_start: 0.7110 (mmm) cc_final: 0.6807 (mmm) REVERT: B 265 SER cc_start: 0.7741 (p) cc_final: 0.7458 (t) REVERT: B 318 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8066 (tp) REVERT: G 21 MET cc_start: 0.8075 (mmm) cc_final: 0.7673 (mmm) REVERT: G 50 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7062 (mt) REVERT: S 46 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7298 (mt-10) REVERT: S 108 PHE cc_start: 0.8508 (m-80) cc_final: 0.8232 (m-80) REVERT: S 191 PHE cc_start: 0.8122 (m-80) cc_final: 0.7726 (m-80) REVERT: S 208 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: S 223 TYR cc_start: 0.6997 (OUTLIER) cc_final: 0.6507 (t80) REVERT: R 27 LEU cc_start: 0.7683 (tp) cc_final: 0.7442 (tm) REVERT: R 136 ILE cc_start: 0.7779 (tt) cc_final: 0.7533 (tp) REVERT: R 150 ILE cc_start: 0.6858 (pp) cc_final: 0.6606 (pt) REVERT: R 191 LEU cc_start: 0.7897 (mt) cc_final: 0.7669 (mp) outliers start: 59 outliers final: 34 residues processed: 237 average time/residue: 0.9566 time to fit residues: 246.2465 Evaluate side-chains 232 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 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 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: 0.7980 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 0.0040 chunk 88 optimal weight: 0.1980 chunk 65 optimal weight: 0.0980 overall best weight: 0.3392 ------------------------------------------------------------------------------- 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 = 0.3995 r_free = 0.3995 target = 0.145447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.127850 restraints weight = 12874.599| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.06 r_work: 0.3650 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9111 Z= 0.134 Angle : 0.574 8.272 12345 Z= 0.300 Chirality : 0.042 0.182 1410 Planarity : 0.005 0.059 1542 Dihedral : 4.980 59.039 1240 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.61 % Allowed : 29.49 % 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: 0.57 (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 0.011 0.001 HIS R 210 PHE 0.042 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 0.03511 ( 489) hydrogen bonds : angle 4.56002 ( 1401) SS BOND : bond 0.00334 ( 3) SS BOND : angle 0.93514 ( 6) covalent geometry : bond 0.00304 ( 9108) covalent geometry : angle 0.57363 (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 257 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 202 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8214 (mtpp) REVERT: A 46 LYS cc_start: 0.6555 (ttpp) cc_final: 0.6171 (ttpp) REVERT: A 198 LYS cc_start: 0.8204 (mmmm) cc_final: 0.7746 (mtpp) REVERT: A 201 ASP cc_start: 0.8045 (t0) cc_final: 0.7640 (t0) REVERT: A 246 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7293 (tm-30) REVERT: B 18 ILE cc_start: 0.8390 (pp) cc_final: 0.8148 (pt) REVERT: B 37 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7824 (tt) REVERT: B 114 CYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7592 (p) REVERT: B 128 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8325 (p) REVERT: B 188 MET cc_start: 0.8257 (mmm) cc_final: 0.7860 (mmm) REVERT: B 230 ASN cc_start: 0.8157 (m-40) cc_final: 0.7849 (m-40) REVERT: B 246 ASP cc_start: 0.7839 (m-30) cc_final: 0.7409 (m-30) REVERT: B 262 MET cc_start: 0.7029 (mmm) cc_final: 0.6761 (mmm) REVERT: B 265 SER cc_start: 0.7725 (p) cc_final: 0.7403 (t) REVERT: G 21 MET cc_start: 0.8026 (mmm) cc_final: 0.7635 (mmm) REVERT: G 50 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6854 (mt) REVERT: S 46 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7296 (mt-10) REVERT: S 208 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: S 223 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.6480 (t80) REVERT: R 27 LEU cc_start: 0.7625 (tp) cc_final: 0.7367 (tm) REVERT: R 136 ILE cc_start: 0.7597 (tt) cc_final: 0.7345 (tp) REVERT: R 219 MET cc_start: 0.6833 (mpp) cc_final: 0.6610 (mmm) outliers start: 55 outliers final: 29 residues processed: 232 average time/residue: 0.8788 time to fit residues: 221.7781 Evaluate side-chains 231 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 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 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 32 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 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 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: 0.9980 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.141569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.123894 restraints weight = 12752.153| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.01 r_work: 0.3602 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 9111 Z= 0.299 Angle : 0.655 8.537 12345 Z= 0.341 Chirality : 0.047 0.227 1410 Planarity : 0.005 0.057 1542 Dihedral : 5.191 59.211 1240 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 7.76 % Allowed : 27.45 % Favored : 64.80 % 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: 0.30 (0.25), residues: 1111 helix: 1.57 (0.25), residues: 419 sheet: -0.45 (0.31), residues: 270 loop : -0.66 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 120 HIS 0.015 0.002 HIS R 210 PHE 0.036 0.002 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 0.04063 ( 489) hydrogen bonds : angle 4.67607 ( 1401) SS BOND : bond 0.00472 ( 3) SS BOND : angle 1.14157 ( 6) covalent geometry : bond 0.00684 ( 9108) covalent geometry : angle 0.65488 (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: 76 poor density : 195 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6696 (ttpp) cc_final: 0.6140 (ttpp) REVERT: A 201 ASP cc_start: 0.8060 (t0) cc_final: 0.7555 (t0) REVERT: A 267 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8193 (mt) REVERT: A 322 THR cc_start: 0.8507 (m) cc_final: 0.8301 (p) REVERT: B 37 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7891 (tt) REVERT: B 114 CYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7762 (p) REVERT: B 128 THR cc_start: 0.8665 (OUTLIER) cc_final: 0.8312 (p) REVERT: B 188 MET cc_start: 0.8325 (mmm) cc_final: 0.7949 (mmm) REVERT: B 262 MET cc_start: 0.7237 (mmm) cc_final: 0.6850 (mmm) REVERT: B 265 SER cc_start: 0.7721 (p) cc_final: 0.7480 (t) REVERT: B 318 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8126 (tp) REVERT: G 21 MET cc_start: 0.8197 (mmm) cc_final: 0.7868 (mmm) REVERT: G 50 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7506 (mt) REVERT: S 46 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7319 (mt-10) REVERT: S 87 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7384 (mtp180) REVERT: S 191 PHE cc_start: 0.8170 (m-80) cc_final: 0.7722 (m-80) REVERT: S 208 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: S 223 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.6585 (t80) REVERT: R 27 LEU cc_start: 0.7849 (tp) cc_final: 0.7621 (tm) REVERT: R 50 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8007 (tt) REVERT: R 136 ILE cc_start: 0.7886 (tt) cc_final: 0.7664 (tp) REVERT: R 190 ILE cc_start: 0.7944 (mm) cc_final: 0.7720 (tp) REVERT: R 277 MET cc_start: 0.6934 (mmm) cc_final: 0.6731 (mmm) outliers start: 76 outliers final: 36 residues processed: 238 average time/residue: 0.9306 time to fit residues: 240.0895 Evaluate side-chains 229 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 267 LEU 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 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 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 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 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: 0.4980 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 39 GLN S 182 ASN R 24 GLN R 210 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.143980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.126208 restraints weight = 12667.104| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.03 r_work: 0.3633 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2155 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= 0.170 Angle : 0.603 8.309 12345 Z= 0.313 Chirality : 0.044 0.196 1410 Planarity : 0.005 0.056 1542 Dihedral : 5.064 57.841 1240 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.82 % Allowed : 30.20 % 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: 0.53 (0.26), residues: 1111 helix: 1.91 (0.26), residues: 412 sheet: -0.48 (0.32), residues: 266 loop : -0.56 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 120 HIS 0.011 0.001 HIS R 210 PHE 0.030 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 0.03710 ( 489) hydrogen bonds : angle 4.60979 ( 1401) SS BOND : bond 0.00365 ( 3) SS BOND : angle 1.02346 ( 6) covalent geometry : bond 0.00386 ( 9108) covalent geometry : angle 0.60269 (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: 57 poor density : 194 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7269 (tm-30) REVERT: A 258 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8126 (ptmm) REVERT: A 322 THR cc_start: 0.8497 (m) cc_final: 0.8287 (p) REVERT: B 37 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7883 (tt) REVERT: B 114 CYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7643 (p) REVERT: B 128 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 188 MET cc_start: 0.8294 (mmm) cc_final: 0.7871 (mmm) REVERT: B 262 MET cc_start: 0.7099 (mmm) cc_final: 0.6849 (mmm) REVERT: B 265 SER cc_start: 0.7737 (p) cc_final: 0.7471 (t) REVERT: G 21 MET cc_start: 0.8150 (mmm) cc_final: 0.7830 (mmm) REVERT: G 50 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7488 (mt) REVERT: S 46 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7341 (mt-10) REVERT: S 87 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7309 (mtp180) REVERT: S 191 PHE cc_start: 0.8155 (m-80) cc_final: 0.7706 (m-80) REVERT: S 208 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: S 223 TYR cc_start: 0.6963 (OUTLIER) cc_final: 0.6513 (t80) REVERT: R 27 LEU cc_start: 0.7750 (tp) cc_final: 0.7520 (tm) REVERT: R 50 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7968 (tt) REVERT: R 136 ILE cc_start: 0.7773 (tt) cc_final: 0.7529 (tp) outliers start: 57 outliers final: 31 residues processed: 225 average time/residue: 0.9789 time to fit residues: 238.2631 Evaluate side-chains 226 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 210 HIS Chi-restraints excluded: chain R residue 231 VAL Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 244 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 0.0770 chunk 15 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.0770 chunk 21 optimal weight: 0.6980 overall best weight: 0.4096 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.144438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.126754 restraints weight = 12794.753| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.04 r_work: 0.3639 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9111 Z= 0.146 Angle : 0.598 8.344 12345 Z= 0.309 Chirality : 0.043 0.197 1410 Planarity : 0.004 0.057 1542 Dihedral : 5.006 58.199 1240 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.92 % Allowed : 29.90 % 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: 0.51 (0.26), residues: 1111 helix: 1.90 (0.26), residues: 419 sheet: -0.49 (0.31), residues: 273 loop : -0.61 (0.30), residues: 419 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 0.027 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 0.03597 ( 489) hydrogen bonds : angle 4.58482 ( 1401) SS BOND : bond 0.00295 ( 3) SS BOND : angle 0.96377 ( 6) covalent geometry : bond 0.00333 ( 9108) covalent geometry : angle 0.59822 (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 254 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 196 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 258 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8110 (ptmm) REVERT: A 322 THR cc_start: 0.8505 (m) cc_final: 0.8266 (p) REVERT: B 37 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7876 (tt) REVERT: B 114 CYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7595 (p) REVERT: B 128 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8284 (p) REVERT: B 188 MET cc_start: 0.8221 (mmm) cc_final: 0.7853 (mmm) REVERT: B 262 MET cc_start: 0.7038 (mmm) cc_final: 0.6810 (mmm) REVERT: B 265 SER cc_start: 0.7741 (p) cc_final: 0.7452 (t) REVERT: B 266 HIS cc_start: 0.7789 (OUTLIER) cc_final: 0.7584 (t-170) REVERT: G 21 MET cc_start: 0.8139 (mmm) cc_final: 0.7828 (mmm) REVERT: G 50 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7431 (mt) REVERT: S 87 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7242 (mtp180) REVERT: S 208 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: S 223 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6509 (t80) REVERT: R 16 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.7166 (pp) REVERT: R 27 LEU cc_start: 0.7699 (tp) cc_final: 0.7484 (tm) REVERT: R 136 ILE cc_start: 0.7753 (tt) cc_final: 0.7504 (tp) outliers start: 58 outliers final: 24 residues processed: 231 average time/residue: 0.9219 time to fit residues: 231.2206 Evaluate side-chains 220 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 244 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 0.0470 chunk 90 optimal weight: 0.0470 chunk 100 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 16 optimal weight: 0.0370 chunk 74 optimal weight: 0.9980 overall best weight: 0.2654 ------------------------------------------------------------------------------- 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** R 24 GLN R 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.145552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.127859 restraints weight = 12947.194| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.08 r_work: 0.3654 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9111 Z= 0.126 Angle : 0.589 8.220 12345 Z= 0.304 Chirality : 0.043 0.206 1410 Planarity : 0.004 0.058 1542 Dihedral : 4.943 59.115 1240 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.08 % Allowed : 32.35 % 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: 0.63 (0.26), residues: 1111 helix: 2.03 (0.25), residues: 418 sheet: -0.39 (0.31), residues: 276 loop : -0.61 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 120 HIS 0.009 0.001 HIS R 210 PHE 0.026 0.001 PHE R 88 TYR 0.025 0.002 TYR R 266 ARG 0.010 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 489) hydrogen bonds : angle 4.51791 ( 1401) SS BOND : bond 0.00245 ( 3) SS BOND : angle 0.85822 ( 6) covalent geometry : bond 0.00283 ( 9108) covalent geometry : angle 0.58859 (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 246 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.6533 (ttpp) cc_final: 0.6120 (ttpp) REVERT: A 201 ASP cc_start: 0.8003 (t0) cc_final: 0.7478 (t0) REVERT: A 246 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7262 (tm-30) REVERT: A 258 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8118 (ptmm) REVERT: B 37 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7854 (tt) REVERT: B 114 CYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7657 (p) REVERT: B 128 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 188 MET cc_start: 0.8178 (mmm) cc_final: 0.7801 (mmm) REVERT: B 262 MET cc_start: 0.7001 (mmm) cc_final: 0.6772 (mmm) REVERT: B 265 SER cc_start: 0.7608 (p) cc_final: 0.7364 (t) REVERT: G 21 MET cc_start: 0.8150 (mmm) cc_final: 0.7844 (mmm) REVERT: G 50 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7363 (mt) REVERT: S 87 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7296 (mtp180) REVERT: S 189 ASP cc_start: 0.7684 (t0) cc_final: 0.7447 (t0) REVERT: S 191 PHE cc_start: 0.8196 (m-80) cc_final: 0.7713 (m-80) REVERT: S 208 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: S 223 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.6482 (t80) REVERT: S 227 PHE cc_start: 0.8565 (m-80) cc_final: 0.8036 (m-80) REVERT: R 16 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7134 (pp) REVERT: R 27 LEU cc_start: 0.7656 (tp) cc_final: 0.7419 (tm) REVERT: R 136 ILE cc_start: 0.7618 (tt) cc_final: 0.7364 (tp) REVERT: R 190 ILE cc_start: 0.7952 (mm) cc_final: 0.7739 (tp) outliers start: 40 outliers final: 24 residues processed: 231 average time/residue: 0.9009 time to fit residues: 226.3440 Evaluate side-chains 228 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 294 CYS Chi-restraints excluded: chain B residue 307 VAL 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 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 Chi-restraints excluded: chain R residue 244 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 0.0670 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 0.0670 overall best weight: 0.4456 ------------------------------------------------------------------------------- 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 R 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.145266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.127759 restraints weight = 12707.004| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.04 r_work: 0.3654 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2342 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= 0.146 Angle : 0.613 8.996 12345 Z= 0.311 Chirality : 0.043 0.205 1410 Planarity : 0.005 0.058 1542 Dihedral : 4.918 58.878 1240 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.39 % Allowed : 33.57 % Favored : 62.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1111 helix: 1.99 (0.25), residues: 420 sheet: -0.40 (0.31), residues: 281 loop : -0.61 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 120 HIS 0.016 0.001 HIS R 210 PHE 0.048 0.002 PHE S 68 TYR 0.026 0.002 TYR R 266 ARG 0.009 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 489) hydrogen bonds : angle 4.50515 ( 1401) SS BOND : bond 0.00271 ( 3) SS BOND : angle 0.92863 ( 6) covalent geometry : bond 0.00334 ( 9108) covalent geometry : angle 0.61241 (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 246 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8279 (mtpp) REVERT: A 46 LYS cc_start: 0.6548 (ttpp) cc_final: 0.6156 (ttpp) REVERT: A 201 ASP cc_start: 0.7981 (t0) cc_final: 0.7487 (t0) REVERT: A 246 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7248 (tm-30) REVERT: A 258 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8118 (ptmm) REVERT: B 37 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7870 (tt) REVERT: B 114 CYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7678 (p) REVERT: B 128 THR cc_start: 0.8556 (OUTLIER) cc_final: 0.8283 (p) REVERT: B 188 MET cc_start: 0.8192 (mmm) cc_final: 0.7817 (mmm) REVERT: B 262 MET cc_start: 0.6982 (mmm) cc_final: 0.6771 (mmm) REVERT: B 265 SER cc_start: 0.7672 (p) cc_final: 0.7455 (t) REVERT: B 266 HIS cc_start: 0.7599 (OUTLIER) cc_final: 0.7362 (t-90) REVERT: G 21 MET cc_start: 0.8152 (mmm) cc_final: 0.7879 (mmm) REVERT: S 87 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7325 (mtp180) REVERT: S 189 ASP cc_start: 0.7669 (t0) cc_final: 0.7437 (t0) REVERT: S 208 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7348 (mp0) REVERT: S 223 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.6457 (t80) REVERT: R 16 LEU cc_start: 0.7386 (OUTLIER) cc_final: 0.7132 (pp) REVERT: R 27 LEU cc_start: 0.7668 (tp) cc_final: 0.7443 (tm) REVERT: R 136 ILE cc_start: 0.7612 (tt) cc_final: 0.7357 (tp) REVERT: R 190 ILE cc_start: 0.7962 (mm) cc_final: 0.7739 (tp) outliers start: 43 outliers final: 29 residues processed: 228 average time/residue: 0.9418 time to fit residues: 232.5864 Evaluate side-chains 239 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS 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 114 CYS Chi-restraints excluded: chain B residue 128 THR 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 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 231 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 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 210 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.144087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.126430 restraints weight = 12828.740| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 2.04 r_work: 0.3637 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2391 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= 0.189 Angle : 0.628 8.361 12345 Z= 0.323 Chirality : 0.044 0.210 1410 Planarity : 0.004 0.057 1542 Dihedral : 4.981 58.742 1240 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.18 % Allowed : 33.27 % 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: 1.93 (0.25), residues: 420 sheet: -0.43 (0.31), residues: 281 loop : -0.57 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 120 HIS 0.006 0.001 HIS R 210 PHE 0.027 0.002 PHE R 88 TYR 0.027 0.002 TYR R 266 ARG 0.010 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 489) hydrogen bonds : angle 4.53577 ( 1401) SS BOND : bond 0.00307 ( 3) SS BOND : angle 0.95182 ( 6) covalent geometry : bond 0.00436 ( 9108) covalent geometry : angle 0.62756 (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 248 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 246 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7261 (tm-30) REVERT: A 258 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8149 (ptmm) REVERT: A 309 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7197 (mt-10) REVERT: B 37 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7888 (tt) REVERT: B 114 CYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7666 (p) REVERT: B 128 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8304 (p) REVERT: B 188 MET cc_start: 0.8240 (mmm) cc_final: 0.7873 (mmm) REVERT: B 255 LEU cc_start: 0.8093 (mt) cc_final: 0.7854 (mp) REVERT: B 265 SER cc_start: 0.7681 (p) cc_final: 0.7398 (t) REVERT: G 21 MET cc_start: 0.8184 (mmm) cc_final: 0.7877 (mmm) REVERT: S 87 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7327 (mtp180) REVERT: S 208 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: S 223 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.6524 (t80) REVERT: R 16 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7143 (pp) REVERT: R 27 LEU cc_start: 0.7717 (tp) cc_final: 0.7490 (tm) REVERT: R 69 CYS cc_start: 0.6508 (OUTLIER) cc_final: 0.6284 (t) REVERT: R 136 ILE cc_start: 0.7671 (tt) cc_final: 0.7419 (tp) REVERT: R 190 ILE cc_start: 0.7991 (mm) cc_final: 0.7769 (tp) outliers start: 41 outliers final: 31 residues processed: 228 average time/residue: 0.9345 time to fit residues: 230.7927 Evaluate side-chains 245 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 48 ARG 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 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 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 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 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 231 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: 0.8980 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 76 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 266 HIS R 210 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.144249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.126711 restraints weight = 12667.886| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.04 r_work: 0.3635 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9111 Z= 0.187 Angle : 0.635 8.343 12345 Z= 0.325 Chirality : 0.044 0.213 1410 Planarity : 0.005 0.057 1542 Dihedral : 5.018 59.002 1240 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.29 % Allowed : 33.27 % Favored : 62.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.26), residues: 1111 helix: 1.97 (0.25), residues: 414 sheet: -0.41 (0.31), residues: 279 loop : -0.59 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 120 HIS 0.013 0.001 HIS R 210 PHE 0.028 0.002 PHE S 68 TYR 0.027 0.002 TYR R 266 ARG 0.009 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03675 ( 489) hydrogen bonds : angle 4.54274 ( 1401) SS BOND : bond 0.00293 ( 3) SS BOND : angle 0.91304 ( 6) covalent geometry : bond 0.00430 ( 9108) covalent geometry : angle 0.63473 (12339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7416.98 seconds wall clock time: 128 minutes 30.89 seconds (7710.89 seconds total)