Starting phenix.real_space_refine on Thu Jan 16 16:25:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5g_38934/01_2025/8y5g_38934.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5g_38934/01_2025/8y5g_38934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y5g_38934/01_2025/8y5g_38934.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5g_38934/01_2025/8y5g_38934.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5g_38934/01_2025/8y5g_38934.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5g_38934/01_2025/8y5g_38934.cif" } resolution = 3.0 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= 0.003 sd= 0.042 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: 5 Type Number sf(0) Gaussians Mg 4 5.21 5 S 60 5.16 5 C 6388 2.51 5 N 1649 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9860 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2876 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "B" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "C" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1936 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 9, 'TRANS': 239} Chain: "D" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2862 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 13, 'TRANS': 344} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SPD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.41, per 1000 atoms: 0.65 Number of scatterers: 9860 At special positions: 0 Unit cell: (84.36, 93.48, 139.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 Mg 4 11.99 O 1759 8.00 N 1649 7.00 C 6388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 10 sheets defined 50.6% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 55 through 65 removed outlier: 3.541A pdb=" N VAL A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 116 removed outlier: 4.908A pdb=" N GLY A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.724A pdb=" N VAL A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 163 Processing helix chain 'A' and resid 179 through 198 removed outlier: 3.579A pdb=" N ASN A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.506A pdb=" N ALA A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 Processing helix chain 'A' and resid 241 through 248 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'B' and resid 8 through 23 removed outlier: 3.534A pdb=" N ILE B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 34 Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 58 through 91 removed outlier: 4.136A pdb=" N VAL B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) Proline residue: B 85 - end of helix Processing helix chain 'B' and resid 97 through 104 Processing helix chain 'B' and resid 105 through 111 Proline residue: B 108 - end of helix removed outlier: 3.508A pdb=" N THR B 111 " --> pdb=" O PRO B 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 111' Processing helix chain 'B' and resid 112 through 124 removed outlier: 3.884A pdb=" N TYR B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 149 through 175 removed outlier: 3.764A pdb=" N VAL B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Proline residue: B 163 - end of helix removed outlier: 3.534A pdb=" N MET B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.727A pdb=" N LEU B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 198 Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.717A pdb=" N LEU B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 221 through 229 removed outlier: 4.286A pdb=" N SER B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 removed outlier: 3.760A pdb=" N VAL B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 279 removed outlier: 3.519A pdb=" N GLY B 253 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 28 Proline residue: C 21 - end of helix Processing helix chain 'C' and resid 44 through 52 removed outlier: 3.618A pdb=" N SER C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 88 removed outlier: 4.003A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 105 Processing helix chain 'C' and resid 107 through 122 Processing helix chain 'C' and resid 127 through 152 Proline residue: C 141 - end of helix Processing helix chain 'C' and resid 156 through 165 removed outlier: 4.235A pdb=" N GLU C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 176 Processing helix chain 'C' and resid 176 through 199 removed outlier: 3.708A pdb=" N LEU C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Proline residue: C 183 - end of helix Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.944A pdb=" N LYS C 223 " --> pdb=" O TYR C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 253 removed outlier: 3.767A pdb=" N ILE C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 239 " --> pdb=" O THR C 235 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL C 245 " --> pdb=" O SER C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 65 Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.600A pdb=" N ARG D 89 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 116 removed outlier: 4.964A pdb=" N GLY D 113 " --> pdb=" O ASN D 109 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LEU D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 135 removed outlier: 3.638A pdb=" N VAL D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 163 Processing helix chain 'D' and resid 179 through 198 removed outlier: 3.821A pdb=" N ASN D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.568A pdb=" N ALA D 211 " --> pdb=" O ASP D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 238 removed outlier: 3.517A pdb=" N TYR D 236 " --> pdb=" O PRO D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 299 removed outlier: 3.548A pdb=" N LEU D 299 " --> pdb=" O PRO D 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 40 removed outlier: 6.636A pdb=" N VAL A 32 " --> pdb=" O CYS A 26 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N CYS A 26 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG A 24 " --> pdb=" O PRO A 34 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LEU A 36 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ILE A 23 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER A 71 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.479A pdb=" N PHE A 45 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL A 219 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THR A 47 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N MET A 221 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 49 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE A 218 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP A 229 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 220 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 279 removed outlier: 6.598A pdb=" N ASN A 270 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL A 258 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 303 removed outlier: 5.661A pdb=" N VAL A 317 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU A 332 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU A 319 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AA6, first strand: chain 'D' and resid 30 through 40 removed outlier: 6.690A pdb=" N VAL D 32 " --> pdb=" O CYS D 26 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N CYS D 26 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ARG D 24 " --> pdb=" O PRO D 34 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N LEU D 36 " --> pdb=" O GLY D 22 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE D 23 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SER D 71 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.440A pdb=" N PHE D 45 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL D 219 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR D 47 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N MET D 221 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU D 49 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE D 218 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ASP D 229 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL D 220 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 274 through 279 removed outlier: 7.503A pdb=" N ARG D 266 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ARG D 261 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG D 268 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 300 through 302 removed outlier: 4.234A pdb=" N ALA D 361 " --> pdb=" O GLU D 302 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 321 through 322 502 hydrogen bonds defined for protein. 1446 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: 2.67 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3187 1.34 - 1.46: 2193 1.46 - 1.58: 4559 1.58 - 1.70: 0 1.70 - 1.82: 111 Bond restraints: 10050 Sorted by residual: bond pdb=" CA VAL D 330 " pdb=" CB VAL D 330 " ideal model delta sigma weight residual 1.531 1.544 -0.013 1.16e-02 7.43e+03 1.31e+00 bond pdb=" CB ASN A 270 " pdb=" CG ASN A 270 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.25e+00 bond pdb=" SD MET A 116 " pdb=" CE MET A 116 " ideal model delta sigma weight residual 1.791 1.764 0.027 2.50e-02 1.60e+03 1.13e+00 bond pdb=" N GLU D 366 " pdb=" CA GLU D 366 " ideal model delta sigma weight residual 1.458 1.473 -0.015 1.37e-02 5.33e+03 1.13e+00 bond pdb=" CG ARG A 233 " pdb=" CD ARG A 233 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 ... (remaining 10045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 13467 2.62 - 5.25: 144 5.25 - 7.87: 8 7.87 - 10.50: 4 10.50 - 13.12: 1 Bond angle restraints: 13624 Sorted by residual: angle pdb=" CB MET D 360 " pdb=" CG MET D 360 " pdb=" SD MET D 360 " ideal model delta sigma weight residual 112.70 125.82 -13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" C SER A 97 " pdb=" N TYR A 98 " pdb=" CA TYR A 98 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C ASN A 270 " pdb=" CA ASN A 270 " pdb=" CB ASN A 270 " ideal model delta sigma weight residual 109.48 115.46 -5.98 1.68e+00 3.54e-01 1.27e+01 angle pdb=" C VAL B 107 " pdb=" CA VAL B 107 " pdb=" CB VAL B 107 " ideal model delta sigma weight residual 114.35 110.60 3.75 1.06e+00 8.90e-01 1.25e+01 angle pdb=" N HIS D 146 " pdb=" CA HIS D 146 " pdb=" C HIS D 146 " ideal model delta sigma weight residual 114.64 109.27 5.37 1.52e+00 4.33e-01 1.25e+01 ... (remaining 13619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 5196 17.69 - 35.38: 629 35.38 - 53.06: 189 53.06 - 70.75: 37 70.75 - 88.44: 6 Dihedral angle restraints: 6057 sinusoidal: 2457 harmonic: 3600 Sorted by residual: dihedral pdb=" CA TRP D 364 " pdb=" C TRP D 364 " pdb=" N VAL D 365 " pdb=" CA VAL D 365 " ideal model delta harmonic sigma weight residual 180.00 -161.86 -18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ALA D 99 " pdb=" C ALA D 99 " pdb=" N LEU D 100 " pdb=" CA LEU D 100 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA THR A 213 " pdb=" C THR A 213 " pdb=" N MET A 214 " pdb=" CA MET A 214 " ideal model delta harmonic sigma weight residual -180.00 -163.23 -16.77 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 6054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 924 0.032 - 0.063: 474 0.063 - 0.095: 109 0.095 - 0.127: 81 0.127 - 0.159: 9 Chirality restraints: 1597 Sorted by residual: chirality pdb=" CG LEU D 313 " pdb=" CB LEU D 313 " pdb=" CD1 LEU D 313 " pdb=" CD2 LEU D 313 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CA PHE C 138 " pdb=" N PHE C 138 " pdb=" C PHE C 138 " pdb=" CB PHE C 138 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA GLU A 189 " pdb=" N GLU A 189 " pdb=" C GLU A 189 " pdb=" CB GLU A 189 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1594 not shown) Planarity restraints: 1723 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 285 " -0.052 5.00e-02 4.00e+02 7.83e-02 9.81e+00 pdb=" N PRO D 286 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO D 286 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 286 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 167 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.56e+00 pdb=" N PRO B 168 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 168 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 168 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 208 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO C 209 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 209 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 209 " -0.032 5.00e-02 4.00e+02 ... (remaining 1720 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 134 2.68 - 3.24: 9027 3.24 - 3.79: 13908 3.79 - 4.35: 18484 4.35 - 4.90: 31962 Nonbonded interactions: 73515 Sorted by model distance: nonbonded pdb=" OD2 ASP D 348 " pdb="MG MG D 402 " model vdw 2.131 2.170 nonbonded pdb=" O PHE D 345 " pdb="MG MG D 401 " model vdw 2.191 2.170 nonbonded pdb=" N ASP C 108 " pdb=" OD1 ASP C 108 " model vdw 2.269 3.120 nonbonded pdb=" O ILE B 146 " pdb=" OG1 THR B 149 " model vdw 2.278 3.040 nonbonded pdb=" NE2 GLN D 154 " pdb=" O SER D 174 " model vdw 2.305 3.120 ... (remaining 73510 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 373 or resid 401 through 402)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.890 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 0.038 10050 Z= 0.286 Angle : 0.674 13.122 13624 Z= 0.365 Chirality : 0.044 0.159 1597 Planarity : 0.006 0.078 1723 Dihedral : 16.922 88.441 3725 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.14 % Favored : 95.78 % Rotamer: Outliers : 2.40 % Allowed : 24.70 % Favored : 72.90 % 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: -0.20 (0.24), residues: 1232 helix: 0.80 (0.22), residues: 575 sheet: 0.63 (0.39), residues: 199 loop : -1.70 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 368 HIS 0.007 0.001 HIS A 146 PHE 0.029 0.002 PHE B 48 TYR 0.013 0.001 TYR D 98 ARG 0.015 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 269 time to evaluate : 1.081 Fit side-chains REVERT: A 28 ASP cc_start: 0.7274 (t70) cc_final: 0.7039 (t70) REVERT: A 75 MET cc_start: 0.7675 (mpt) cc_final: 0.7430 (mmt) REVERT: A 152 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7341 (mt0) REVERT: A 185 GLN cc_start: 0.7572 (tt0) cc_final: 0.7026 (tt0) REVERT: A 186 MET cc_start: 0.8160 (mtm) cc_final: 0.7864 (mtm) REVERT: A 189 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6806 (mp0) REVERT: A 297 GLU cc_start: 0.8268 (pm20) cc_final: 0.8056 (mp0) REVERT: A 343 GLU cc_start: 0.7349 (pt0) cc_final: 0.7096 (pt0) REVERT: C 173 LEU cc_start: 0.7477 (mp) cc_final: 0.7266 (mp) REVERT: D 129 MET cc_start: 0.8584 (mmm) cc_final: 0.8369 (mmt) outliers start: 26 outliers final: 20 residues processed: 288 average time/residue: 1.2916 time to fit residues: 396.8923 Evaluate side-chains 286 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 265 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 253 ARG Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 214 MET Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.0000 chunk 95 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 206 HIS A 358 GLN D 42 ASN D 255 ASN D 321 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.124739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.106552 restraints weight = 13376.706| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.16 r_work: 0.3241 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10050 Z= 0.198 Angle : 0.587 10.740 13624 Z= 0.304 Chirality : 0.043 0.150 1597 Planarity : 0.005 0.060 1723 Dihedral : 6.923 57.401 1391 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 4.42 % Allowed : 20.65 % Favored : 74.93 % 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: 0.59 (0.24), residues: 1232 helix: 1.82 (0.22), residues: 583 sheet: 0.51 (0.38), residues: 202 loop : -1.66 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 136 HIS 0.009 0.001 HIS A 146 PHE 0.024 0.001 PHE B 133 TYR 0.014 0.001 TYR C 17 ARG 0.007 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 248 time to evaluate : 1.071 Fit side-chains REVERT: A 75 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7739 (mpt) REVERT: B 133 PHE cc_start: 0.8060 (t80) cc_final: 0.7744 (t80) REVERT: B 137 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8218 (mp) REVERT: C 43 THR cc_start: 0.8296 (t) cc_final: 0.7906 (m) REVERT: C 121 LEU cc_start: 0.8268 (tt) cc_final: 0.7967 (tt) REVERT: D 37 ASP cc_start: 0.8445 (m-30) cc_final: 0.8219 (m-30) REVERT: D 140 PHE cc_start: 0.8097 (m-10) cc_final: 0.7778 (m-80) REVERT: D 207 ASP cc_start: 0.7756 (t0) cc_final: 0.7526 (t0) outliers start: 48 outliers final: 20 residues processed: 275 average time/residue: 1.2131 time to fit residues: 357.2061 Evaluate side-chains 248 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 331 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 117 GLN A 142 GLN A 185 GLN A 187 GLN A 358 GLN D 42 ASN D 147 GLN D 255 ASN D 321 ASN D 335 ASN D 346 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.124707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.106344 restraints weight = 13590.074| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.21 r_work: 0.3235 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10050 Z= 0.207 Angle : 0.573 11.356 13624 Z= 0.291 Chirality : 0.043 0.212 1597 Planarity : 0.005 0.054 1723 Dihedral : 5.455 57.712 1359 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.73 % Favored : 96.19 % Rotamer: Outliers : 4.88 % Allowed : 21.75 % Favored : 73.36 % 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: 0.72 (0.25), residues: 1232 helix: 2.08 (0.22), residues: 579 sheet: 0.38 (0.38), residues: 205 loop : -1.71 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 136 HIS 0.009 0.001 HIS A 146 PHE 0.023 0.001 PHE C 138 TYR 0.011 0.001 TYR B 223 ARG 0.008 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 233 time to evaluate : 1.132 Fit side-chains REVERT: A 75 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7517 (mpt) REVERT: B 133 PHE cc_start: 0.8088 (t80) cc_final: 0.7706 (t80) REVERT: B 137 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8180 (mp) REVERT: B 215 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7537 (tmm) REVERT: D 37 ASP cc_start: 0.8435 (m-30) cc_final: 0.8218 (m-30) REVERT: D 140 PHE cc_start: 0.8137 (m-10) cc_final: 0.7827 (m-80) REVERT: D 207 ASP cc_start: 0.7723 (t0) cc_final: 0.7460 (t0) REVERT: D 330 VAL cc_start: 0.8778 (p) cc_final: 0.8551 (m) outliers start: 53 outliers final: 24 residues processed: 264 average time/residue: 1.2493 time to fit residues: 352.7454 Evaluate side-chains 253 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 255 ASN Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 42 ASN A 142 GLN A 358 GLN D 42 ASN D 255 ASN D 277 ASN D 321 ASN D 335 ASN D 358 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.124658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.106312 restraints weight = 13488.705| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.18 r_work: 0.3232 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10050 Z= 0.215 Angle : 0.570 11.587 13624 Z= 0.288 Chirality : 0.043 0.199 1597 Planarity : 0.005 0.051 1723 Dihedral : 4.867 58.718 1351 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.94 % Rotamer: Outliers : 4.79 % Allowed : 22.86 % Favored : 72.35 % 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: 0.71 (0.25), residues: 1232 helix: 2.04 (0.23), residues: 589 sheet: 0.38 (0.38), residues: 200 loop : -1.73 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 368 HIS 0.005 0.001 HIS A 146 PHE 0.023 0.001 PHE C 138 TYR 0.012 0.001 TYR B 223 ARG 0.012 0.001 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 240 time to evaluate : 1.091 Fit side-chains REVERT: A 75 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7562 (mpt) REVERT: B 133 PHE cc_start: 0.8097 (t80) cc_final: 0.7714 (t80) REVERT: B 137 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8150 (mp) REVERT: B 215 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7586 (tmm) REVERT: D 37 ASP cc_start: 0.8447 (m-30) cc_final: 0.8230 (m-30) REVERT: D 140 PHE cc_start: 0.7974 (m-10) cc_final: 0.7698 (m-80) REVERT: D 148 LEU cc_start: 0.8550 (mp) cc_final: 0.8316 (mt) REVERT: D 207 ASP cc_start: 0.7708 (t0) cc_final: 0.7432 (t0) REVERT: D 330 VAL cc_start: 0.8781 (p) cc_final: 0.8532 (m) outliers start: 52 outliers final: 28 residues processed: 272 average time/residue: 1.2467 time to fit residues: 363.5541 Evaluate side-chains 264 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 57 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 185 GLN A 208 GLN A 358 GLN D 42 ASN D 255 ASN D 321 ASN D 335 ASN D 346 ASN D 358 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104900 restraints weight = 13533.993| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.18 r_work: 0.3209 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10050 Z= 0.298 Angle : 0.605 12.834 13624 Z= 0.306 Chirality : 0.044 0.193 1597 Planarity : 0.005 0.049 1723 Dihedral : 4.950 59.176 1351 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 4.88 % Allowed : 23.04 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.25), residues: 1232 helix: 2.00 (0.23), residues: 587 sheet: 0.35 (0.38), residues: 200 loop : -1.77 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 129 HIS 0.005 0.001 HIS A 103 PHE 0.025 0.002 PHE C 138 TYR 0.015 0.001 TYR D 98 ARG 0.010 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 242 time to evaluate : 1.082 Fit side-chains REVERT: A 75 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7643 (mpt) REVERT: A 116 MET cc_start: 0.8278 (mpp) cc_final: 0.7963 (mpp) REVERT: A 143 ARG cc_start: 0.8271 (mtp85) cc_final: 0.8007 (mtp-110) REVERT: A 268 ARG cc_start: 0.7203 (mtp85) cc_final: 0.6987 (mtp85) REVERT: B 133 PHE cc_start: 0.8119 (t80) cc_final: 0.7739 (t80) REVERT: B 137 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8119 (mp) REVERT: B 215 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7596 (tmm) REVERT: C 173 LEU cc_start: 0.7978 (mp) cc_final: 0.7697 (mp) REVERT: D 37 ASP cc_start: 0.8444 (m-30) cc_final: 0.8227 (m-30) REVERT: D 130 GLU cc_start: 0.8122 (tt0) cc_final: 0.7915 (tt0) REVERT: D 140 PHE cc_start: 0.8007 (m-10) cc_final: 0.7724 (m-80) REVERT: D 207 ASP cc_start: 0.7781 (t0) cc_final: 0.7517 (t0) REVERT: D 330 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8568 (m) outliers start: 53 outliers final: 32 residues processed: 275 average time/residue: 1.2482 time to fit residues: 367.0135 Evaluate side-chains 271 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 235 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 42 ASN A 185 GLN A 358 GLN D 42 ASN D 255 ASN D 321 ASN D 335 ASN D 346 ASN D 358 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.124297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106146 restraints weight = 13681.291| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.25 r_work: 0.3166 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 10050 Z= 0.453 Angle : 0.668 13.104 13624 Z= 0.341 Chirality : 0.048 0.241 1597 Planarity : 0.006 0.050 1723 Dihedral : 5.189 58.638 1351 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 5.53 % Allowed : 22.67 % Favored : 71.80 % 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: 0.37 (0.24), residues: 1232 helix: 1.69 (0.22), residues: 593 sheet: 0.26 (0.38), residues: 200 loop : -1.84 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 129 HIS 0.007 0.001 HIS A 103 PHE 0.028 0.002 PHE C 138 TYR 0.019 0.002 TYR B 223 ARG 0.011 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 1.169 Fit side-chains REVERT: A 27 PHE cc_start: 0.7258 (t80) cc_final: 0.6937 (t80) REVERT: A 28 ASP cc_start: 0.7629 (t70) cc_final: 0.7349 (t70) REVERT: A 116 MET cc_start: 0.8310 (mpp) cc_final: 0.7912 (mpp) REVERT: A 143 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8176 (mtp180) REVERT: A 268 ARG cc_start: 0.7278 (mtp85) cc_final: 0.7000 (mtp85) REVERT: B 137 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8141 (mp) REVERT: B 215 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7655 (tmm) REVERT: C 25 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7997 (mt) REVERT: C 173 LEU cc_start: 0.8007 (mp) cc_final: 0.7787 (mp) REVERT: D 60 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7897 (mp) REVERT: D 148 LEU cc_start: 0.8617 (mp) cc_final: 0.8408 (mt) REVERT: D 207 ASP cc_start: 0.7855 (t0) cc_final: 0.7579 (t0) REVERT: D 330 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8587 (m) REVERT: D 371 VAL cc_start: 0.8414 (t) cc_final: 0.8051 (m) outliers start: 60 outliers final: 36 residues processed: 287 average time/residue: 1.3230 time to fit residues: 404.9681 Evaluate side-chains 298 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 257 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Chi-restraints excluded: chain D residue 368 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 44 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 358 GLN D 321 ASN D 358 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.123928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105623 restraints weight = 13598.372| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.19 r_work: 0.3224 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10050 Z= 0.205 Angle : 0.588 13.308 13624 Z= 0.296 Chirality : 0.043 0.175 1597 Planarity : 0.005 0.049 1723 Dihedral : 4.470 54.786 1346 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 4.61 % Allowed : 24.79 % Favored : 70.60 % 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: 0.61 (0.25), residues: 1232 helix: 1.99 (0.22), residues: 588 sheet: 0.23 (0.38), residues: 200 loop : -1.77 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 129 HIS 0.003 0.001 HIS A 146 PHE 0.025 0.001 PHE B 133 TYR 0.011 0.001 TYR B 223 ARG 0.010 0.001 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 252 time to evaluate : 1.112 Fit side-chains REVERT: A 27 PHE cc_start: 0.7211 (t80) cc_final: 0.6884 (t80) REVERT: A 28 ASP cc_start: 0.7619 (t70) cc_final: 0.7349 (t70) REVERT: A 75 MET cc_start: 0.8069 (mpt) cc_final: 0.7843 (mpt) REVERT: A 116 MET cc_start: 0.8277 (mpp) cc_final: 0.7912 (mpp) REVERT: A 268 ARG cc_start: 0.7217 (mtp85) cc_final: 0.6950 (mtp85) REVERT: A 277 ASN cc_start: 0.8120 (m-40) cc_final: 0.7792 (p0) REVERT: B 133 PHE cc_start: 0.8113 (t80) cc_final: 0.7751 (t80) REVERT: B 137 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8109 (mp) REVERT: B 215 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7547 (tmm) REVERT: C 173 LEU cc_start: 0.8053 (mp) cc_final: 0.7802 (mp) REVERT: D 37 ASP cc_start: 0.8420 (m-30) cc_final: 0.8190 (m-30) REVERT: D 67 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8434 (mt-10) REVERT: D 117 GLN cc_start: 0.8242 (mt0) cc_final: 0.8032 (mt0) REVERT: D 140 PHE cc_start: 0.8014 (m-10) cc_final: 0.7784 (m-80) REVERT: D 148 LEU cc_start: 0.8582 (mp) cc_final: 0.8350 (mt) REVERT: D 207 ASP cc_start: 0.7786 (t0) cc_final: 0.7532 (t0) REVERT: D 330 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8506 (m) REVERT: D 371 VAL cc_start: 0.8399 (t) cc_final: 0.8058 (m) outliers start: 50 outliers final: 32 residues processed: 277 average time/residue: 1.2265 time to fit residues: 363.7293 Evaluate side-chains 282 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 247 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 174 ARG Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 185 GLN A 358 GLN D 358 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.106023 restraints weight = 13623.565| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.19 r_work: 0.3229 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10050 Z= 0.206 Angle : 0.587 12.650 13624 Z= 0.295 Chirality : 0.043 0.169 1597 Planarity : 0.005 0.052 1723 Dihedral : 4.371 54.712 1346 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 3.96 % Allowed : 26.08 % Favored : 69.95 % 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: 0.70 (0.25), residues: 1232 helix: 2.13 (0.22), residues: 582 sheet: 0.22 (0.38), residues: 200 loop : -1.76 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 129 HIS 0.003 0.001 HIS A 146 PHE 0.023 0.001 PHE B 133 TYR 0.011 0.001 TYR B 223 ARG 0.016 0.001 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 1.043 Fit side-chains REVERT: A 27 PHE cc_start: 0.7225 (t80) cc_final: 0.6891 (t80) REVERT: A 28 ASP cc_start: 0.7629 (t70) cc_final: 0.7355 (t70) REVERT: A 268 ARG cc_start: 0.7213 (mtp85) cc_final: 0.6936 (mtp85) REVERT: A 277 ASN cc_start: 0.8130 (m-40) cc_final: 0.7777 (p0) REVERT: B 137 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8148 (mp) REVERT: B 215 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7597 (tmm) REVERT: B 277 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6918 (mm) REVERT: D 37 ASP cc_start: 0.8422 (m-30) cc_final: 0.8188 (m-30) REVERT: D 67 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8460 (mt-10) REVERT: D 140 PHE cc_start: 0.7994 (m-10) cc_final: 0.7766 (m-80) REVERT: D 148 LEU cc_start: 0.8556 (mp) cc_final: 0.8332 (mt) REVERT: D 330 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8548 (m) REVERT: D 371 VAL cc_start: 0.8395 (t) cc_final: 0.8049 (m) outliers start: 43 outliers final: 28 residues processed: 275 average time/residue: 1.2660 time to fit residues: 373.1181 Evaluate side-chains 279 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 247 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 33 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 89 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 42 ASN A 142 GLN A 358 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.125326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.107093 restraints weight = 13413.150| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.17 r_work: 0.3246 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10050 Z= 0.203 Angle : 0.601 12.704 13624 Z= 0.301 Chirality : 0.043 0.157 1597 Planarity : 0.005 0.056 1723 Dihedral : 4.323 54.409 1346 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.46 % Favored : 95.45 % Rotamer: Outliers : 3.69 % Allowed : 26.27 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1232 helix: 2.19 (0.22), residues: 582 sheet: 0.23 (0.37), residues: 199 loop : -1.75 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 368 HIS 0.003 0.001 HIS A 146 PHE 0.029 0.001 PHE B 133 TYR 0.012 0.001 TYR D 98 ARG 0.016 0.001 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 246 time to evaluate : 1.069 Fit side-chains REVERT: A 27 PHE cc_start: 0.7236 (t80) cc_final: 0.6908 (t80) REVERT: A 28 ASP cc_start: 0.7668 (t70) cc_final: 0.7397 (t70) REVERT: A 268 ARG cc_start: 0.7231 (mtp85) cc_final: 0.6955 (mtp85) REVERT: B 137 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8168 (mp) REVERT: B 215 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7546 (tmm) REVERT: B 277 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6833 (mm) REVERT: C 173 LEU cc_start: 0.8093 (mt) cc_final: 0.7723 (mp) REVERT: D 37 ASP cc_start: 0.8397 (m-30) cc_final: 0.8161 (m-30) REVERT: D 67 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8432 (mt-10) REVERT: D 140 PHE cc_start: 0.7988 (m-10) cc_final: 0.7774 (m-80) REVERT: D 148 LEU cc_start: 0.8549 (mp) cc_final: 0.8330 (mt) REVERT: D 330 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8534 (m) outliers start: 40 outliers final: 30 residues processed: 264 average time/residue: 1.2819 time to fit residues: 361.2234 Evaluate side-chains 271 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 237 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 121 optimal weight: 0.3980 chunk 75 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 42 ASN A 358 GLN C 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.126041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.107776 restraints weight = 13452.625| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.17 r_work: 0.3256 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10050 Z= 0.189 Angle : 0.594 11.046 13624 Z= 0.297 Chirality : 0.043 0.152 1597 Planarity : 0.005 0.060 1723 Dihedral : 4.231 54.093 1346 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 3.59 % Allowed : 27.00 % Favored : 69.40 % 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: 0.83 (0.25), residues: 1232 helix: 2.28 (0.22), residues: 582 sheet: 0.17 (0.37), residues: 200 loop : -1.69 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 364 HIS 0.003 0.001 HIS A 146 PHE 0.030 0.001 PHE B 133 TYR 0.011 0.001 TYR D 98 ARG 0.016 0.001 ARG D 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 240 time to evaluate : 1.078 Fit side-chains REVERT: A 27 PHE cc_start: 0.7234 (t80) cc_final: 0.6884 (t80) REVERT: A 28 ASP cc_start: 0.7673 (t70) cc_final: 0.7396 (t70) REVERT: A 268 ARG cc_start: 0.7239 (mtp85) cc_final: 0.6949 (mtp85) REVERT: B 137 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8179 (mp) REVERT: B 215 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7545 (tmm) REVERT: B 277 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6734 (mm) REVERT: C 173 LEU cc_start: 0.8092 (mt) cc_final: 0.7670 (mp) REVERT: D 37 ASP cc_start: 0.8408 (m-30) cc_final: 0.8174 (m-30) REVERT: D 140 PHE cc_start: 0.7991 (m-10) cc_final: 0.7776 (m-80) REVERT: D 148 LEU cc_start: 0.8529 (mp) cc_final: 0.8321 (mt) REVERT: D 330 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8511 (m) outliers start: 39 outliers final: 30 residues processed: 257 average time/residue: 1.2107 time to fit residues: 333.4417 Evaluate side-chains 274 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 240 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 7 ARG Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 351 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 30 optimal weight: 0.0670 chunk 72 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 88 optimal weight: 0.0170 chunk 21 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 42 ASN A 154 GLN A 358 GLN C 28 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.108070 restraints weight = 13384.689| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.18 r_work: 0.3260 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10050 Z= 0.184 Angle : 0.590 12.722 13624 Z= 0.295 Chirality : 0.042 0.144 1597 Planarity : 0.005 0.061 1723 Dihedral : 4.179 53.838 1346 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.30 % Favored : 95.62 % Rotamer: Outliers : 3.41 % Allowed : 27.28 % Favored : 69.31 % 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: 0.90 (0.25), residues: 1232 helix: 2.37 (0.22), residues: 581 sheet: 0.20 (0.38), residues: 200 loop : -1.69 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 368 HIS 0.003 0.000 HIS A 146 PHE 0.031 0.001 PHE B 133 TYR 0.012 0.001 TYR D 98 ARG 0.015 0.001 ARG D 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7831.87 seconds wall clock time: 138 minutes 53.38 seconds (8333.38 seconds total)